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What could the etymology of Phallodriline be?


I'm reading about a series of gutless worms described in several papers as phallodrilines. A search in the World Register of Marine Species shows that there is a subfamily called "Phallodrilinae", but then, in at least one paper this term is used to collectively describe gutless worms in several taxa including Oligochaeta, Annelida, and Clitellata. Since they're also described as club-headed I'm assuming that "Phallo-" is from the Latin for penis, but what would be the rest?


Phallus in Latin means penis, while drilus is the New Latin word for Greek

δρῖλος (drîlos)

which means both worm or erect penis.

Here you can check some sources corroborating my claim:

Merriam Webster dictionary

Wiktionary: δρῖλος (drîlos) means verpus

Liddel & Scott Lexicon

Drîlos meaning penis in Greek


-o-linking vowel indicates Greek.-i-is Latin, unless the second word starts with a vowel (many-ectomywords for example). This is irrespective of declension or gender. Weird I know.

In fact, Latin phallus is from φαλλός.

The second part is worm δρῖλος (drilos). Actually it can also mean penis, but let's gloss over that…


The study of the origin of life

If a species can develop only from a preexisting species, then how did life originate? Among the many philosophical and religious ideas advanced to answer that question, one of the most popular was the theory of spontaneous generation, according to which, as already mentioned, living organisms could originate from nonliving matter. With the increasing tempo of discovery during the 17th and 18th centuries, however, investigators began to examine more critically the Greek belief that flies and other small animals arose from the mud at the bottom of streams and ponds by spontaneous generation. Then, when Harvey announced his biological dictum ex ovo omnia (“everything comes from the egg”), it appeared that he had solved the problem, at least insofar as it pertained to flowering plants and the higher animals, all of which develop from an egg. But Leeuwenhoek’s subsequent disquieting discovery of animalcules demonstrated the existence of a densely populated but previously invisible world of organisms that had to be explained.

The Italian physician and poet Francesco Redi was one of the first to question the spontaneous origin of living things. Having observed the development of maggots and flies on decaying meat, Redi in 1668 devised a number of experiments, all pointing to the same conclusion: if flies are excluded from rotten meat, maggots do not develop. On meat exposed to air, however, eggs laid by flies develop into maggots. Nonetheless, in 1745 support for spontaneous generation was renewed with the publication of An Account of Some New Microscopical Discoveries by the English naturalist and Roman Catholic divine John Turberville Needham. Needham found that large numbers of organisms subsequently developed in prepared infusions of many different substances that had been exposed to intense heat in sealed tubes for 30 minutes. Assuming that such heat treatment must have killed any previous organisms, Needham explained the presence of the new population on the grounds of spontaneous generation. The experiments appeared irrefutable until the Italian physiologist Lazzaro Spallanzani repeated them and obtained conflicting results. He published his findings around 1775, claiming that Needham had not heated his tubes long enough, nor had he sealed them in a satisfactory manner. Although Spallanzani’s results should have been convincing, Needham had the support of the influential French naturalist Buffon hence, the matter of spontaneous generation remained unresolved.


Quantum physicists in the 1920s helped found field of quantum biology

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In 1944, quantum physicist Erwin Schroedinger wrote a short book called What Is Life: The Physical Aspect of the Living Cell, exploring how the relatively new field of quantum mechanics might play a role in biological processes. It is considered by many to be one of the earliest forays into "quantum biology," a rarefied field that attempts to apply quantum principles to living systems. But the field actually dates back to the earliest days of quantum mechanics in the 1920s, according to a recent paper published in the Proceedings of the Royal Society A.

"Quantum biology is wrongly regarded as a very new scientific discipline, when it actually began before the Second World War," said co-author Johnjoe McFadden, a microbiologist at the University of Surrey and co-director of its Centre for Quantum Biology, along with his Surrey colleague and co-author Jim Al-Khalili. "Back then, a few quantum physicists tried to understand what was special about life itself and whether quantum mechanics might shed any light on the matter."

Frankly, quantum biology has suffered from a lack of credibility until the last decade or so, when a number of intriguing studies suggested that there might be something to the idea after all. For instance, there is growing evidence that photosynthesis relies on quantum effects to help plants turn sunlight into fuel. Migratory birds might have an internal "quantum compass" that helps them sense Earth's magnetic fields as a means of navigation. Quantum effects might play a role in the human sense of smell, helping us distinguish between different scents.

More controversially, mathematical physicist Roger Penrose suggested in 1989 that mysterious proteins called "microtubules" might exploit quantum effects and hold the secret to human consciousness. Few researchers believe this is actually true, but Matthew Fisher, a physicist at the University of California, Santa Barbara, has recently proposed that the nuclear spins of phosphorus atoms might function as simple "qubits" in the brain. Consciousness, in other words, would work much like a quantum computer.

That's why McFadden and Al-Khalili wrote their bestselling popular science book, Life on the Edge: The Coming of Age of Quantum Biology in 2015. One of the chapters that didn't make it into the final book—exploring the historical origins of the field—ended up forming the basis for this latest paper. "We've forgotten that there were these mavericks even before Schroedinger who were asking these deep questions that we are only now able to test a bit more carefully," said Al-Khalili.

By 1927, physicists had laid out the mathematical framework for the new theory of quantum mechanics. "Flushed with their success at taming the atomic world, and with the arrogance of youth on their side, many quantum pioneers struck out of their physics laboratories and away from their blackboards to seek new areas of science to conquer," the authors write. And since microbiology and the related fledgling field of genetics remained largely unexplored, the intellectually restless physicists naturally gravitated there.

There was even a Theoretical Biology Club at Cambridge in 1932 its members included physicists, philosophers (like Karl Popper), and biologists. "They were all united in the idea that there's something special about life," said Al-Khalili. "They felt that maybe principles in physics and chemistry yet to be discovered could help distinguish the transition between chemistry and biology." Granted, it was more of a hobby for many of them, and Al-Khalili concedes they didn't make much progress. But those early discussions certainly had a great influence on Schroedinger.

Niels Bohr was not entirely convinced that the principles of physics and chemistry would be sufficient to explain living systems, but a lecture he gave at the Scandinavian Meeting of Natural Scientists in 1929 briefly mentioned the possibility. Among those inspired to delve further was a German physicist named Pascual Jordan, one of three authors of the seminal paper laying out the mathematical foundations of quantum mechanics. He was using the term "quantumbiologie" in the late 1930s and published Physics and the Secret of Organic Life—in which he explored the question of whether atomic and quantum physics is essential for life—the year before Schroedinger published What Is Life.

Unfortunately, Jordan was a devout member of the Nazi party, although his defense of Jewish scientists like Einstein meant he was deemed "politically unreliable" by that regime. His attempts to link his theories on quantum biology to the Nazi philosophy—even claiming that a single dictatorial leader (führer) was a central principle of life—served to discredit those theories in the eyes of his fellow scientists.

"Had it been other physicists, maybe people would have taken more notice [of quantum biology] and carried on thinking about some of these problems," said Al-Khalili. "But because of Jordan's background, it was deemed an unsavory area of research."

So it fell to Schroedinger the keep the flame of quantum biology alive. "There's a famous image from one of his notebooks where he drew diagrams of chromosomes, trying to understand how they're able to store information," said Al-Khalili. "He wanted to know what it was that kept life in this highly ordered state." In What Is Life, Schroedinger argued that, unlike inanimate matter, living matter can be influenced by single quantum events. After all, cool certain materials down to near absolute zero and they exhibit quantum effects like superconductivity, in which the electrical resistance disappears. According to Schroedinger, living matter could also exhibit these kinds of effects at room temperatures, perhaps because it's so highly ordered.

Specifically, he pondered how fruit flies, for instance, managed to produce order from disorder, decreasing entropy (in seeming violation of the second law of thermodynamics) by "continually sucking orderliness from the environment." Entropy always increases in a closed system, according to physics, but living things are not isolated systems. A fruit fly might extract order from disorder, but there is a corresponding increase in entropy in its environment. Schroedinger also suggested an "aperiodic crystal" might contain genetic information and that mutations occur via "quantum leaps."

What Is Life was hugely influential at the time Francis Crick and James Watson claimed it helped inspire them to think about the double helix structure of DNA, along with Rosalind Franklin's X-ray diffraction experiments. But quantum biology fell out of favor after that as an area of credible research. The general consensus among physicists in the ensuing decades was that living systems were simply too noisy and quantum effects just too delicate to persist in a complicated environment like a living cell.

The issue is quantum decoherence. Entanglement is key for quantum effects: connecting two or more objects in such a way that they can only be described with reference to each other, even if separated over large distances. Albert Einstein famously dubbed it "spooky action at a distance." But the slightest interaction (colliding with a single photon, for instance) with the surrounding environment will destroy that entanglement.

"Usually we think that the more complex the environment, the faster it decoheres, like a hot object will cool down in a cold environment," said Al-Khalili. "If it didn't, we would have built a quantum computer by now. So how do you maintain these delicate quantum effects long enough for them to be useful?"

Current thinking holds that there may be some living systems where quantum processes could play a role before decoherence kicks in. That's because such systems depend on the dynamics of small numbers of molecules at tiny scales (just a few nanometers), keeping them sufficiently isolated. In fact, the authors contend that recent work in quantum information theory demonstrates that noise might actually support quantum coherence in some systems. Maybe, over billions of years of evolution, nature has learned the trick of maintaining quantum coherence to make use of such effects, and we just don't yet understand how.

These are concepts Al-Khalili himself is only beginning to explore seriously in his research at the Centre for Quantum Biology. "For me, quantum biology is an excuse to look into the foundations of quantum mechanics the fact that it's inside biological systems is almost incidental," he said. "When I first started thinking about quantum biology, it was really just a hobby. I didn't really believe it. I can't say I even 100 percent believe it now, but I think it's an interesting enough problem that we have to rule it out. We've got to stop just waving our hands about and do some careful research."


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The Greek word nýmphē has the primary meaning of "young woman bride, young wife" but is not usually associated with deities in particular. Yet the etymology of the noun nýmphē remains uncertain. The Doric and Aeolic (Homeric) form is nýmfa ( νύμφα ). [3]

Modern usage more often applies to young women at the peak of their attractiveness, contrasting with parthenos ( παρθένος ) "a virgin (of any age)", and generically as kore ( κόρη < κόρϝα ) "maiden, girl". The term is sometimes used by women to address each other and remains the regular Modern Greek term for "bride".

Nymphs were sometimes beloved by many and dwelt in specific areas related to the natural environment: e.g. mountainous regions forests springs. Other nymphs were part of the retinue of a god (such as Dionysus, Hermes, or Pan) or of a goddess (generally the huntress Artemis). [4]

The Greek nymphs were also spirits invariably bound to places, not unlike the Latin genius loci, and sometimes this produced complicated myths like the cult of Arethusa to Sicily. In some of the works of the Greek-educated Latin poets, the nymphs gradually absorbed into their ranks the indigenous Italian divinities of springs and streams (Juturna, Egeria, Carmentis, Fontus) while the Lymphae (originally Lumpae), Italian water goddesses, owing to the accidental similarity of their names, could be identified with the Greek Nymphae. The classical mythologies of the Roman poets were unlikely to have affected the rites and cults of individual nymphs venerated by country people in the springs and clefts of Latium. Among the Roman literate class, their sphere of influence was restricted and they appear almost exclusively as divinities of the watery element. [ citation needed ]

The ancient Greek belief in nymphs survived in many parts of the country into the early years of the twentieth century when they were usually known as "nereids". [5] Nymphs often tended to frequent areas distant from humans but could be encountered by lone travelers outside the village, where their music might be heard, and the traveler could spy on their dancing or bathing in a stream or pool, either during the noon heat or in the middle of the night. They might appear in a whirlwind. Such encounters could be dangerous, bringing dumbness, besotted infatuation, madness or stroke to the unfortunate human. When parents believed their child to be nereid-struck, they would pray to Saint Artemidos. [6] [7]

Nymphs are often depicted in classic works across art, literature, mythology, and fiction. They are often associated with the medieval romances or Renaissance literature of the elusive fairies or elves. [8] [9]

A motif that entered European art during the Renaissance was the idea of a statue of a nymph sleeping in a grotto or spring. [10] [11] [12] This motif supposedly came from an Italian report of a Roman sculpture of a nymph at a fountain above the River Danube. [13] The report, and an accompanying poem supposedly on the fountain describing the sleeping nymph, are now generally concluded to be a fifteenth-century forgery, but the motif proved influential among artists and landscape gardeners for several centuries after, with copies seen at neoclassical gardens such as the grotto at Stourhead. [14] [15] [16]

All the names for various classes of nymphs have plural feminine adjectives, most agreeing with the substantive numbers and groups of nymphai. There is no single adopted classification that could be seen as canonical and exhaustive. [17] Some classes of nymphs tend to overlap, which complicates the task of precise classification. e.g. Dryads and hamadryads as nymphs of trees generally, meliai as nymphs of ash trees, and naiads as nymphs of water, but no others specifically. [17]

By type of dwelling Edit

The following is not the authentic Greek classification, but is intended simply as a guide:

