Category: systematics

Duhhh. . . . Guardian touts a “new” finding that thylacines are more closely related to kangaroos than to dingos

December 11, 2017 • 1:15 pm

Below is the headline of a new science piece in the Guardian (click on screenshot to read it), reporting on a paper that was just published in Nature. I haven’t read that paper, so I won’t comment on it; rather, I’ll comment on the science writing, which in this case is abysmal. It’s sensationalistic, misleading, and, sadly, the scientists whose work is reported appear complicit in the sensationalism.

But what’s a thylacine? It’s a fascinating creature: a carnivorous Australian/Tasmanian marsupial (Thylacinus cynocephalus) that looked like a dog. It’s been called the “Tasmanian wolf” or, because it was striped on the back, the “Tasmanian tiger.” The species lived until recently, going extinct in Australia about 2000 years ago (sightings are reported in the 1830s, though), and on Tasmania until 1930, when the last known one was shot. (Sightings are still reported there, but none have been credible.) Here are two from a Washington, D.C. zoo in 1906:

Why did they go extinct? Certainly hunting was a major factor, but others that have been suggested are disease, habitat loss, and competition with dingos. Dingos are the descendants of wild canids introduced into Australia, and are, unlike thylacines, placental mammals. The physical resemblance between the thylacine and a canid is an independent evolution of form, or an evolutionary convergence. 

There are two results given the headline: “genetic weakness” of the thylacine and “the closer relationship of the thylacine to kangaroos than dingos”. We’ll take these in order.

First, the “weakness”, which I take to mean “lack of genetic variation”, which could make a species more susceptible to extinction because it can’t evolve in a way that would help it cope to new environments or conditions like disease. (Evolution requires genetic variation.) The paper reports a genomic sequencing of a preserved, 106-year old thylacine. Since I haven’t read the paper, the lack of variation in the species would have to have been deduced by finding that this individual was largely invariant in its genome: that both copies of every gene were more similar than in other species.  But earlier work in 2012, based on several thylacines, already told us that they were largely invariant in their mitochondrial DNA. So this conclusion isn’t new.

Did the thylacine go extinct because it was genetically depauperate, though? We have no idea, and the Guardian even suggests it didn’t:

“But what we found is that the population declined about 70,000 years ago, long before it was isolated meaning it probably had more to do with changes in the climate back then.”

While overhunting was “without doubt” responsible for the animal’s extinction in 1936, Pask said its genetic weakness would have made it more susceptible to disease had it survived.

Yes, and if my aunt had testes she’d be my uncle. What we have here is pure speculation. It does appear that thylacines were genetically depauperate, but whether that played a role in their extinction is unknown. After all, they were shot willy-nilly.

But the worst part is the second “conclusion”: the breathless report that thylacines are more closely related to kangaroos than to dingos, with a quote from associate professor Andrew Pask from the University of Melbourne (my emphasis):

The researchers also found that despite its similarities to the Australian dingo, the thylacine’s DNA actually has more in common with the kangaroo.

Scientists consider the thylacine and the dingo as one of the best examples of what’s known as “convergent evolution”, the process where organisms that are not closely related independently evolve to look the same as a result of having to adapt to similar environments or ecological niches.

Because of their hunting technique and diet of fresh meat, their skulls and body shape became similar despite the Tasmanian tiger’s DNA having more in common with a kangaroo.

Pask said the genome showed the Tasmanian tiger was an “unbelievable” example of convergent evolution, because it proved how distant the two species were.

“Their similarities are absolutely astounding because they haven’t shared a common ancestor since the Jurassic period, 160m years ago,” he said.

For crying out loud, WE ALREADY KNEW THIS! Thylacines are marsupials, like kangaroos, and dingos are placentals, like dogs and most other mammals we know. They belong to different infraclasses of mammals (the next level below the class Mammalia), and their ancestors separated about 159 million years ago. In contrast, the thylacine and kangaroo last shared a common ancestor about 62 million years ago. We’ve known that this is a case of convergent evolution for decades, and no biologist would be surprised at the subheadline above. They’d say, like Greg, Matthew, and I did, “Yeah, so?”

You can attribute that subheadline, perhaps, to a nonbiologist interested in writing clickbait, but it appears that Dr. Pask is guilty for fostering some of this hype, for he knows full well that the relatedness and time data have been around for years.