Classification by type of dwelling
Type / Group / Individuals Location Relations and Notes
Celestial nymphs
Aurae (breezes) also called Aetae or Pnoae [ citation needed ] , daughters of Boreas [18]
Asteriae (stars) mainly comprising the Atlantides (daughters of Atlas)
1. Hesperides Far West nymphs of the sunset, the West, and the evening daughters of Atlas also had attributes of the Hamadryads [19]
• Aegle ditto
• Arethusa ditto
• Erytheia (or Eratheis) ditto mother of Eurytion by Ares [20]
• Hesperia (or Hispereia) ditto
2. Hyades (star cluster sent rain) Boeotia (probably) daughters of Atlas by either Pleione or Aethra [21]
3. Pleiades Boeotia (probably) daughters of Atlas and Pleione [22] constellation also were classed as Oreads
• Maia Mt. Cyllene, Arcadia partner of Zeus and mother of Hermes [23]
• Electra Mt. Saon, Samothrace mother of Dardanus and Iasion by Zeus [24]
• Taygete Taygetos Mts., Laconia mother of Lacedaemon by Zeus [25]
• Alcyone Mt. Cithaeron, Boeotia mother of Hyperes and Anthas by Poseidon [26]
• Celaeno Mt. Cithaeron, Boeotia or Euboea mother of Lycus and Nycteus by Poseidon [27]
• Asterope Pisa, Elis mother of Oenomaus by Ares [28]
• Merope Corinth wife of Sisyphus and mother of Glaucus [29]
Nephele (clouds) daughters of Oceanus [30] and/or Tethys [31] or of Aither [32]
Land nymphs
Alseides (groves) [33]
Auloniades (valley pastures, glens)
Leimakides or Leimonides (meadows)
Napaeae (dells) [34]
Oreads (mountains, grottoes), also Orodemniades
Wood and plant nymphs
Anthousai (flowers)
Dryades (trees)
Hamadryades or Hadryades
1. Daphnaeae (laurel tree)
2. Epimeliades or Epimelides (apple tree also protected flocks) other name variants include Meliades, Maliades and Hamameliades same as these are also the Boucolai (Pastoral Nymphs)
3. Kissiae (ivy)
4. Meliae (manna-ash tree) born from the drops of blood that fell on Gaia when Cronus castrated Uranus [35]
Hyleoroi (watchers of woods)
Water nymphs (Hydriades or Ephydriades)
Haliae (sea and seashores)
1. Nereids Mediterranean Sea 50 daughters of Nereus and Doris [36]
Naiads or Naides (fresh water)
1. Crinaeae (fountains)
2. Eleionomae (wetlands)
3. Limnades or Limnatides (lakes)
4. Pegaeae (springs)
5. Potameides (rivers)
• Tágides Tagus River
Oceanids daughters of Oceanus and Tethys, [37] any freshwater, typically clouds and rain. see List of Oceanids
Underworld nymphs
Lampades Hades torch bearers in the retinue of Hecate
• Orphne Hades is a representation of the darkness of the river Styx, the river of hatred, but is not to be confused with the goddess Styx herself, but she is associated with both Styx and Nyx. She is the consort of Acheron, (the god of the river in Hades), and the mother of Ascalaphus, (the orchardist of Hades). [38]
• Leuce (white poplar tree) Hades daughter of Oceanus and lover of Hades [39]
• Minthe (mint) Cocytus River probably a daughter of Cocytus, lover of Hades and rival of Persephone [40] [41]
• Melinoe Hades Orphic nymph, daughter of Persephone and "Zeus disguised as Pluto". [42] Her name is a possible epithet of Hecate.
Other nymphs
Hecaterides (rustic dance) daughters of Hecaterus by a daughter of Phoroneus sisters of the Dactyls and mothers of the Oreads and the Satyrs [43]
Kabeirides daughters of Cadmilus and sisters of the Kabeiroi [44] or of Hephaestus and Cabeiro [45]
Maenads or Bacchai or Bacchantes frenzied nymphs in the retinue of Dionysus
1. Lenai (wine-press)
2. Mimallones (music)
3. Naides (Naiads)
4. Thyiai or Thyiades (thyrsus bearers)
Melissae (honey) likely a subgroup of Oreades or Epimelides

By location Edit

The following is a list of groups of nymphs associated with this or that particular location. Nymphs in such groupings could belong to any of the classes mentioned above (Naiades, Oreades, and so on).

Location-specific groupings of nymphs
Groups and Individuals Location Relations and Notes
Aeaean Nymphs Aeaea Island handmaidens of Circe
Aegaeides Aegaeus River on the island of Scheria
Aesepides Aesepus River in Anatolia
• Abarbarea ditto
Acheloides Achelous River in Acarnania
• Callirhoe, second wife of Alcmaeon ditto
Acmenes Stadium in Olympia, Elis
Amnisiades Amnisos River on the island of Crete entered the retinue of Artemis
Anigrides Anigros River in Elis believed to cure skin diseases
Asopides Asopus River in Sicyonia and Boeotia
• Aegina Island of Aegina mother of Menoetius by Actor, and Aeacus by Zeus
• Asopis
• Chalcis Chalcis, Euboea regarded as the mother of the Curetes and Corybantes perhaps the same as Combe and Euboea below
• Cleone Cleonae, Argos
• Combe Island of Euboea consort of Socus and mother by him of the seven Corybantes
• Corcyra Island of Corcyra mother of Phaiax by Poseidon
• Euboea Island of Euboea abducted by Poseidon
• Gargaphia or Plataia or Oeroe Plataea, Boeotia carried off by Zeus
• Harmonia Akmonian Wood, near Themiscyra mother of the Amazons by Ares [46] [47]
• Harpina Pisa, Elis mother of Oenomaus by Ares
• Ismene Ismenian spring of Thebes, Boeotia wife of Argus, eponymous king of Argus and thus, mother of Argus Panoptes and Iasus.
• Nemea Nemea, Argolis others called her the daughter of Zeus and Selene
• Ornea Ornia, Sicyon
• Peirene Corinth others called her father to be Oebalus or Achelous by Poseidon she became the mother of Lecheas and Cenchrias
• Salamis Island of Salamis mother of Cychreus by Poseidon
• Sinope Sinope, Anatolia mother of Syrus by Apollo
• Tanagra Tanagra, Boeotia mother of Leucippus and Ephippus by Poemander
• Thebe Thebes, Boeotia wife of Zethus and also said to have consorted with Zeus
• Carmentis,or Carmenta Arcadia She had a son with Hermes, called Evander. Her son was the founder of the Pallantium. Pallantium became one of the cities that was merged later into the ancient Rome. Romans called her, Carmenta. [48]
• Thespeia Thespia, Boeotia abducted by Apollo
Astakides Lake Astacus, Bithynia appeared in the myth of Nicaea
• Nicaea Nicaea, Bithynia
Asterionides Asterion River, Argos daughters of the river god Asterion nurses of the infant goddess Hera
• Acraea ditto
• Euboea ditto
• Prosymna ditto
Carian Naiades (Caria) Caria
• Salmacis Halicarnassus, Caria
Nymphs of Ceos Island of Ceos
Corycian Nymphs (Corycian Cave) Corycian cave, Delphi, Phocis daughters of the river god Pleistos
• Kleodora (or Cleodora) Mt. Parnassus, Phocis mother of Parnassus by Poseidon
• Corycia Corycian cave, Delphi, Phocis mother of Lycoreus by Apollo
• Daphnis Mt. Parnassus, Phocis
• Melaina Dephi, Phocis mother of Delphos by Apollo
Cydnides River Cydnus in Cilicia
Cyrenaean Nymphs City of Cyrene, Libya
Cypriae Nymphs Island of Cyprus
Cyrtonian Nymphs Town of Cyrtone, Boeotia Κυρτωνιαι
Deliades Island of Delos daughters of Inopus, god of the river Inopus
Dodonides Oracle at Dodona
Erasinides Erasinos River, Argos daughters of the river god Erasinos attendants of the goddess Britomartis.
• Anchiroe ditto
• Byze ditto
• Maera ditto
• Melite ditto
Nymphs of the river Granicus River Granicus daughters of the river-god Granicus
• Alexirhoe ditto mother of Aesacus by Priam
• Pegasis ditto mother of Atymnios by Emathion
Heliades River Eridanos daughters of Helios who were changed into trees
Himeriai Naiades Local springs at the town of Himera, Sicily
Hydaspides Hydaspers River, India nurses of infant Zagreus
Idaean Nymphs Mount Ida, Crete nurses of infant Zeus
• Ida ditto
• Adrasteia ditto
Inachides Inachos River, Argos daughters of the river god Inachus
• Io ditto mother of Epaphus by Zeus
• Amymone ditto
• Philodice ditto wife of Leucippus of Messenia by whom she became the mother of Hilaeira, Phoebe and possibly Arsinoe
• Messeis ditto
• Hyperia ditto
• Mycene ditto wife of Arestor and by him probably the mother of Argus Panoptes eponym of Mycenae
Ionides Kytheros River in Elis daughters of the river god Cytherus
• Calliphaea ditto
• Iasis ditto
• Pegaea ditto
• Synallaxis ditto
Ithacian Nymphs Local springs and caves on the island of Ithaca
Ladonides Ladon River
Lamides or Lamusides Lamos River in Cilicia possible nurses of infant Dionysus
Leibethrides Mounts Helicon and Leibethrios in Boeotia or Mount Leibethros in Thrace)
• Libethrias
• Petra
Lelegeides Lycia, Anatolia
Lycaean Nymphs Mount Lycaeus nurses of infant Zeus, perhaps a subgroup of the Oceanides
Melian Nymphs Island of Melos transformed into frogs by Zeus not to be confused with the Meliae (ash tree nymphs
Mycalessides Mount Mycale in Caria, Anatolia
Mysian Nymphs Spring of Pegai near Lake Askanios in Bithynia who abducted Hylas
• Euneica
• Malis
• Nycheia
Naxian Nymphs Mount Drios on the island of Naxos nurses of infant Dionysus were syncretized with the Hyades
• Cleide
• Coronis
• Philia
Neaerides Thrinacia Island daughters of Helios and Neaera, watched over Helios' cattle
Nymphaeides Nymphaeus River in Paphlagonia
Nysiads Mount Nysa nurses of infant Dionysos, identified with Hyades
Ogygian Nymphs Island of Ogygia four handmaidens of Calypso
Ortygian Nymphs Local springs of Syracuse, Sicily named for the island of Ortygia
Othreides Mount Othrys a local group of Hamadryads
Pactolides Pactolus River
• Euryanassa wife of Tantalus
Pelionides Mount Pelion nurses of the Centaurs
Phaethonides a synonym for the Heliades
Phaseides Phasis River
Rhyndacides Rhyndacus River in Mysia
Sithnides Fountain at the town of Megara
Spercheides River Spercheios one of them, Diopatra, was loved by Poseidon and the others were changed by him into trees
Sphragitides, or Cithaeronides Mount Cithaeron
Tagids, Tajids, Thaejids or Thaegids River Tagus in Portugal and Spain
Thessalides Peneus River in Thessaly
Thriae Mount Parnassos prophets and nurses of Apollo
Trojan Nymphs Local springs of Troy

Others Edit

The following is a selection of names of the nymphs whose class was not specified in the source texts. For lists of Naiads, Oceanids, Dryades etc. see respective articles.


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The word crocodile comes from the Ancient Greek krokódilos ( κροκόδιλος ) meaning 'lizard', used in the phrase ho krokódilos tou potamoú, "the lizard of the (Nile) river". There are several variant Greek forms of the word attested, including the later form krokódeilos ( κροκόδειλος ) [4] found cited in many English reference works. [5] In the Koine Greek of Roman times, krokodilos and krokodeilos would have been pronounced identically, and either or both may be the source of the Latinized form crocodīlus used by the ancient Romans. It has been suggested, but it is not certain that the word crocodilos or crocodeilos is a compound of krokè ('pebbles'), and drilos/dreilos ('worm'), although drilos is only attested as a colloquial term for 'penis'. [5] It is ascribed to Herodotus, and supposedly describes the basking habits of the Egyptian crocodile. [6]

The form crocodrillus is attested in Medieval Latin. [5] It is not clear whether this is a medieval corruption or derives from alternative Greco-Latin forms (late Greek corcodrillos and corcodrillion are attested). A (further) corrupted form cocodrille is found in Old French and was borrowed into Middle English as cocodril(le). The Modern English form crocodile was adapted directly from the Classical Latin crocodīlus in the 16th century, replacing the earlier form. The use of -y- in the scientific name Crocodylus (and forms derived from it) is a corruption introduced by Laurenti (1768).

A total of 16 extant species have been recognized. Further genetic study is needed for the confirmation of proposed species under the genus Osteolaemus, which is currently monotypic.

Species name Image Distribution Description/Comments
American crocodile ( Crocodylus acutus ) Throughout the Caribbean Basin, including many of the Caribbean islands and South Florida. A larger sized species, with a greyish colour and a prominent V-shaped snout. Prefers brackish water, but also inhabits lower stretches of rivers and true marine environments. This is one of the rare species that exhibits regular sea-going behaviour, which explains the great distribution throughout the Caribbean. It is also found in hypersaline lakes such as Lago Enriquillo, in the Dominican Republic, which has one of the largest populations of this species. [7] Diet consists mostly of aquatic and terrestrial vertebrates. Classified as Vulnerable, but certain local populations under greater threat.
Hall's New Guinea crocodile (Crocodylus halli) The island of New Guinea, south of the New Guinea Highlands A smaller species that closely resembles and was long classified under the New Guinea crocodile, which it is now considered to be genetically distinct from. It lives south of the mountain barrier that divides the two species' ranges. It can be physically distinguished from the New Guinea crocodile by its shorter maxilla and enlarged postcranial elements. Cranial elements can still widely vary within the species, with populations from Lake Murray having much wider heads than those from the Aramia River. [8]
Orinoco crocodile ( Crocodylus intermedius ) Colombia and Venezuela This is a large species with a relatively elongated snout and a pale tan coloration with scattered dark brown markings. Lives primarily in the Orinoco Basin. Despite having a rather narrow snout, preys on a wide variety of vertebrates, including large mammals. It is a Critically Endangered species.
Freshwater crocodile ( Crocodylus johnstoni ) Northern Australia A smaller species with a narrow and elongated snout. It has light brown coloration with darker bands on body and tail. Lives in rivers with considerable distance from the sea, to avoid confrontations with saltwater crocodiles. Feeds mostly on fish and other small vertebrates.
Philippine crocodile ( Crocodylus mindorensis ) Endemic to the Philippines This is a relatively small species with a rather broader snout. It has heavy dorsal armour and a golden-brown colour that darkens as the animal matures. Prefers freshwater habitats and feeds on a variety of small to medium sized vertebrates. This species is Critically Endangered and the most severely threatened species of crocodile. [9]
Morelet's crocodile ( Crocodylus moreletii ) Atlantic regions of Mexico, Belize and Guatemala A small to medium sized crocodile with a rather broad snout. It has a dark greyish-brown colour and is found in mostly various freshwater habitats. Feeds on mammals, birds and reptiles. It is listed as Least Concern.
Nile crocodile ( Crocodylus niloticus ) Sub-saharan Africa A large and aggressive species with a broad snout, especially in older animals. It has a dark bronze coloration and darkens as the animal matures. Lives in a variety of freshwater habitats but is also found in brackish water. It is an apex predator that is capable of taking a wide array of African vertebrates, including large ungulates and other predators. [10] This species is listed as Least Concern.
New Guinea crocodile ( Crocodylus novaeguineae) The island of New Guinea, north of the New Guinea Highlands A smaller species of crocodile with a grey-brown colour and dark brown to black markings on the tail. The young have a narrower V-shaped snout that becomes wider as the animal matures. Prefers freshwater habitats, even though is tolerant to salt water, in order to avoid competition and predation by the saltwater crocodile. This species feeds on small to mid-sized vertebrates.
Mugger crocodile ( Crocodylus palustris ) The Indian subcontinent and surrounding countries This is a modest sized crocodile with a very broad snout and an alligator-like appearance. It has dark-grey to brown coloration. Enlarged scutes around the neck make it a heavily armoured species. Prefers slow moving rivers, swamps and lakes. It can also be found in coastal swamps but avoids areas populated by saltwater crocodiles. [11] Feeds on a wide array of vertebrates.
Saltwater crocodile ( Crocodylus porosus ) Throughout Southeast Asia , Northern Australia and surrounding waters The largest living reptile and most aggressive of all crocodiles. It is a big-headed species and has a relatively broad snout, especially when older. The coloration is pale yellow with black stripes when young but dark greenish-drab coloured as adults. Lives in brackish and marine environments as well as lower stretches of rivers. This species has the greatest distribution of all crocodiles. Tagged specimens showed long-distance marine travelling behaviour. It is the apex predator throughout its range and preys on virtually any animal within its reach. It is classified as Least Concern with several populations under greater risk. [12]
Borneo crocodile (Crocodylus raninus) Island of Borneo in Southeast Asia A freshwater species of crocodile that has been considered a synonym of the saltwater crocodile.
Cuban crocodile ( Crocodylus rhombifer ) Found only in the Zapata Swamp and Isle of Youth of Cuba It is a small but extremely aggressive species of crocodile that prefers freshwater swamps. [13] The coloration is vibrant even as adults and the scales have a "pebbled" appearance. It is a relatively terrestrial species with agile locomotion on land, and sometimes displays terrestrial hunting. The snout is broad with a thick upper-jaw and large teeth. The unique characteristics and fossil record indicates a rather specialized diet in the past, preying on megafauna such as the giant sloth. This species sometimes displays pack-hunting behaviour, which might have been the key to hunting large species in the past, despite its small size. [14] Today most prey are small to medium sized vertebrates. It is Critically Endangered, and the remaining wild population is under threat of hybridization. [15]
Siamese crocodile ( Crocodylus siamensis ) Indonesia, Brunei, East Malaysia and southern Indochina A fairly small crocodile that prefers freshwater habitats. It has a relatively broad snout and olive-green to dark green coloration. It feeds on a variety of small to mid-sized vertebrates. Listed as Critically Endangered, but might be already extinct in the wild status is unknown. [16]
West African crocodile ( Crocodylus suchus ) Western and Central Africa Recent studies revealed that this is distinct species from the larger Nile crocodile. [17] [18] It has a slightly narrower snout and is much smaller compared to its larger cousin.
Dwarf crocodile ( Osteolaemus tetraspis ) Western Africa It is the smallest of all living crocodiles. It belongs to its own monotypic genus however, new studies indicate there might be two or even three distinct species. [19] It is a heavily armoured species with uniform black coloration in adults, while juveniles have a lighter brown banding. Lives in the tropical forests of Western Africa. Feeds on small vertebrates and large aquatic invertebrates. It is a fairly terrestrial species and exhibits terrestrial hunting, especially at night. This species is classified as Vulnerable.
West African slender-snouted crocodile ( Mecistops cataphractus ) Western Africa A medium sized species with a narrow and elongated snout. Lives in freshwater habitats within tropical forests of the continent. Feeds mostly on fish but also other small to medium sized vertebrates. It is a Critically Endangered species.
Central African slender-snouted crocodile (Mecistops leptorhynchus) Central Africa A medium sized species found in watery areas in dense rainforest. Feeds largely on fish. Insufficient conservation data, but was classified as Critically Endangered when lumped with M. cataphractus, although M. leptorhynchus is doing better in its home range.

A crocodile's physical traits allow it to be a successful predator. Its external morphology is a sign of its aquatic and predatory lifestyle. Its streamlined body enables it to swim swiftly it also tucks its feet to the side while swimming, making it faster by decreasing water resistance. Crocodiles have webbed feet which, though not used to propel them through the water, allow them to make fast turns and sudden moves in the water or initiate swimming. Webbed feet are an advantage in shallow water, where the animals sometimes move around by walking. Crocodiles have a palatal flap, a rigid tissue at the back of the mouth that blocks the entry of water. The palate has a special path from the nostril to the glottis that bypasses the mouth. The nostrils are closed during submergence.

Like other archosaurs, crocodilians are diapsid, although their post-temporal fenestrae are reduced. The walls of the braincase are bony but lack supratemporal and postfrontal bones. [20] Their tongues are not free, but held in place by a membrane that limits movement as a result, crocodiles are unable to stick out their tongues. [21] Crocodiles have smooth skin on their bellies and sides, while their dorsal surfaces are armoured with large osteoderms. The armoured skin has scales and is thick and rugged, providing some protection. They are still able to absorb heat through this armour, as a network of small capillaries allows blood through the scales to absorb heat. The osteoderms are highly vascularised and aid in calcium balance, both to neutralize acids while the animal cannot breathe underwater [22] and to provide calcium for eggshell formation. [23] Crocodilian tegument have pores believed to be sensory in function, analogous to the lateral line in fishes. They are particularly seen on their upper and lower jaws. Another possibility is that they are secretory, as they produce an oily substance which appears to flush mud off. [20]

Size greatly varies among species, from the dwarf crocodile to the saltwater crocodile. Species of the dwarf crocodile Osteolaemus grow to an adult size of just 1.5 to 1.9 m (4.9 to 6.2 ft), [24] whereas the saltwater crocodile can grow to sizes over 7 m (23 ft) and weigh 1,000 kg (2,200 lb). [25] Several other large species can reach over 5.2 m (17 ft) long and weigh over 900 kg (2,000 lb). Crocodilians show pronounced sexual dimorphism, with males growing much larger and more rapidly than females. [20] Despite their large adult sizes, crocodiles start their lives at around 20 cm (7.9 in) long. The largest species of crocodile is the saltwater crocodile, found in eastern India, northern Australia, throughout South-east Asia, and in the surrounding waters.

The brain volume of two adult crocodiles was 5.6 cm 3 for a spectacled caiman and 8.5 cm 3 for a larger Nile crocodile. [26]

The largest crocodile ever held in captivity is a saltwater–Siamese hybrid named Yai (Thai: ใหญ่ , meaning big born 10 June 1972) at the Samutprakarn Crocodile Farm and Zoo, Thailand. This animal measures 6 m (20 ft) in length and weighs 1,114 kg (2,456 lb). [27]

The longest crocodile captured alive was Lolong, a saltwater crocodile which was measured at 6.17 m (20.2 ft) and weighed at 1,075 kg (2,370 lb) by a National Geographic team in Agusan del Sur Province, Philippines. [28] [29] [30]

Teeth

Crocodiles are polyphyodonts they are able to replace each of their 80 teeth up to 50 times in their 35- to 75-year lifespan. [31] [32] Next to each full-grown tooth, there is a small replacement tooth and an odontogenic stem cell in the dental lamina in standby that can be activated if required. [33]

Crocodilians are more closely related to birds and dinosaurs than to most animals classified as reptiles, the three families being included in the group Archosauria ('ruling reptiles'). Despite their prehistoric look, crocodiles are among the more biologically complex reptiles. Unlike other reptiles, a crocodile has a cerebral cortex and a four-chambered heart. Crocodilians also have the functional equivalent of a diaphragm by incorporating muscles used for aquatic locomotion into respiration. [34] Salt glands are present in the tongues of crocodiles and they have a pore opening on the surface of the tongue, a trait that separates them from alligators. Salt glands are dysfunctional in Alligatoridae. [20] Their function appears to be similar to that of salt glands in marine turtles. Crocodiles do not have sweat glands and release heat through their mouths. They often sleep with their mouths open and may pant like a dog. [35] Four species of freshwater crocodile climb trees to bask in areas lacking a shoreline. [36]

Senses

Crocodiles have acute senses, an evolutionary advantage that makes them successful predators. The eyes, ears and nostrils are located on top of the head, allowing the crocodile to lie low in the water, almost totally submerged and hidden from prey.

Vision

Crocodiles have very good night vision, and are mostly nocturnal hunters. They use the disadvantage of most prey animals' poor nocturnal vision to their advantage. The light receptors in crocodilians' eyes include cones and numerous rods, so it is assumed all crocodilians can see colours. [37] Crocodiles have vertical-slit shaped pupils, similar to those of domestic cats. One explanation for the evolution of slit pupils is that they exclude light more effectively than a circular pupil, helping to protect the eyes during daylight. [38] On the rear wall of the eye is a tapetum lucidum, which reflects incoming light back onto the retina, thus utilizing the small amount of light available at night to best advantage. In addition to the protection of the upper and lower eyelids, crocodiles have a nictitating membrane (sometimes called a "third eye-lid") that can be drawn over the eye from the inner corner while the lids are open. The eyeball surface is thus protected under the water while a certain degree of vision is still possible. [39]

Olfaction

Crocodilian sense of smell is also very well developed, aiding them to detect prey or animal carcasses that are either on land or in water, from far away. It is possible that crocodiles use olfaction in the egg prior to hatching. [39]

Chemoreception in crocodiles is especially interesting because they hunt in both terrestrial and aquatic surroundings. Crocodiles have only one olfactory chamber and the vomeronasal organ is absent in the adults [40] indicating all olfactory perception is limited to the olfactory system. Behavioural and olfactometer experiments indicate that crocodiles detect both air-borne and water-soluble chemicals and use their olfactory system for hunting. When above water, crocodiles enhance their ability to detect volatile odorants by gular pumping, a rhythmic movement of the floor of the pharynx. [41] [42] Crocodiles close their nostrils when submerged, so olfaction underwater is unlikely. Underwater food detection is presumably gustatory and tactile. [43]

Hearing

Crocodiles can hear well their tympanic membranes are concealed by flat flaps that may be raised or lowered by muscles. [20]

Touch

Cranial: The upper and lower jaws are covered with sensory pits, visible as small, black speckles on the skin, the crocodilian version of the lateral line organs seen in fish and many amphibians, though arising from a completely different origin. These pigmented nodules encase bundles of nerve fibers innervated beneath by branches of the trigeminal nerve. They respond to the slightest disturbance in surface water, detecting vibrations and small pressure changes as small as a single drop. [44] This makes it possible for crocodiles to detect prey, danger and intruders, even in total darkness. These sense organs are known as domed pressure receptors (DPRs). [45]

Post-Cranial: While alligators and caimans have DPRs only on their jaws, crocodiles have similar organs on almost every scale on their bodies. The function of the DPRs on the jaws is clear to catch prey, but it is still not clear what the function is of the organs on the rest of the body. The receptors flatten when exposed to increased osmotic pressure, such as that experienced when swimming in sea water hyperosmotic to the body fluids. When contact between the integument and the surrounding sea water solution is blocked, crocodiles are found to lose their ability to discriminate salinities. It has been proposed that the flattening of the sensory organ in hyperosmotic sea water is sensed by the animal as "touch", but interpreted as chemical information about its surroundings. [45] This might be why in alligators they are absent on the rest of the body. [46]

Hunting and diet

Crocodiles are ambush predators, waiting for fish or land animals to come close, then rushing out to attack. Crocodiles mostly eat fish, amphibians, crustaceans, molluscs, birds, reptiles, and mammals, and they occasionally cannibalize smaller crocodiles. What a crocodile eats varies greatly with species, size and age. From the mostly fish-eating species, like the slender-snouted and freshwater crocodiles, to the larger species like the Nile crocodile and the saltwater crocodile that prey on large mammals, such as buffalo, deer and wild boar, diet shows great diversity. Diet is also greatly affected by the size and age of the individual within the same species. All young crocodiles hunt mostly invertebrates and small fish, gradually moving on to larger prey. Being ectothermic (cold-blooded) predators, they have a very slow metabolism, so they can survive long periods without food. Despite their appearance of being slow, crocodiles have a very fast strike and are top predators in their environment, and various species have been observed attacking and killing other predators such as sharks and big cats. [47] [48] Crocodiles are also known to be aggressive scavengers who feed upon carrion and steal from other predators. [49] Evidence suggests that crocodiles also feed upon fruits, based on the discovery of seeds in stools and stomachs from many subjects as well as accounts of them feeding. [50] [51]

Crocodiles have the most acidic stomach of any vertebrate. They can easily digest bones, hooves and horns. The BBC TV [52] reported that a Nile crocodile that has lurked a long time underwater to catch prey builds up a large oxygen debt. When it has caught and eaten that prey, it closes its right aortic arch and uses its left aortic arch to flush blood loaded with carbon dioxide from its muscles directly to its stomach the resulting excess acidity in its blood supply makes it much easier for the stomach lining to secrete more stomach acid to quickly dissolve bulks of swallowed prey flesh and bone. Many large crocodilians swallow stones (called gastroliths or stomach stones), which may act as ballast to balance their bodies or assist in crushing food, [20] similar to grit ingested by birds. Herodotus claimed that Nile crocodiles had a symbiotic relationship with certain birds, such as the Egyptian plover, which enter the crocodile's mouth and pick leeches feeding on the crocodile's blood with no evidence of this interaction actually occurring in any crocodile species, it is most likely mythical or allegorical fiction. [53]

Since they feed by grabbing and holding onto their prey, they have evolved sharp teeth for piercing and holding onto flesh, and powerful muscles to close the jaws and hold them shut. The teeth are not well-suited to tearing flesh off of large prey items as are the dentition and claws of many mammalian carnivores, the hooked bills and talons of raptorial birds, or the serrated teeth of sharks. However, this is an advantage rather than a disadvantage to the crocodile since the properties of the teeth allow it to hold onto prey with the least possibility of the prey animal escaping. Cutting teeth, combined with the exceptionally high bite force, would pass through flesh easily enough to leave an escape opportunity for prey. The jaws can bite down with immense force, by far the strongest bite of any animal. The force of a large crocodile's bite is more than 5,000 lbf (22,000 N), which was measured in a 5.5 m (18 ft) Nile crocodile, in the field [54] comparing to 335 lbf (1,490 N) for a Rottweiler, 800 lbf (3,600 N) for a hyena, 2,200 lbf (9,800 N) for an American alligator, [55] [ failed verification ] and 4,095 lbf (18,220 N) for the largest confirmed great white shark. [56] A 5.2 m (17 ft) long saltwater crocodile has been confirmed as having the strongest bite force ever recorded for an animal in a laboratory setting. It was able to apply a bite force value of 3,700 lbf (16,000 N), and thus surpassed the previous record of 2,125 lbf (9,450 N) made by a 3.9 m (13 ft) long American alligator. [57] [58] Taking the measurements of several 5.2 m (17 ft) crocodiles as reference, the bite forces of 6-m individuals were estimated at 7,700 lbf (34,000 N). [59] The study, led by Dr. Gregory M. Erickson, also shed light on the larger, extinct species of crocodilians. Since crocodile anatomy has changed only slightly over the last 80 million years, current data on modern crocodilians can be used to estimate the bite force of extinct species. An 11-to-12-metre (36–39 ft) Deinosuchus would apply a force of 23,100 lbf (103,000 N), nearly twice that of the latest, higher bite force estimations of Tyrannosaurus (12,814 lbf (57,000 N)). [7] [60] [61] [62] The extraordinary bite of crocodilians is a result of their anatomy. The space for the jaw muscle in the skull is very large, which is easily visible from the outside as a bulge at each side. The muscle is so stiff, it is almost as hard as bone to touch, as if it were the continuum of the skull. Another trait is that most of the muscle in a crocodile's jaw is arranged for clamping down. Despite the strong muscles to close the jaw, crocodiles have extremely small and weak muscles to open the jaw. Crocodiles can thus be subdued for study or transport by taping their jaws or holding their jaws shut with large rubber bands cut from automobile inner tubes.