As Greg said when we were discussing this piece (it was sent by Matthew Cobb), “Any scientist who can pretend, in order to garner press attention, that it’s a novel discovery that Tasmanian tigers are indeed marsupials should be shunned as a publicity-seeking charlatan.”

Amen!

Whence the beaver? They’re kangaroo rats, not squirrels!

March 9, 2017 • 1:00 pm

Of course the title is clickbait, but it does express a new finding: that, among Rodentia (yes, beavers are rodents), whose phylogeny was till now a bit unclear, we now learn that beavers are more closely related to kangaroo rats than to squirrels. For a long time, beavers had been thought to be closely related to squirrels (the “sciurid rodents”) because of the similar arrangement of their masseter muscles—the muscles that close the jaw. Recently, there was some slight but not completely convincing evidence, however, that beavers may be more closely related to kangaroo rats: those cute hopping mice in the family Heteromyidae. (Heteromyids also include pocket mice, kangaroo mice, and spiny pocket mice.) The molecular evidence was based on a similar piece of DNA in beavers and heteromyids: a single “retrotransposon,” a “jumping gene” that moves around the DNA by being transcribed from its RNA and then stuck in different places in the genome.

So we have a muscle similarity coming up against a single molecular similarity. Well, a new paper in Nature Scientific Reports by Liliya Doronina et al. (reference below; free download), using a lot more molecular data, shows that the kangaroo-rat affinity wins. This is based on a phylogeny constructed from both DNA sequences as well as the presence and position of retrotransposons.

It turns out that beavers, compared to other groups of rodents, share seven new retrotransposons with the kangaroo rat, and none with other groups of rodents. This shows that beavers and kangaroo rats are monophyletic: they have a common ancestor that is not a common ancestor with any other rodent. Below you can see what the new rodent phylogeny looks like, and you can also see, along the right, the similarity of the muscles between squirrels and beavers.

Note that they used the Eurasian beaver (Castor fiber), rather than its good old New World counterpart, the North American beaver (Castor canadensis). But that doesn’t matter, for the two species of beavers—there are only two and they diverged about 9 million years ago—are more closely related to each other than to kangaroo rats or any other rodent.

Before I give the reveal, here are the animals:

A Eurasian beaver:

A North American beaver (much cuter!):

A kangaroo rat (Dipodomys sp.):

It turns out that a similar arrangement of the masseter muscle evolved three times independently in rodents, so that’s not a good character to use for making evolutionary trees; it’s an “evolutionary convergence” that doesn’t tell us much about ancestry. DNA is much better, and here’s the final tree:

(From paper): 3,780 potential phylogenetically informative retroposons were extracted from the beaver reference assembly and projected onto sequence information of other rodent genomes and onto PCR-amplified orthologs from Anomaluromorpha. These newly revealed markers are shown as enlarged red balls. Previously identified phylogenetically diagnostic retroposon markers are indicated by black and two conflicting yellow balls. The two screening strategies and the resulting diagnostic presence/absence patterns are indicated for Castorimorpha and also the mouse-related clade. The myomorphous, sciurimorphous, and hystricomorphous zygomasseteric systems are illustrated to the right (blue and red lines show anterior parts of medial and lateral masseter, respectively; for details of zygomasseteric systems in rodents see Potapova27). The mandible types20 are noted: sciurognathous and hystricognathous. For the squirrel-related clade, only the zygomasseteric system of Sciuridae is presented. The rodent paintings were provided by Jón Baldur Hlíðberg.

At last we can rest easy, knowing that the beaver is not a close relative of the squirrel. The similarity of their muscle configuration undoubtedly comes from their similar habits of gnawing tough stuff, which led to a convergent arrangement of strong jaw muscles.

h/t: Matthew Cobb

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Doronina, L., A. Matzke, G. Churakov, M. Stoll, A. Huge, and J. Schmitz. 2017. The beaver’s phylogenetic lineage illuminated by retroposon reads. Nature Scientific Reports 7, Article number: 43562 (2017) doi:10.1038/srep43562

PBS: How many species of giraffes are there?

November 2, 2016 • 8:30 am

A while back I discussed a paper in Current Biology by Julian Fennessy et al. . That paper used genetic analysis (the total genetic divergence among groups) to claim that there are actually four species of giraffe instead of a single species with nine subspecies. Using the Biological Species Concept (BSC), however, I argued that there was no objective basis for recognizing four distinct species on the basis of genetic distance and monophyly alone, for such recognition is purely subjective. How much genetic divergence between geographically isolated groups is necessary before we call them “separate species”? Any decision must necessarily be subjective, since no cut-off point of genetic distance is biologically meaningful.