Locomotion

Crocodiles can move quickly over short distances, even out of water. The land speed record for a crocodile is 17 km/h (11 mph) measured in a galloping Australian freshwater crocodile. [63] Maximum speed varies between species. Some species can gallop, including Cuban crocodiles, Johnston's crocodiles, New Guinea crocodiles, African dwarf crocodiles, and even small Nile crocodiles. The fastest means by which most species can move is a "belly run", in which the body moves in a snake-like (sinusoidal) fashion, limbs splayed out to either side paddling away frantically while the tail whips to and fro. Crocodiles can reach speeds of 10–11 km/h (6–7 mph) when they "belly run", and often faster if slipping down muddy riverbanks. When a crocodile walks quickly, it holds its legs in a straighter and more upright position under its body, which is called the "high walk". This walk allows a speed of up to 5 km/h. [64]

Crocodiles may possess a homing instinct. In northern Australia, three rogue saltwater crocodiles were relocated 400 km (249 mi) by helicopter, but returned to their original locations within three weeks, based on data obtained from tracking devices attached to them. [65]

Longevity

Measuring crocodile age is unreliable, although several techniques are used to derive a reasonable guess. The most common method is to measure lamellar growth rings in bones and teeth—each ring corresponds to a change in growth rate which typically occurs once a year between dry and wet seasons. [66] Bearing these inaccuracies in mind, it can be safely said that all crocodile species have an average lifespan of at least 30–40 years, and in the case of larger species an average of 60–70 years. The oldest crocodiles appear to be the largest species. C. porosus is estimated to live around 70 years on average, with limited evidence of some individuals exceeding 100 years. [67]

In captivity, some individuals are claimed to have lived for over a century. A male crocodile lived to an estimated age of 110–115 years in a Russian zoo in Yekaterinburg. [68] Named Kolya, he joined the zoo around 1913 to 1915, fully grown, after touring in an animal show, and lived until 1995. [68] A male freshwater crocodile lived to an estimated age of 120–140 years at the Australia Zoo. [69] Known affectionately as "Mr. Freshie", he was rescued around 1970 by Bob Irwin and Steve Irwin, after being shot twice by hunters and losing an eye as a result, and lived until 2010. [69] Crocworld Conservation Centre, in Scottburgh, South Africa, claims to have a male Nile crocodile that was born in 1900. Named Henry, the crocodile is said to have lived in Botswana along the Okavango River, according to centre director Martin Rodrigues. [70] [71]

Social behaviour and vocalization

Crocodiles are the most social of reptiles. Even though they do not form social groups, many species congregate in certain sections of rivers, tolerating each other at times of feeding and basking. Most species are not highly territorial, with the exception of the saltwater crocodile, which is a highly territorial and aggressive species: a mature, male saltwater crocodile will not tolerate any other males at any time of the year, but most other species are more flexible. There is a certain form of hierarchy in crocodiles: the largest and heaviest males are at the top, having access to the best basking site, while females are priority during a group feeding of a big kill or carcass. A good example of the hierarchy in crocodiles would be the case of the Nile crocodile. This species clearly displays all of these behaviours. Studies in this area are not thorough, however, and many species are yet to be studied in greater detail. [72] Mugger crocodiles are also known to show toleration in group feedings and tend to congregate in certain areas. However, males of all species are aggressive towards each other during mating season, to gain access to females.

Crocodiles are also the most vocal of all reptiles, producing a wide variety of sounds during various situations and conditions, depending on species, age, size and sex. Depending on the context, some species can communicate over 20 different messages through vocalizations alone. [73] Some of these vocalizations are made during social communication, especially during territorial displays towards the same sex and courtship with the opposite sex the common concern being reproduction. Therefore most conspecific vocalization is made during the breeding season, with the exception being year-round territorial behaviour in some species and quarrels during feeding. Crocodiles also produce different distress calls and in aggressive displays to their own kind and other animals notably other predators during interspecific predatory confrontations over carcasses and terrestrial kills.

Specific vocalisations include —

  • Chirp: When about to hatch, the young make a "peeping" noise, which encourages the female to excavate the nest. The female then gathers the hatchlings in her mouth and transports them to the water, where they remain in a group for several months, protected by the female [74]
  • Distress call: A high-pitched call used mostly by younger animals to alert other crocodiles to imminent danger or an animal being attacked.
  • Threat call: A hissing sound that has also been described as a coughing noise.
  • Hatching call: Emitted by a female when breeding to alert other crocodiles that she has laid eggs in her nest.
  • Bellowing: Male crocodiles are especially vociferous. Bellowing choruses occur most often in the spring when breeding groups congregate, but can occur at any time of year. To bellow, males noticeably inflate as they raise the tail and head out of water, slowly waving the tail back and forth. They then puff out the throat and with a closed mouth, begin to vibrate air. Just before bellowing, males project an infrasonic signal at about 10 Hz through the water, which vibrates the ground and nearby objects. These low-frequency vibrations travel great distances through both air and water to advertise the male's presence and are so powerful they result in the water's appearing to "dance". [75]

Reproduction

Crocodiles lay eggs, which are laid in either holes or mound nests, depending on species. A hole nest is usually excavated in sand and a mound nest is usually constructed out of vegetation. Nesting periods range from a few weeks up to six months. Courtship takes place in a series of behavioural interactions that include a variety of snout rubbing and submissive display that can take a long time. Mating always takes place in water, where the pair can be observed mating several times. Females can build or dig several trial nests which appear incomplete and abandoned later. Egg-laying usually takes place at night and about 30–40 minutes. [76] Females are highly protective of their nests and young. The eggs are hard shelled, but translucent at the time of egg-laying. Depending on the species of crocodile, 7 to 95 eggs are laid. Crocodile embryos do not have sex chromosomes, and unlike humans, sex is not determined genetically. Sex is determined by temperature, where at 30 °C (86 °F) or less most hatchlings are females and at 31 °C (88 °F), offspring are of both sexes. A temperature of 32 to 33 °C (90 to 91 °F) gives mostly males whereas above 33 °C (91 °F) in some species continues to give males, but in other species resulting in females, which are sometimes called high-temperature females. [77] Temperature also affects growth and survival rate of the young, which may explain the sexual dimorphism in crocodiles. The average incubation period is around 80 days, and also is dependent on temperature and species that usually ranges from 65 to 95 days. The eggshell structure is very conservative through evolution but there are enough changes to tell different species apart by their eggshell microstructure. [78] Scutes may play a role in calcium storage for eggshell formation. [23]

At the time of hatching, the young start calling within the eggs. They have an egg-tooth at the tip of their snouts, which is developed from the skin, and that helps them pierce out of the shell. Hearing the calls, the female usually excavates the nest and sometimes takes the unhatched eggs in her mouth, slowly rolling the eggs to help the process. The young is usually carried to the water in the mouth. She would then introduce her hatchlings to the water and even feed them. [79] The mother would then take care of her young for over a year before the next mating season. In the absence of the mother crocodile, the father would act in her place to take care of the young. [80] However, even with a sophisticated parental nurturing, young crocodiles have a very high mortality rate due to their vulnerability to predation. [81] A group of hatchlings is called a pod or crèche and may be protected for months. [76]

Cognition

Crocodiles possess some advanced cognitive abilities. [82] [83] [84] They can observe and use patterns of prey behaviour, such as when prey come to the river to drink at the same time each day. Vladimir Dinets of the University of Tennessee, observed that crocodiles use twigs as bait for birds looking for nesting material. [85] They place sticks on their snouts and partly submerge themselves. When the birds swooped in to get the sticks, the crocodiles then catch the birds. Crocodiles only do this in spring nesting seasons of the birds, when there is high demand for sticks to be used for building nests. Vladimir also discovered other similar observations from various scientists, some dating back to the 19th century. [82] [84] Aside from using sticks, crocodiles are also capable of cooperative hunting. [84] [86] Large numbers of crocodiles swim in circles to trap fish and take turns snatching them. In hunting larger prey, crocodiles swarm in, with one holding the prey down as the others rip it apart.

According to a 2015 study, crocodiles engage in all three main types of play behaviour recorded in animals: locomotor play, play with objects and social play. Play with objects is reported most often, but locomotor play such as repeatedly sliding down slopes, and social play such as riding on the backs of other crocodiles is also reported. This behaviour was exhibited with conspecifics and mammals and is apparently not uncommon, though has been difficult to observe and interpret in the past due to obvious dangers of interacting with large carnivores. [87]

Crocodylidae contains two subfamilies: Crocodylinae and Osteolaeminae. [88] Crocodylinae contains 13-14 living species, as well as 6 extinct species. Osteolaeminae was named by Christopher Brochu in 2003 as a subfamily of Crocodylidae separate from Crocodylinae, [89] and contains the two extant genera Osteolaemus and Mecistops, along with several extinct genera. The number of extant species within Osteolaeminae is currently in question. [19]


New study unravels Darwin's 'abominable mystery' surrounding origin of flowering plants

The origin of flowering plants famously puzzled Charles Darwin, who described their sudden appearance in the fossil record from relatively recent geological times as an "abominable mystery." This mystery has further deepened with an inexplicable discrepancy between the relatively recent fossil record and a much older time of origin of flowering plants estimated using genome data.

Now a team of scientists from Switzerland, Sweden, the UK, and China may have solved the puzzle. Their results show flowering plants indeed originated in the Jurassic or earlier, that is millions of years earlier than their oldest undisputed fossil evidence, according to a new study published in the scientific journal Nature Ecology & Evolution. The lack of older fossils, according to their results, might instead be the product of low probability of fossilization and the rarity of early flowering plants.

"A diverse group of flowering plants had been living for a very long time shadowed by ferns and gymnosperms, which were dominating ancient ecosystems. This reminds me of how modern mammals lived for a long time laying low in the age of dinosaurs, before becoming a dominant component of modern faunas," said lead author Dr Daniele Silvestro, from the University of Fribourg in Switzerland.

Flowering plants are by far the most abundant and diverse group of plants globally in modern ecosystems, far outnumbering ferns and gymnosperms, and including almost all crops sustaining human livelihood. The fossil record shows this pattern was established over the past 80-100 million years, while earlier flowering plants are thought to have been small and rare. The new results show that flowering plants have been around for as many as 100 million years before they finally came to dominance.

"While we do not expect our study to put an end to the debate about angiosperm origin, it does provide a strong motivation for what some consider a hunt for the snark -- a Jurassic flowering plant. Rather than a mythical artefact of genome-based analyses, Jurassic angiosperms are an expectation of our interpretation of the fossil record," said co-author Professor Philip Donoghue, from the University of Bristol in the UK.

The research conclusions are based on complex modelling using a large global database of fossil occurrences, which Dr Yaowu Xing and his team at the Xishuangbanna Tropical Botanical Garden compiled from more than 700 publications. These records, amounting to more than 15,000, included members of many groups of plants including representatives of palms, orchids, sunflowers, and peas.

"Scientific debate has long been polarised between palaeontologists who estimate the antiquity of angiosperms based on the age of the oldest fossils, versus molecular biologists who use this information to calibrate molecular evolution to geologic time. Our study shows that these views are too simplistic the fossil record has to be interpreted," said co-author Dr Christine Bacon, from the University of Gothenburg in Sweden.

"A literal reading of the fossil record cannot be used to estimate realistically the time of origin of a group. Instead, we had to develop new mathematical models and use computer simulations to solve this problem in a robust way."

Even 140 years after Darwin's conundrum about the origin of flowering plants, the debate has maintained a central place in the scientific arena. In particular, many studies based on phylogenetic analyses of modern plants and their genomes estimated that the group originated significantly earlier than indicated by the fossil record, a finding widely disputed in palaeontological research. The new study, which was based exclusively on fossils and did not include genome data or evolutionary trees, shows an earlier age of flowering plants is not an artifact of phylogenetic analyses, but is in fact supported by palaeontological data as well.

Co-author Professor Alexandre Antonelli, Director of Science at the Royal Botanic Gardens, Kew in the UK, added: "Understanding when flowering plants went from being an insignificant group into becoming the cornerstone of most terrestrial ecosystems shows us that nature is dynamic. The devastating human impact on climate and biodiversity could mean that the successful species in the future will be very different to the ones we are accustomed to now."


Origin of Life: Modern Theory of Origin of Life

According to this theory life originated on early earth through physico-chemical pro­cesses of atoms combining to form molecules, molecules in turn reacting to produce inor­ganic and organic compounds. Organic compounds interacted to produce all types of macromolecules which organised to form the first living system or cells.

Image Courtesy : upload.wikimedia.org/wikipedia/commons/6/6f/Blacksmoker_in_Atlantic_Ocean.jpg

Thus according to this theory ‘life’ originated upon our earth spontaneously from non-­living matter. First inorganic compounds and then organic compounds were formed in accordance with ever-changing environmental conditions. This is called chemical evolution which cannot occur under present environmental conditions upon earth. Conditions suitable for origin of life existed only upon primitive earth.

Oparin-Haldane theory is also called chemical theory or naturalistic theory. A. I. Oparin (1894-1980) was a Russian Scientist. He published his book “The origin of Life” in 1936 and an English edition in 1938. J.B.S. Haldane (1892-1964) was born in England but migrated to India in July 1957 and settled in Bhubaneswar, Orissa. He was biologist, biochemist and geneticist. Both Oparin (1938) and Haldane (1929) gave similar views regarding the origin of life.

Modem views regarding the origin of life include chemical evolution and biological evolution:

A. Chemical Evolution (Chemogeny):

1. The Atomic Phase:

Early earth had innumerable atoms of all those elements (e.g., hydrogen, oxygen, carbon, nitrogen, sulphur, phosphorus, etc.) which are essential for the formation of protoplasm. Atoms were segregated in three concentric masses according to their weights, (a) The heaviest atoms of iron, nickel, copper, etc. were found in the centre of the earth, (b) Medium weight atoms of sodium, potassium, silicon, magnesium, alu­minium, phosphorus, chlorine, fluorine, sulphur, etc. were collected in the core of the earth, (c) The lightest atoms of nitrogen, hydrogen, oxygen, carbon etc. formed the primitive atmosphere.

2. Formation of Inorganic Molecules:

Free atoms combined to form inorganic molecules such as H2 (Hydrogen), N2 (Nitrogen), H20 (Water vapour), CH4 (Methane), NH3 (Ammonia), C02 (Carbon dioxide). Hydrogen atoms were most numerous and most reactive in primitive atmosphere.

First hydrogen atoms combined with all oxygen atoms to form water and leaving no free oxygen. Thus primitive atmosphere was reducing atmosphere (without free oxygen) unlike the present oxidising atmosphere (with free oxygen).

Hydrogen atoms also combined with nitrogen, forming ammonia (NH3). So water and ammonia were probably the first molecules of primitive earth.

3. Formation of Simple Organic Molecules (Monomers):

The early inorganic molecules interacted and produced simple organic molecules such as simple sugars (e.g., ribose, deoxyribose, glucose, etc.), nitrogenous bases (e.g., purines, pyrimidines), amino acids, glycerol, fatty acids, etc.

Torrential rains must have fallen. As the water rushed down, it must have dissolved away and carried with it salts and minerals, and ultimately accumulated in the form of oceans. Thus ancient oceanic water contained large amounts of dissolved NH3, CH4, HCN, nitrides, carbides, various gases and elements.

CH4 + C02 + H20 —> Sugars + Glycerol + Fatty Acids

CH4 + HCN + NH3 + H20 —> Purines + Pyrimidines

Some external sources must have been acting on the mixture for reactions. These external sources might be (i) solar radiations such as ultra-violet light, X-rays, etc., (ii) energy from electrical discharges like lightning, (iii) high energy radiations are other sources of energies (probably unstable isotopes on the primitive earth). There was no ozone layer in the atmosphere.

A soup-like broth of chemicals formed in oceans of the early earth from which living cells are believed to have appeared, was termed by J.B. Haldane (1920) as ‘prebiotic soup’ (also called ‘hot dilute soup’). Thus the stage was set for combination of various chemical elements. Once formed, the organic molecules accumulated in water be­cause their degradation was extremely slow in the absence of any life or enzyme catalysts.

Experimental Evidence for Abiogenic Molecular Evolution of Life:

Stanley Miller in 1953, who was then a graduate student of Harold Urey (1893-1981) at the University of Chicago, demonstrated it clearly that ultra-violet radiation or electrical discharges or heat or a combination of these can produce complex organic compounds from a mixture of methane, ammonia, water (stream of water), and hydrogen. The ratio of methane, ammonia and hydrogen in Miller’s experiment was 2:1:2.

Miller circulated four gases— methane, ammonia, hydrogen and water vapour in an air tight apparatus and passed electrical dis­charges from electrodes at 800°C. He passed the mixture through a condenser.

He circulated the gases continuously in this way for one week and then analysed the chemical composition of the liquid inside the apparatus. He found a large number of simple organic compounds including some amino acids such as alanine, glycine and aspartic acid. Miller conducted the experiment to test the idea that organic molecules could be synthesized in a reducing environment.

Other substances, such as urea, hydrogen cyanide, lactic acid and acetic acid were also present. In another experiment Miller circulated the mixture of the gases in the same way but he did not pass the electric discharge. He could not get the significant yield of the organic compounds.

Later on many investigators have syn­thesized a great variety of organic compounds including purines, pyrimidine’s and simple sugars, etc. It is considered that the essential ‘building blocks’ such as nucleotides, amino ac­ids, etc. of living organisms could thus have formed on the primitive earth.

4. Formation of Com­plex Organic Molecules (Macromolecules):

A variety of amino acids, fatty acids, hydrocarbons, purines and py­rimidine bases, simple sugars and other organic compounds accumulated in the ancient seas. In the primeval atmosphere electrical discharge, lightning, solar energy, ATP and polyphosphates might have provided the source of energy for polymerisation reactions of organic synthesis.

S.W. Fox of the University of Miami has demonstrated that if a nearly dry mixture of amino acids is heated, polypeptide molecules are synthesized. Similarly simple sugars could form polysaccharides and fatty acids could combine to produce fats. Amino acids could form proteins, when other factors were involved.

Thus the small simple organic molecules combined to form large complex organic molecules, e.g., amino acid units joined to form polypeptides and proteins, simple sugar units combined to form polysaccharides, fatty acids and glycerol united to form fats, sugars, nitrogenous bases, and phosphates combined into nucleotides which polymer­ized into nucleic acids in the ancient oceans.

Nitrogenous Bases + Pentose Sugars + Phosphates ———> Nucleotides

Nucleotides + Nucleotides ———–> Nucleic Acids

Which came First RNA or Protein?

The RNA first Hypothesis:

In the early 1980s three scientists (Leslia orgel, Francis Crick and Carl Woese) independently proposed the RNA World as the first stage in the evolution of life in which RNA catalysed all molecules necessary for survival and replication. Thomas Ceck and Sidney Altman shared Nobel Prize in chemistry in 1989 because they discovered that RNA can be both a substrate and an enzyme.

If the first cells used RNA as their hereditary molecule, DNA evolved from an RNA template. DNA probably did not evolve as a hereditary molecule un tills RNA based life became enclosed in membrane. Once cells evolved DNA probably replaced RNA as the genetic code for most organisms.

The Protein First Hypothesis:

A number of authors (for example Sidney Fox, 1978) claimed that a protein catalytic system must have developed before a nucleic acid replicative system. Sidney Fox had shown that amino acids polymerized abiotically when exposed to dry heat to form proteinoids.

Cairns-Smith’s Hypothesis:

It was proposed by Graham Caims-Smith, according to which both proteins and RNA originated at the same time.

Formation of Nucleoproteins:

The giant nucleoprotein molecules were formed by the union of nucleic acid and protein molecules. These nucleoprotein particles were described as free living genes. Nucleoproteins gave most probably the first sign of life.

B. Biological Evolution (Biogeny):

Conditions for the Origin of Life:

For origin of life, at least three conditions are needed.

(a) There must have been a supply of replicators, i.e., self-producing molecules.

(b) Copying of these replicators must have been subject to error through mutation.

(c) The system of replicators must have required a continuous supply of free energy and partial isolation from the general environment.

The high temperature in early earth would have fulfilled the requirement of mutation.

1. Protobionts or Protocells:

These are at least two types of fairly simple laboratory produced structures— Oparin’s coacervates and Fox’s microspheres which possess some of the basic prerequisites of proto cells.

Although these structures were created artificially, they point to the likelihood that non-biological membrane enclosures (proto cells) could have sustained reactive systems for at least short periods of time and led to research on the experimental production of membrane bound vesicles containing molecules, i.e., proto cells.

The first hypothesis was proposed by Oparin (1920). According to this hypothesis early proto cell could have been a coacervate. Oparin gave the term coacer­vates. These were non-living structures that led to the formation of the first living cells from which the more complex cells have today evolved.

Oparin speculated that a proto cell consisted a carbohydrates, proteins, lipids and nucleic acids that accumulated to form a coacervate. Such a structure could have consisted of a collection of organic macromolecules surrounded by a film of water molecules.

This arrangement of water molecules, although not a membrane, could have functioned as a physical barrier between the organic molecules and their surroundings. They could selectively take in materials from their sur­roundings and incorporate them into their structure.

Coacervates have been synthesized in the laboratory. They can selectively absorb chemicals from the surrounding water and incorpo­rate them into their structure. Some coacervates contain enzymes that direct a specific type of chemical reaction.

Because they lack a definite membrane, no one claims coacervates are alive, but they do exhibit some life like characters. They have a simple but persistent orga­nization. They can remain in solution for extended periods. They have the ability to increase in size.

An another hypothesis is that early proto cell could have been a microsphere. A microsphere is a non-living collection of organic macromolecules with double layered outer boundary. The term microsphere was given by Sydney Fox (1958-1964).

Sidney Fox demonstrated the ability to build microspheres from proteinoids. Proteinoids are protein like structures consisting of branched chains of amino acids. Proteinoids are formed by the dehydration synthesis of amino acids at a temperature of 180°C. Fox, from the University of Miami, showed that it is feasible to combine single amino acids into polymers of proteinoids. He also demonstrated the ability to build microspheres from these proteinoids.

Fox observed small spherical cell-like units that had arisen from aggregations of proteinoids. These molecular aggregates were called proteinoid microspheres. The first non-cellular forms of life could have originated 3 billion years back. They would have been giant molecules (RNA, Proteins, Polysaccharides etc.).

Microspheres can be formed when proteinoids are placed in boiling water and slowly allowed to cool. Some of the proteinoid material produces a double-boundary structure that encloses the microsphere. Although these walls do not contain lipids, they do exhibit some membrane like characteristics and suggest the structure of a cellular membrane.

Microspheres swell or shrink depending on the osmotic potential in the surrounding solution. They also display a type of internal movement (streaming) similar to that exhibited by cells and contain some proteinoids that function as enzymes. Using ATP as a source of energy, microspheres can direct the formation of polypeptides and nucleic acids. They can absorb material from the surrounding medium.

They have the ability of motility, growth, binary fission into two particles and a capacity of reproduction by budding and fragmentation. Superficially, their budding resembles with those of bacteria and fungi.

According to some investigators, microspheres can be considered first living cells.

2. Origin of Prokaryotes:

Prokaryotes were originated from proto cells about 3.5 billion years ago in the sea. The atmosphere was anaerobic because free oxygen was absent in the atmosphere. Prokaryotes do not have nuclear membrane, cytoskeleton or complex organelles. They divide by binary fission. Some of the oldest known fossil cells appear as parts of stromatolites. Stromatolites are formed today from sediments and photosynthetic prokaryotes (mainly filamentous cynobacteria— blue green algae).

3. Evolution of Modes of Nutrition:

The earliest prokaryotes presumably obtained energy by the fermen­tation of organic molecules from the sea broth in oxygen free atmosphere (reducing atmosphere). They required readymade organic material as food and thus they were heterotrophs.

Due to rapid increase in the number of heterotrophs the nutrient from sea water began to disappear and gradually exhausted. That led to the evolution of autotrophs. These organisms were capable of producing their own organic molecules by chemosynthesis or photosynthesis.

Drop in temperature stopped synthesis of organic molecules in the sea water. Some of the early prokaryotes got converted into chemoautotrophs which prepared organic food by using energy released during certain inorganic chemical reactions. These anaerobic chemoautotrophs were like present anaerobic bacteria. They released CO2 in the atmosphere.

Evolution of chlorophyll molecule enabled certain protocells to utilize light energy and synthesize carbohydrates. These were anaerobic photoautotrophs. They did not use water as a hydrogen source. They were similar to present day sulphur bacteria in which hydrogen sulphide split into hydrogen and sulphur. Hydrogen was used in food manufacture and sulphur was released as a waste product.

Aerobic photoautotrophs used water as a source of hydrogen and carbon dioxide as source of carbon to synthesize carbohydrate in the presence of solar energy. The first aerobic photoautotrophs were cyanobacteria (blue green algae) like forms which had chlo­rophyll. They released oxygen in the atmosphere as the by product of photosynthesis. The main source of genetic variation was mutation.

As the number of photoautotrophs increased, oxygen was released in the sea and atmosphere. Free oxygen than reacted with methane and ammonia present in the primitive atmosphere and transformed methane and ammonia into carbon dioxide and free nitrogen.

The oldest fossil belonging to blue green algae, named Archaeospheroides barbertonensis which is 3.2 billion years old. Oxygen releasing prokaryotes first appeared at least 2.5 billion years ago.

4. Formation of Ozone Layer:

As oxygen accumulated in the atmosphere, the ultra­violet light changed some of oxygen into ozone.

The ozone formed a layer in the atmosphere, blocking the ultraviolet light and leaving the visible light as the main source of energy.

5. Origin of Eukaryotes:

The eukaryotes developed from primitive prokaryotic cells about 1.5 billion years ago. There are two views regarding the origin of eukaryotes.

According to Margulis (1970-1981) of Boston Uni­versity, some anaerobic predator host cells engulfed primitive aerobic bacte­ria but did not digest them. These aerobic bacteria established themselves inside the host cells as symbionts. Such preda­tor host cells became the first eukaryotic cells.

The predator host cells that engulfed aerobic bacteria evolved into animal cells while those that captured both aerobic bacteria and blue-green algae became eukaryotic plant cells. The aerobic bacteria established them­selves as mitochondria and blue green algae as chloroplasts.

(ii) Origin by Invagination:

Ac­cording to this view cell organelles of eukaryotic cells might have originated by invagination of surface membrane of primitive prokaryotic cells.


Communicating with Predators

Other studies are less easy to reconcile with an evolutionary worldview. Researchers have found that plant volatile emission does not just affect other plants for herbivore defense it also may attract the natural predators of the herbivore to come feed on the pest. In one study, bean plants infested with aphids were planted in the same pot as plants without aphids. The non-infected plants were then shown to release the same compounds that made them attractive to a parasitic wasp that preys on aphids as infested plants. This also applied when uninfested plants were grown in a hydroponic solution which had previously contained infested plants.6 This would appear to indicate that the volatiles were passed from plant to plant by means of the soil, as this occurred even when the roots did not touch or did not share the same container simultaneously.

The cress plant, a common model organism in botany, releases volatiles in response to predation by the caterpillars of cabbage white butterflies. As the caterpillars chew on the cress, it releases volatiles that attract a parasitic wasp. The parasitic wasps responded more to plants damaged specifically by cabbage white caterpillars, though they also were attracted to plants which had been damaged manually and those with generic herbivore damage.7 This result could indicate that the cress was able to recognize the herbivore feeding on it and tune its volatile release to attract the right predator to deal with it.

Another particularly clever experiment was done with lima beans, corn, and tobacco. Rather than assume that the uninfested plants that sensed volatiles had a better defense against herbivores, these researchers tested the idea by placing non-infested tobacco plants in a wind tunnel and placing lima bean plants down wind. Then, the lima beans were deliberately infested with herbivorous mites and the tobacco plants removed. New, uninfected lima bean plants were then introduced. After a period of days, the herbivorous mites were introduced to the uninfected plants. The same process was applied to the corn plants, except with a different herbivore-predator combination. It was found that, in a lab environment with air flow, uninfected plants were more resistant to their herbivores, while in a greenhouse environment with no air flow, there was no difference.8 This is expected as plant volatiles are carried by wind above ground and normally have a range of a few centimeters even in the best conditions.


Part 2: Choanoflagellate colonies, bacterial signals and animal origins

00:00:07.22 So, Hello.
00:00:09.01 My name is Nicole King.
00:00:10.11 I'm an investigator in the Howard Hughes Medical Institute
00:00:12.02 and a professor at the
00:00:13.26 University of California at Berkeley,
00:00:15.20 and I'm excited to be here today
00:00:17.17 to tell you about organisms
00:00:19.15 that we study in my laboratory, the choanoflagellates,
00:00:23.01 and tell you about how they interact with bacteria
00:00:24.09 and how these interactions
00:00:26.11 might inform us about animal origins.
00:00:29.27 Now, I want to provide a little bit of introduction
00:00:32.10 to the motivation for the research in my lab.
00:00:34.25 There's been a lot of focus in the past
00:00:37.20 on understanding how different animal body forms diversified,
00:00:41.21 and understanding how different animals
00:00:43.18 are related to each other on the phylogenetic tree.
00:00:45.29 But, in fact, we know relatively little
00:00:47.29 about the nature of the organisms
00:00:49.22 from which animals first evolved,
00:00:51.25 and in my laboratory we're particularly interested
00:00:53.28 in understanding the genomic innovations
00:00:56.19 and the influences of cell biology
00:00:59.29 and interspecies interactions
00:01:01.29 and understanding how that might have contributed
00:01:04.10 to what we call the transition to multicellularity.
00:01:06.13 That is, how did ancestrally unicellular organisms
00:01:10.15 evolve into organisms
00:01:13.05 that are capable of simple multicellularity,
00:01:15.09 such as this hypothetical colony.
00:01:18.26 In Part I of my talk,
00:01:23.22 I previously spoke about how
00:01:26.05 an unusual group of organisms called the choanoflagellates
00:01:29.03 can help us understand animal origins,
00:01:31.24 and I told you that
00:01:34.13 the first animals likely had genes in their genomes
00:01:37.25 that had evolved much earlier.
00:01:39.15 And so, by comparing choanoflagellates to animals,
00:01:43.06 we're learning about the nature of the first animals.
00:01:45.22 In this part of my talk,
00:01:47.29 I'm going to focus on one particular species
00:01:50.16 of choanoflagellate,
00:01:52.15 and I'm going to tell you that this choanoflagellate
00:01:54.09 actually can transition from being single-celled
00:01:56.17 to having simple multicellularity,
00:01:58.29 and I'm going to tell you about how we've been developing this
00:02:01.29 into a new model system
00:02:03.24 so that we can learn about how that transition,
00:02:06.02 from being single-celled to multicellular,
00:02:08.09 is regulated.
00:02:09.23 And, what we don't know now,
00:02:11.19 but we hope to learn,
00:02:13.05 is whether the regulation of multicellularity in this organism
00:02:15.21 might give us specific insights into the ancestry
00:02:18.14 of multicellularity in animals.
00:02:22.08 Now, the organisms that we study
00:02:24.16 are in fact not animals.
00:02:26.18 They are the sister group of animals.
00:02:28.11 They are called choanoflagellates
00:02:30.06 and they sit on this very special part of the phylogenetic tree
00:02:32.26 because they are the closest living relatives of animals.
00:02:36.04 And our understanding that choanoflagellates
00:02:38.19 sit here on the tree,
00:02:40.07 and that they are our, essentially, evolutionary cousins,
00:02:42.04 comes from multiple lines of evidence.
00:02:44.08 It comes from comparisons of the cell biology
00:02:46.15 of choanoflagellates to the cell biology of animals.
00:02:50.02 It comes from many different independent types
00:02:52.11 of phylogenetic analyses.
00:02:54.12 And it comes from comparisons between
00:02:56.24 the genomes of choanoflagellates and the genomes of animals.
00:03:00.05 From all of these different sets of data,
00:03:02.03 it's now become very clear
00:03:04.11 that the study of choanoflagellates,
00:03:06.14 our closest living relatives,
00:03:08.24 tells us about the biology of our last common ancestor.
00:03:14.05 So, I introduced this in Part I,
00:03:16.24 but I just want to quickly
00:03:19.21 review the biology of choanoflagellates
00:03:22.00 because it becomes essential for understanding
00:03:24.00 what I'm about to tell you in the later part of this talk.
00:03:28.09 Choanoflagellates are microbial eukaryotes.
00:03:31.05 They have a spheroid.
00:03:34.05 spherical or ovoid cell body,
00:03:36.14 an apical collar of actin-filled microvilli,
00:03:39.11 and a long apical flagellum.
00:03:41.14 And this flagellum can undulate
00:03:43.26 from side to side,
00:03:45.21 and this undulation creates water currents
00:03:47.26 that allow choanoflagellates
00:03:50.26 to swim through the water column,
00:03:53.22 but these water currents also pull water
00:03:57.27 from the media up against the collar,
00:04:00.04 and those water currents can carry bacteria,
00:04:02.22 and bacteria are actually the primary prey target
00:04:06.10 for choanoflagellates.
00:04:07.28 Choanoflagellates are voracious bacteriovores.
00:04:10.12 They love eating bacteria,
00:04:11.27 they're very good at,
00:04:13.22 and this is an essential part of their biology
00:04:15.28 - their ability to capture and ingest bacteria.
00:04:19.24 So, choanoflagellates have a lot of really interesting aspects
00:04:22.10 to their biology,
00:04:24.13 one of which, obviously, is this ability to eat bacteria,
00:04:27.02 but one of the aspects of their biology
00:04:29.03 which really excited me when I first learned about it
00:04:31.13 as a postdoc
00:04:33.04 is that some choanoflagellates can form
00:04:35.11 these beautiful multi-celled colonies.
00:04:38.04 These colonies are in fact, to me,
00:04:40.18 reminiscent of some types of marine invertebrate embryos,
00:04:44.19 and these colonies
00:04:47.11 raise all sorts of questions about
00:04:49.29 how do the cells interact
00:04:52.03 and how is this process regulated?
00:04:55.05 Moreover, you'll remember that I told you
00:04:58.21 that one of the major questions in my laboratory
00:05:00.28 is how, evolutionarily,
00:05:03.09 did the ancestors of animals evolve the ability
00:05:06.08 to form simple multicellular morphologies.
00:05:08.25 And here we have, in living color,
00:05:11.08 an organism that actually does it,
00:05:13.08 every day.
00:05:15.12 And so, what we've been doing in my laboratory
00:05:17.02 is to understand.
00:05:18.23 is to study this process
00:05:21.07 in minute detail the same way
00:05:24.23 that a Drosophila biologist might try to study
00:05:26.29 how a fruit fly goes from an egg
00:05:29.00 to an embryo to an adult,
00:05:31.23 or a mouse biologist
00:05:34.07 studies the same process of development.
00:05:36.02 We're trying to study, in mechanistic detail,
00:05:38.22 the process by which this organism, S. rosetta,
00:05:41.16 goes from being a single cell
00:05:44.05 to a multi-celled colony.
00:05:46.19 And, in particular,
00:05:47.25 we're focusing on trying to understand
00:05:50.13 the mechanisms of cell adhesion and cell signaling
00:05:52.03 within the colony.
00:05:53.09 We're trying to understand
00:05:54.24 what triggers this transition
00:05:56.13 from being single-celled to colonial,
00:05:58.11 and eventually we hope to learn
00:06:02.00 whether the mechanisms underlying this transition
00:06:03.22 in choanoflagellates
00:06:05.15 are related to mechanisms underlying animal development,
00:06:08.02 in which case we would infer
00:06:10.01 that they are ancient and evolved
00:06:12.07 before the origin and diversification of animals.
00:06:14.23 So, I'm going to tell you a lot
00:06:17.18 about this organism, S. rosetta.
00:06:19.14 And, the first thing I need to tell you
00:06:21.23 is that it does a lot of exciting things.
00:06:24.20 You know, I think many of us think
00:06:26.27 about protozoa as being simple organisms
00:06:31.01 that lead a rather mundane life,
00:06:34.07 but this organism not only can switch between
00:06:37.18 being single-celled and colonial,
00:06:39.20 it actually has a really wild and crazy life history.
00:06:42.18 It has many different morphologies
00:06:45.24 that it can produce,
00:06:47.22 and these are all coming
00:06:51.28 from an organism.
00:06:53.14 a single genotype is encoding
00:06:55.03 for all of these different forms,
00:06:57.09 and many of these forms
00:06:59.10 can differentiate into other forms.
00:07:02.02 So, this cell in the center
00:07:04.02 we call the 'slow swimmer',
00:07:06.08 and cultures that only have slow swimmers in them
00:07:09.03 are capable of producing rosette colonies,
00:07:13.02 chain colonies,
00:07:14.26 fast swimmer cells.
00:07:16.15 and these fast swimmers can differentiate
00:07:18.16 into these attached cells.
00:07:20.20 So, there's a lot of dynamic cell differentiation that's going on,
00:07:23.09 and it seems to have at least some
00:07:26.00 environmental component because we can,
00:07:28.05 in the laboratory, push the choanoflagellate
00:07:30.22 toward different types of cells
00:07:33.14 by changing the environmental conditions
00:07:35.10 in which we grow the cells.
00:07:37.23 For the sake of simplicity
00:07:39.11 and also to focus on things that we know the most about,
00:07:41.16 today, I'm only going to focus on
00:07:44.07 this part of the life history,
00:07:46.16 and try to understand,
00:07:48.25 what is it that allows this cell to differentiate
00:07:52.01 into these other multicellular forms.
00:07:54.16 In particular,
00:07:57.12 we're going to talk about the rosette form,
00:07:59.19 because this is the form in which S. rosetta
00:08:01.28 was actually isolated from nature,
00:08:04.03 and this is the one that is most similar
00:08:07.12 to the multicellular form
00:08:09.22 that we hypothesize
00:08:12.01 was required for the ancestry of animals.
00:08:14.21 So, we want to know,
00:08:16.21 how do rosettes form?
00:08:19.09 Are they forming
00:08:21.14 from multiple cells swimming together and sticking?
00:08:24.14 And that would be similar
00:08:26.05 to the slime mold Dictyostelium.
00:08:28.11 or are they more similar to animals
00:08:30.09 in the way in which they form?
00:08:31.24 That is to say,
00:08:33.12 does a single cell divide repeatedly
00:08:35.11 to form a rosette.
00:08:37.14 We also like to know,
00:08:39.08 how are the cells inside of the rosette
00:08:41.10 adhering to each other?
00:08:42.25 How do you get that stable structure?
00:08:44.20 Again, trying to draw analogies to embryogenesis.
00:08:48.09 And finally, we have this enigma,
00:08:52.09 which is that this single cell
00:08:54.10 is capable of producing three different types of morphologies.
00:08:59.22 It can divide to produce more copies of itself,
00:09:02.14 it can produce these chains,
00:09:05.26 or it can produce rosettes,
00:09:07.29 and we'd like to know
00:09:10.01 how is that differentiation process regulated.
00:09:13.14 So, let me start with question number 1:
00:09:15.13 how are these rosettes forming?
00:09:18.07 To investigate this
00:09:19.26 we used multiple different approaches,
00:09:21.23 but I think the simplest one is to just watch,
00:09:24.09 and what we found is that
00:09:27.00 when cultures were shifting
00:09:29.07 from having only single-celled individuals
00:09:31.29 to rosettes
00:09:34.11 it always happened through cell division.
00:09:36.29 And so, what you're going to see in this movie here
00:09:39.15 is that this is a founding cell that's going to divide repeatedly
00:09:42.23 to produce a spherical multi-celled colony.
00:09:45.18 So let's watch.
00:09:48.05 The single cell divides over and over again.
00:09:50.12 The cells remain attached,
00:09:52.18 and in the end of this 15 hour movie
00:09:55.28 we have a spherical colony.
00:09:58.01 And, this I think is also nicely shown here
00:10:00.10 in these stills taken by confocal microscopy.
00:10:04.04 Now, I want to make the point
00:10:06.27 that even though this looks 2-dimensional,
00:10:08.24 these colonies are actually 3-dimensional
00:10:10.23 and are producing a nice sphere.
00:10:14.06 Okay, so, the answer to our first question, then,
00:10:16.11 is that the rosettes are forming through cell division,
00:10:19.12 and that provides a very nice parallel
00:10:21.21 to the way in which embryos of animals form,
00:10:24.12 in which you have a single cell, the zygote,
00:10:27.03 and that zygote divides over and over again
00:10:29.07 to produce a multicellular embryo.
00:10:31.20 How are the cells in choanoflagellate colonies
00:10:34.22 actually sticking together?
00:10:36.11 And, to answer this,
00:10:38.14 we had to use electron microscopy.
00:10:41.14 If you look at choanoflagellate cells
00:10:43.20 using a scanning electron microscope,
00:10:45.29 what you see is that the cells are actually connected
00:10:49.11 by these fine intercellular bridges that you can see here,
00:10:52.28 and we think, although we don't know yet,
00:10:55.20 but we think that these are the product of
00:10:57.27 incomplete cytokinesis.
00:10:59.13 That is to say that the cleavage plane
00:11:01.14 that forms when cells are dividing
00:11:03.25 doesn't close completely,
00:11:05.09 and so there's a little remnant of membrane
00:11:07.23 that remains between those cells
00:11:10.01 and it produces this intercellular bridge.
00:11:14.11 But that's not the only source of cell adhesion
00:11:17.13 between these cells.
00:11:20.07 If you examine the cells under different conditions,
00:11:22.25 and then look at them either in SEM or in TEM,
00:11:27.28 what you can see is that there is
00:11:30.21 a fine meshwork of material covering the cells
00:11:33.12 and also filling the inside of the colony,
00:11:35.25 and this is actually extracellular matrix, or ECM.
00:11:38.29 And so, it's the combination of the intercellular bridges
00:11:45.07 and extracellular matrix
00:11:47.14 that is contributing to the structural integrity of the rosette.
00:11:51.21 Okay, so just to summarize, then,
00:11:53.18 I've just told you that when choanoflagellates form.
00:11:56.26 when S. rosetta forms rosette colonies
00:11:59.20 it forms it through incomplete cytokinesis,
00:12:02.05 and what I've also told you
00:12:05.00 is that the cells in these rosettes
00:12:06.22 are adhering through a combination
00:12:08.17 of intercellular bridges and extracellular matrix,
00:12:11.14 but of course I think the question
00:12:13.18 we should all be interested in and wondering about is,
00:12:16.24 how is this transition regulated?
00:12:19.28 And what determines
00:12:22.18 whether this single-celled form of S. rosetta
00:12:25.17 divides to produce more of itself,
00:12:28.15 or produces chains,
00:12:30.25 or produces rosettes?
00:12:32.20 What is determining the regulation
00:12:35.03 of this developmental switch?
00:12:37.10 And here's where I was really stymied in my research.
00:12:40.01 And so, what I need to tell you
00:12:42.16 is a story of frustration
00:12:45.04 that finally ended with serendipity
00:12:47.08 and I think an exciting new discovery.
00:12:50.27 So, let me back up and tell you
00:12:53.23 about how I started studying S. rosetta.
00:12:56.13 When I began my postdoc,
00:12:58.06 there were no labs out that were studying choanoflagellates,
00:13:01.25 and so I was fortunate to be taken into the lab
00:13:04.18 of a leading evo-devo researcher,
00:13:07.14 Sean Carroll,
00:13:09.06 but I had to go to the ATCC,
00:13:11.03 the American Type Culture Collection,
00:13:13.17 to work with a protistologist named Tom Nerad,
00:13:16.06 to learn how to study choanoflagellates.
00:13:18.00 And while I was there,
00:13:19.27 he and a group of other scientists
00:13:21.28 were studying diverse microbial eukaryotes
00:13:23.21 from the environment,
00:13:25.16 and he observed one choanoflagellate
00:13:27.08 that was capable of forming beautiful rosette colonies,
00:13:30.08 and this is S. rosetta.
00:13:32.12 So, he was kind enough to put S. rosetta into culture.
00:13:35.29 He isolated a single colony, grew it up,
00:13:38.18 and froze it down so that I could study
00:13:41.07 S. rosetta in perpetuity.
00:13:43.07 So, I brought it back to Madison,
00:13:45.10 where I was doing my postdoc,
00:13:47.02 and started growing this choanoflagellate.
00:13:49.02 And, let me tell you,
00:13:51.01 it was a very frustrating finding when I brought it back to Madison,
00:13:54.22 because S. rosetta cultures, in the laboratory,
00:13:57.29 rarely have rosettes.
00:13:59.24 They were largely unicellular,
00:14:01.22 and so you can see, here would be a best case scenario.
00:14:03.29 Lots of single-celled choanoflagellates,
00:14:06.04 you can see the round cells,
00:14:08.20 and only the occasional rosette colony,
00:14:11.28 and lots of bacteria.
00:14:13.20 And so, no matter what I did,
00:14:16.08 these cultures would not robustly form rosette colonies,
00:14:18.24 and so that meant that I wasn't going to be able
00:14:23.07 to do the types of experiments that I wanted to do
00:14:24.28 to study the mechanisms of rosette development.
00:14:27.26 So, I worked on this for a long time,
00:14:29.22 without success,
00:14:31.21 and then ended up bringing.
00:14:33.25 fortunately, other things worked,
00:14:36.11 but S. rosetta was recalcitrant,
00:14:38.21 and so I brought it with me when I started my own lab at Berkeley
00:14:41.24 and continued to experience frustration,
00:14:46.12 and continued to be unable
00:14:49.10 to get this thing to form rosettes
00:14:51.08 in any robust or predictable way.
00:14:53.06 And so, finally, I switched my research objectives
00:14:56.17 and decided that if I couldn't get rosette colonies
00:15:00.05 from this species,
00:15:02.12 at least I could sequence its genome,
00:15:04.09 and that might tell me something,
00:15:06.00 by comparing its genome to the
00:15:08.03 genomes of single-celled choanoflagellates,
00:15:09.11 might tell me something about the mechanisms regulating development.
00:15:12.17 And so, an undergraduate in the lab at the time,
00:15:15.03 Rick Zuzow, helped me to get this choanoflagellate
00:15:17.07 ready for genome sequencing,
00:15:19.17 and at one point.
00:15:20.20 one challenge I need to point out is that
00:15:22.21 because choanoflagellates eat bacteria,
00:15:24.29 this creates a real problem for genome sequencing
00:15:27.11 because the bacterial DNA
00:15:30.27 can make it difficult
00:15:34.29 to get a high-quality genome assembly from the choanoflagellate.
00:15:38.02 So, the first thing he had to do, then,
00:15:40.03 was to treat these cultures with cocktails of antibiotics,
00:15:45.24 and he tried two different cocktails of antibiotics
00:15:49.12 and they gave two very interesting results.
00:15:51.28 So, one cocktail of antibiotics,
00:15:54.11 actually, when he treated, when he used that,
00:15:57.28 it resulted in a culture that had a bloom of rosette development.
00:16:00.23 And so, you can imagine, we were thrilled!
00:16:03.00 It was so exciting and we had no idea
00:16:05.15 why this treatment with antibiotics
00:16:08.05 led to rosette development, but it did.
00:16:11.08 Perhaps even more interestingly,
00:16:13.08 when he treated with a different cocktail of antibiotics,
00:16:17.01 he recovered a culture that produced no rosettes, ever.
00:16:21.09 And so, we find that.
00:16:23.24 we found that different cocktails of antibiotics
00:16:26.04 led to different results,
00:16:29.14 and we started to wonder what was going on.
00:16:32.12 Now, it could have been
00:16:35.06 any of a number of possible explanations.
00:16:37.25 It could have been that the antibiotics
00:16:40.15 were directly stressing the choanoflagellates in different ways.
00:16:43.10 It could be that the choanoflagellates
00:16:45.13 were starving
00:16:48.27 when exposed to one set of antibiotics, but not the other.
00:16:51.20 But, it was hard to reconcile these different observations,
00:16:54.08 but the one possible explanation
00:16:57.12 that sort of was consistent with what we were seeing
00:17:00.11 was the possibility that bacteria from the environment
00:17:03.06 were actually regulating the switch to rosette development.
00:17:06.06 And so, to test that,
00:17:08.06 Rick took bacteria from the original environmental sample
00:17:11.15 and added them to this culture
00:17:14.01 that didn't form rosettes,
00:17:16.08 and asked whether those environmental bacteria
00:17:19.17 could stimulate rosette development
00:17:21.17 in these non-rosette forming cultures.
00:17:23.19 And, in fact, that did work.
00:17:26.22 So, environmental bacteria
00:17:29.00 were sufficient to induce rosette development.
00:17:31.20 So, that was very exciting,
00:17:33.21 very unexpected,
00:17:35.11 and of course the next thing we wanted to know was,
00:17:38.05 which bacteria were actually
00:17:41.19 providing this stimulus for rosette development?
00:17:44.00 And so, what Rick and other members of the lab did
00:17:47.00 was to go into this original environmental sample
00:17:48.29 and isolate multiple independent strains of bacteria
00:17:54.25 and test them one at a time
00:17:57.07 in this rosette-deficient culture,
00:17:59.10 and ask whether those bacteria
00:18:01.22 were capable of inducing rosette development.
00:18:04.20 And so, we tested 64 different environmental isolates,
00:18:09.12 one at a time,
00:18:11.12 and what we found in the end was that,
00:18:13.07 of all of these, only one species
00:18:15.13 was capable of inducing rosette development.
00:18:19.00 So, what was that species?
00:18:22.14 It was the previously undescribed
00:18:25.12 bacterial speices Algoriphagus machipongonensis.
00:18:29.01 So, we can add Algoriphagus to cultures
00:18:32.05 of single-celled choanoflagellates,
00:18:34.02 and that is sufficient to induce them
00:18:36.02 to form rosette colonies.
00:18:38.04 I need to make a couple of important points
00:18:40.12 about Algoriphagus.
00:18:42.22 First of all, it was co-isolated with S. rosetta,
00:18:45.03 so it's a natural environment co-habitant with S. rosetta,
00:18:49.00 and it's also a sufficient prey target.
00:18:52.13 So, we can grow S. rosetta
00:18:54.25 only in the presence of Algoriphagus
00:18:56.24 and it's perfectly viable
00:18:58.21 and it happily form rosette colonies.
00:19:00.26 The other exciting and interesting thing about Algoriphagus
00:19:03.22 is that it's a member of a much larger group of bacteria
00:19:06.04 called the Bacteroidetes,
00:19:08.15 and Bacteroidetes bacteria
00:19:11.15 are some of the most abundant bacteria in your gut,
00:19:14.06 and they're also abundant and important bacteria
00:19:17.09 in diverse environmental settings,
00:19:19.16 including the oceans and soil.
00:19:22.08 And, in each of these settings,
00:19:24.01 there's a growing interest in the ways in which
00:19:26.15 bacteria might be influencing the biology of eukaryotes
00:19:29.07 with which they're associated.
00:19:31.15 So, we're excited about the possibility
00:19:34.02 that this interaction which I've just described to you
00:19:36.12 might be used to help understand
00:19:39.16 the mechanisms underlying interactions
00:19:41.10 between bacteria and eukaryotes.
00:19:43.26 Now, why.
00:19:46.01 why would we be so excited about bacteria?
00:19:47.27 And I've hinted at that a little bit,
00:19:49.13 but I want to tell you.
00:19:51.05 I want to back up and give you a little bit of context
00:19:53.03 for why bacteria are such an important factor
00:19:58.08 to try to investigate
00:20:00.12 when you're thinking about animal origins.
00:20:01.23 And, to do that, I need to go in the way-back machine.
00:20:04.06 I need to remind you about the history of life on Earth.
00:20:08.06 And, to that do,
00:20:10.13 I'm going to use this time chart
00:20:12.13 in which we're thinking about life, the history of life,
00:20:14.07 starting with the present here on the top,
00:20:16.09 going back to the start of Earth
00:20:19.09 and the solidification of the crust,
00:20:21.13 and say that we think that the last universal common ancestor
00:20:24.25 of life
00:20:26.16 lived on the order of over 3 billion years ago.
00:20:29.05 And, the earliest fossil evidence
00:20:32.00 we have for life
00:20:34.00 is that of stromatolites.
00:20:36.16 These are large multicellular
00:20:38.26 aggregations of bacteria.
00:20:40.23 They are essentially a bacterial biofilm,
00:20:43.01 and we preserve representatives of these types of morphologies,
00:20:46.17 here, today.
00:20:48.25 Here is an example of a modern stromatolite,
00:20:50.26 and these complex forms
00:20:53.10 are produced by bacteria,
00:20:55.16 and there's a lot of really terrific work
00:20:57.19 that's being done to address
00:21:01.00 the ways in which bacterial metabolism
00:21:04.04 has influenced the geochemistry of Earth,
00:21:07.23 but also the life of other organisms.
00:21:10.27 And, what we now realize,
00:21:13.26 is that animals whose fossils
00:21:17.05 have not been recovered.
00:21:19.01 you know, the oldest animal fossils
00:21:21.16 are no older than about 5-600 million years old
00:21:24.17 and the oldest multicellular eukaryotes in general
00:21:27.14 are on the order of a billion years old,
00:21:29.16 those multicellular eukaryotes
00:21:31.20 evolved in environments that were already dominated
00:21:36.10 by teeming hoards of bacteria.
00:21:38.22 If we're going to understand the origin
00:21:40.24 of multicellular eukaryotes,
00:21:42.20 we need to understand how their progenitors
00:21:45.02 coped with a world
00:21:47.09 that was already populated and colonized by bacteria.
00:21:51.19 So, that's one important point that I want to make
00:21:53.21 about the bacterial context of animal origins.
00:21:56.18 The second point that I want to make
00:21:58.20 harkens back to something I talked about in Part I,
00:22:01.02 and that is that,
00:22:02.19 through the study of choanoflagellates,
00:22:04.09 we've been able to reconstruct
00:22:06.14 some important aspects of the biology of the first animals.
00:22:08.29 And so, you may remember that I mentioned
00:22:11.02 that we think the first animals
00:22:13.08 probably had collar cells
00:22:15.06 and, more importantly,
00:22:17.28 that those first animals were involved in bacterivory,
00:22:21.05 that is to say, they ate bacteria.
00:22:23.08 They make a living by eating bacteria.
00:22:25.15 And so, we now know think that interactions with bacteria
00:22:29.03 were an obligate part of the life history
00:22:31.17 of the first animals.
00:22:33.28 The final point that I want to make
00:22:38.28 is that, if you look at living animals,
00:22:41.19 what you can see is that development
00:22:43.25 in many of these diverse organisms
00:22:45.27 is regulated by bacterial signals.
00:22:48.19 The challenge in these cases.
00:22:50.18 now, obviously, there's been a lot of interest,
00:22:52.28 but the challenge has been that we're looking at
00:22:55.05 large, complex multicellular organisms
00:22:57.28 that are growing in association
00:23:00.04 with diverse and complex communities of microbiota,
00:23:04.19 and this has made it very difficult
00:23:06.22 to try to learn something about the mechanisms
00:23:08.29 underlying these important interactions.
00:23:11.25 And so, what we are now doing
00:23:15.02 is using this interaction
00:23:17.21 between the bacteria Algoriphagus and the choanoflagellate S. rosetta
00:23:21.01 as a simple bioassay
00:23:24.09 to discover bacterial signaling molecules
00:23:26.11 that we think will help us understand
00:23:28.20 the regulation of this developmental switch,
00:23:31.16 but will potentially have relevance
00:23:33.29 to other systems as well.
00:23:35.20 Now, I have to say that
00:23:38.01 this has been a very exciting but also challenging process,
00:23:41.15 in part because we had absolutely no idea
00:23:44.03 what the nature of the signaling molecules were.
00:23:48.20 After casting about in the dark for a little while,
00:23:51.14 we had a hint that came from looking
00:23:55.06 at what is unusual about the Bacteroidetes,
00:23:57.11 which are the bacteria. the large group of bacteria
00:23:59.22 of which Algoriphagus is a member.
00:24:03.25 So, Bacteroidetes
00:24:06.25 actually have, like other members of this group,
00:24:08.20 an outer membrane and an inner membrane.
00:24:11.28 They have components called LPS and peptidoglycan,
00:24:14.17 which are known inducers
00:24:18.09 of immune system components in animals,
00:24:22.04 but they also have an unusual group of lipids
00:24:24.18 called the sphingolipids
00:24:26.23 and the closely related sulfonolipids,
00:24:28.29 and I say that these are unusual,
00:24:30.26 but in fact they're quite common in eukaryotes.
00:24:32.29 It's in bacteria in which
00:24:36.15 you don't often see these types of lipids.
00:24:39.13 And so, for a variety of reasons,
00:24:42.02 we focused on this group of lipids as a potential source
00:24:45.12 of the signaling activity.
00:24:48.01 And, to do this,
00:24:50.14 we have established really one of the best collaborations
00:24:53.27 in my career.
00:24:55.12 It's been a fantastic experience.
00:24:57.01 We're been collaborating with Jon Clardy,
00:24:58.24 who's at Harvard Medical School
00:25:01.01 and has done fantastic work in many systems
00:25:04.17 in recovering bioactive molecules.
00:25:07.07 And so, what he and his group did
00:25:10.10 was they took Algoriphagus,
00:25:12.18 they extracted the sphingolipid fraction
00:25:16.10 from its outer membrane,
00:25:18.13 and then.
00:25:21.21 these sphingolipids are very difficult to deal with,
00:25:23.20 so at our first pass,
00:25:25.23 we've now started using different approaches,
00:25:28.01 but in the fist pass people from his lab
00:25:31.18 used a process called prep-TLC,
00:25:34.05 and this is thin layer chromatography,
00:25:36.19 to separate out all those sphingolipids,
00:25:39.28 and then they would scrape them off of this plate
00:25:43.01 and send them to my lab where we would test them
00:25:45.00 in the bioassay
00:25:46.27 and see whether those fractions were capable of
00:25:49.23 inducing rosettes or not.
00:25:51.10 And, based on that,
00:25:53.03 then we could take the fractions that were capable of inducing
00:25:55.23 and analyze them by mass spectroscopy.
00:25:58.25 And so, this was an iterative process.
00:26:01.09 We would send the bacterial samples,
00:26:03.09 they would fractionate them,
00:26:04.27 they would send us the fractions,
00:26:06.20 we would test them, we would send them the information.
00:26:08.02 it was back and forth,
00:26:11.01 and through a long series of analyses
00:26:13.23 we eventually were able to identify
00:26:15.18 the first bacterial molecule that was capable
00:26:18.12 of inducing rosette development
00:26:20.15 and that is this molecule.
00:26:22.17 We've name it RIF-1 for rosette-inducing factor 1,
00:26:25.00 and we now have a structure for it,
00:26:26.23 which is very exciting,
00:26:28.18 and we also know something about its chemistry.
00:26:31.28 So, RIF-1 is not a sphingolipid.
00:26:35.01 It is in fact in a different class of molecules
00:26:37.16 called the sulfonolipids,
00:26:39.14 and the sulfonolipids differ from sphingolipids
00:26:42.23 in that they have a sulfonic acid headgroup
00:26:45.13 at one end.
00:26:47.16 This class of molecules
00:26:50.09 has not previously been shown to be involved in signaling,
00:26:52.21 so this is exciting because it's the tip of the iceberg.
00:26:55.04 These types of molecules
00:26:57.09 might have wide-ranging roles
00:26:59.05 and we can just start to study them now.
00:27:01.06 What is known is that, in bacteria,
00:27:03.06 they seem to have a role in regulating gliding motility.
00:27:07.28 So, this molecule
00:27:11.01 we can fractionate and isolate from bacteria,
00:27:12.26 but it is actually functioning in a way
00:27:15.10 that is consistent with it having a real role in the environment.
00:27:18.09 And so, we took purified RIF-1
00:27:21.11 and tried to determine
00:27:24.15 the concentration of the molecule
00:27:26.13 that was required to induce rosette development,
00:27:28.19 and the exciting result is that in fact
00:27:32.03 RIF-1 is tremendously potent.
00:27:34.14 It is able to induce rosette development.
00:27:36.21 here again I'm showing you
00:27:39.10 the extent of rosette development along the y-axis
00:27:41.25 and the concentration of RIF-1 along the x-axis,
00:27:46.09 and what I hope you can see is that
00:27:48.00 we are getting maximal induction of rosette development
00:27:50.22 at concentrations that are in the femtomolar range,
00:27:54.16 and so this.
00:27:56.10 not only is it active at these levels,
00:27:58.12 but these are the levels in which we find RIF-1
00:28:01.19 in the conditioned media,
00:28:03.09 and so the activity of RIF-1 is entirely consistent
00:28:06.03 with it having an important function
00:28:08.09 at environmental concentrations.
00:28:10.04 So, that was very exciting.
00:28:11.27 So, it's a new class of signaling molecule,
00:28:13.22 it's active at environmentally-relevant concentrations,
00:28:16.26 that's all good, but now we get to the nitty-gritty.
00:28:20.01 I want to show you that, in fact,
00:28:22.08 the maximal induction that we're seeing
00:28:24.07 is only on the order of about 5% of cells
00:28:27.04 going into rosettes,
00:28:29.02 so it suggests that RIF-1 is important,
00:28:31.00 it's sufficient for rosette induction,
00:28:32.28 but it's not the whole story.
00:28:34.27 And so, what we've now done
00:28:37.20 is go back to our simple bioassay
00:28:39.20 to see, now, if we can more rapidly discover
00:28:42.00 other potential bacterial signaling molecules,
00:28:44.15 and in fact we have.
00:28:47.15 So, again this is through our collaboration
00:28:49.16 with the Clardy lab.
00:28:51.01 We've gone back now
00:28:53.09 and analyzed more broadly,
00:28:55.07 not just the sphingolipids,
00:28:57.11 but the entire lipid fraction,
00:29:01.02 and we've been able, through this process,
00:29:02.27 to find other bioactive signaling molecules.
00:29:05.19 Here in this part of the eluate we find RIF-1,
00:29:10.24 but also many, many other sulfonolipids,
00:29:13.15 all of which are inactive,
00:29:15.08 and that makes an important point.
00:29:17.02 RIF-1 isn't active because it's a sulfonolipid.
00:29:19.22 RIF-1 is a special sulfonolipid.
00:29:22.09 Most other sulfonolipids can't induce (rosette development).
00:29:25.25 So, there's a tight structure-activity relationship
00:29:28.00 between RIF-1 and its ability to regulate rosette development.
00:29:31.11 But, what we've also found is that there are
00:29:33.28 other classes of sulfonolipids
00:29:36.04 that are structurally similar to RIF-1
00:29:38.00 that are also capable of inducing.
00:29:40.07 There's an entirely different class of lipids
00:29:42.16 called the LPEs, or the lysophosphatidylethanolamines.
00:29:45.22 These are able to synergize with RIF-1
00:29:48.18 and the other sulfonolipids
00:29:50.17 to promote rosette development.
00:29:52.18 And finally, there's another type of lipids
00:29:54.29 that's an antagonist of the RIFs,
00:29:58.07 and if you incubate it with the choanoflagellate
00:30:02.03 and then add RIF-1, -2, or -3,
00:30:04.23 you find that you block rosette development.
00:30:07.05 So, there are many different, diverse bioactive lipids
00:30:10.08 available in Algoriphagus,
00:30:12.15 and we can mix them together
00:30:14.17 and reconstitute the full induction activity
00:30:17.00 that you normally get from live Algoriphagus bacteria.
00:30:21.02 So, there are diverse bioactive molecules
00:30:23.13 that we have discovered already using our bioassay,
00:30:26.04 just from Algoriphagus,
00:30:27.26 but in addition
00:30:30.13 we've also surveyed lots of other diverse bacteria,
00:30:33.13 and biologists will do this and what I'm going to tell you is,
00:30:36.01 I'm showing you a phylogenetic tree of diverse bacteria
00:30:39.05 and you don't need to worry about the fact that
00:30:41.20 you can't read which bacteria I'm showing you.
00:30:43.24 The point I want to make is that there's a lot of diverse bacteria
00:30:45.27 we've tested now,
00:30:47.26 and shown in these squares
00:30:50.04 I'm indicating whether they induce rosettes or not.
00:30:53.04 Those shown with black do induce.
00:30:54.29 Those shown with white don't,
00:30:57.25 and those in grey induce at a low level.
00:31:00.03 And so, we're find that across the tree of bacterial diversity,
00:31:02.28 we're finding many different bacteria
00:31:05.28 that induce and some of them seem to use
00:31:08.12 different types of bioactive molecules
00:31:10.22 to induce rosette development.
00:31:13.00 Finally, we'd like to know
00:31:15.16 whether this bioassay might help us
00:31:18.07 find something that's of biomedical relevance,
00:31:20.02 and so we've actually surveyed
00:31:22.18 the bacteria of the vertebrate gut system,
00:31:24.23 looking at different parts of the intestinal tract,
00:31:27.13 and testing whether they're capable of
00:31:29.28 inducing rosette development,
00:31:31.20 and we find, in fact, that they can.
00:31:33.17 So, bacteria from the stomach and the small intestine
00:31:35.29 do not induce rosette development,
00:31:38.08 but bacteria from the cecum and the colon do,
00:31:41.12 and if we follow the strategy that we followed previously
00:31:44.04 in the discovery of Algoriphagus,
00:31:46.14 we can do it here
00:31:48.27 and culture these bacteria and see if we can identify
00:31:51.05 the species that induce rosette development,
00:31:53.12 and so we've done that,
00:31:55.08 and we've now discovered the specific bacteria
00:31:57.10 from the gut system
00:31:59.06 that are capable of inducing rosette development
00:32:00.27 and we're focusing on isolating the bioactive molecules
00:32:03.27 from these organisms as well.
00:32:06.25 Okay, so let me just recap what I've told you.
00:32:10.16 I've told you that rosette development is regulated.
00:32:13.21 is the process of incomplete cytokinesis,
00:32:16.24 and cells in rosettes
00:32:19.04 are held together through a combination
00:32:21.24 of intercellular bridges and ECM.
00:32:24.09 Moreover, what we're discovered,
00:32:26.00 and it was quite unexpected,
00:32:28.04 we found that the developmental switch
00:32:30.07 that controls whether a single cell
00:32:32.10 is going to form a rosette, chain colonies,
00:32:35.26 or another single cell,
00:32:37.20 that's regulated not solely by genetics
00:32:40.18 of the choanoflagellate,
00:32:42.09 but actually, importantly,
00:32:44.18 by signals that are released
00:32:47.02 by environmental bacteria.
00:32:50.24 So, over Part I and Part II,
00:32:53.27 I've been telling you about these
00:32:56.18 really interesting organisms, the choanoflagellates,
00:32:59.16 that were discovered in the 1800s,
00:33:01.29 that we've now brought into the molecular
00:33:03.23 and genomic era.
00:33:05.15 And, through the study of choanoflagellates,
00:33:06.28 we're finding that we're able to reconstruct
00:33:09.02 the biology of the first animals
00:33:11.28 in increasingly resolution,
00:33:13.29 and one of the most exciting things
00:33:16.11 I think we've found through these types of studies
00:33:18.20 is that many of the genes that are essential
00:33:20.27 for regulating cell-cell interactions in animals
00:33:23.21 and regulating the process of development
00:33:26.08 actually evolved before the origin of animals
00:33:29.00 and are conserved in the genomes
00:33:30.28 of living choanoflagellates.
00:33:32.13 So, that's been great,
00:33:34.05 to learn that choanoflagellates provide this window
00:33:36.00 into animal origins.
00:33:38.27 In addition, I told you about
00:33:42.00 a transition to multicellularity
00:33:44.02 that actually happens in the life history of
00:33:46.04 a living choanoflagellate, the choanoflagellate S. rosetta.
00:33:49.06 And, the very exciting discovery that we've made
00:33:52.03 by studying this process in mechanistic detail
00:33:56.02 is that the developmental switch
00:33:59.00 to form multicelled rosette colonies
00:34:01.08 is actually regulated by environmental bacteria.
00:34:04.23 So, it's been very exciting,
00:34:07.04 we've been collaborating with Jon Clardy
00:34:09.11 to uncover bioactive molecules,
00:34:11.06 and this now bring us to the point in which
00:34:13.24 we can start thinking
00:34:15.10 about the choanoflagellate side of the story.
00:34:16.03 How is it that choanoflagellates
00:34:18.09 are actually sensing these bacterial signaling molecules?
00:34:21.12 Moreover, we're curious about whether this interaction
00:34:24.25 is something special to the choanoflagellate lineage
00:34:28.01 or whether it actually is informative
00:34:30.06 about mechanisms underlying animal origins.
00:34:32.21 And so, to that end,
00:34:33.29 in the long run we'd like to know
00:34:36.06 whether the mechanisms regulating this signaling interaction
00:34:40.15 between bacteria and choanoflagellates
00:34:43.03 might be conserved in the interactions
00:34:45.06 between animals and their commensal bacteria.
00:34:49.00 So, it's been a real pleasure
00:34:51.10 telling you about this work
00:34:53.07 and I want to take this opportunity to thank
00:34:55.12 a number of people, many of which,
00:34:58.11 you know, I can't list all of them,
00:35:00.00 but I really want to thank everybody in my lab
00:35:01.26 and I've highlighted here, in yellow,
00:35:03.26 the people who have actually contributed to the work
00:35:05.21 that I discussed here.
00:35:07.17 One current member, Arielle Woznika,
00:35:09.11 and many different alumni
00:35:11.29 who have been essential to this project.
00:35:14.05 Moreover, I have to express my gratitude
00:35:17.10 to Jon Clardy,
00:35:19.19 who's been a really fantastic collaborator
00:35:21.05 and I've learned so much from him
00:35:23.02 and it's been a wonderful experience,
00:35:24.29 and then of course our funding agencies.
00:35:26.29 If you find yourself fascinated by choanoflagellates
00:35:28.29 and you want to learn more,
00:35:32.17 we invite many, many people, we want to grow this community,
00:35:35.02 and you can learn more about choanoflagellates
00:35:37.13 in these various locations,
00:35:39.06 and importantly we have a choanoflagellate workshop
00:35:41.10 every two years, so please come and join us.
00:35:44.17 And it's been a pleasure talking to you.

  • />Part 1: The origin of animal multicellularity

Diversity (n.)

mid-14c., diversite , "variety, diverseness" late 14c., "quality of being diverse, fact of difference between two or more things or kinds variety separateness that in which two or more things differ," mostly in a neutral sense, from Old French diversete "difference, diversity, unique feature, oddness:" also "wickedness, perversity" (12c., Modern French diversité ), from Latin diversitatem (nominative diversitas ) "contrariety, contradiction, disagreement" also, as a secondary sense, "difference, diversity," from diversus "turned different ways" (in Late Latin "various"), past participle of divertere (see divert).

A negative meaning, "perverseness, being contrary to what is agreeable or right conflict, strife perversity, evil" existed in English from late 14c. but was obsolete from 17c. Diversity as a virtue in a nation is an idea from the rise of modern democracies in the 1790s, where it kept one faction from arrogating all power (but this was not quite the modern sense, as ethnicity, gender, sexual identity, etc. were not the qualities in mind):

Specific focus (in a positive sense) on race, gender, etc., "inclusion and visibility of persons of previously under-represented minority identities" is by 1992.


Watch the video: Λιαντίνης: ο Εφιάλτης θα φανεί στο τέλος (November 2021).