I concluded that although the press gave the Fennessy et al. paper a ton of publicity, there’s no good reason to recognize four instead of one species of giraffe so long as all the “species” are geographically isolated from one another. (Greg Mayer and Matthew Cobb, my biology co-writers here, agreed.)

Now, mirabile dictu, the Public Broadcasting Service (PBS) in the U.S. has taken up the issue, and I had several conversations about speciation with writer Becca Cudmore, who proved to be one of the more inquisitive and savvy science journalists I’ve encountered. And, miracle of miracles again, she gives substantial publicity to the idea that giraffes may not really comprise four species.

In her PBS NatureNow article “How many giraffe species are there, really?” Cudmore gives a good airing of the BSC and my take on the giraffes. The gist:

Unlike Coyne’s approach, the study used genetic differences to separate the giraffes. This is a method of defining species by their “phylogenetics,”or by their shared traits. In this case, Goethe University researcher Axel Janke found genetic markers, such as mutations, that were common among certain giraffes and not shared by the others. This suggested to him that there has been very little gene sharing between the groups.

But by Coyne’s definition, this doesn’t prove that giraffes are reproductively isolated. “The only way to show whether or not they are separate would be to move the wild giraffes into the same area and see if they produce a fertile offspring,” he says. While the different subspecies are known to hybridize in captivity, there is very little evidence of this in the wild.

“The Biological Species Concept is more meaningful because it helps to explain one of evolutionary biology’s most profound questions”: Why is nature discontinuous? he says—why is it not all “one big smear” that can exchange genes?

And so on. There is of course some pushback:

Still, with what we know about hybrids between species in the wild, Janke calls Coyne’s approach too “pure” and says that it’s going out-of-date.

Janke is just wrong here. (I have no idea what he means by “too pure”!) The fact that some species exchange genes is not a serious problem for a concept based on reproductive isolation between entire genomes, and in fact most closely related species do not exchange genes. The cases of gene exchange between biological species, while widely publicized, are not the rule but the exception. (See Coyne & Orr, Speciation, for the evidence.)

Most tellingly, virtually every paper I’ve seen on the process of speciation—that is, on the ways that new species come into being—deals not with the accumulation of genetic distance per se, but on the development of reproductive barriers that eventually prevent populations from exchanging genes. That’s a tacit admission of the importance of the BSC.

I think the impetus behind naming more giraffe species is largely connected with conservation, for with more named species we can put more species on the endangered list and save more of the phenotypic and genetic diversity in what was formerly one species. But while that may be an admirable goal, it should not be a motivation for recognizing species in nature.

It may not be a coincidence that Fennessy works for the Giraffe Conservation Foundation. Cudmore notes this:

Whether one, four, or six species, giraffes have experienced a 40 percent plummet in population over the past 15 years. They’re currently listed as a species of “least concern” by the IUCN [International Union for Conservation of Nature] and unlike alarm bells ringing for Africa’s elephants, gorillas, and rhinos amid the poaching crisis, they receive relatively little attention.

and the press release for the paper gives a quote from Fennessy:

“With now four distinct species, the conservation status of each of these can be better defined and in turn added to the IUCN Red List,” said study co-author Julian Fennessy of the Giraffe Conservation Foundation in a release. For example, said Fennessy, there are now less than 4,750 Northern giraffes and fewer than 8,700 reticulated giraffes in the wild. “As distinct species, [this] makes them some of the most endangered large mammals in the world.”

This makes me suspect that behind the “splitting” of giraffes is a conservationist motivation, not an attempt to partition out nature in biologically and evolutionarily meaningful ways.

giraffe_collage_1-1280x512
(from PBS article) A recent study proposed that giraffes are actually comprised of four main species (from left to right): reticulated, northern, southern and Masaai.

The exciting “new phylum” of Dendrogramma turns out to be an old one

June 8, 2016 • 8:45 am

Time for a correction. On September 7, 2014, I put up a post about a weird new creature, Dendrogramma, two species of which were dredged up from the deep seas of Australia. Here’s one of them:

screen-shot-2014-09-06-at-12-55-41-pm

Thse species, which had stalks and inflexible disks, weren’t considered members of existing phyla like ctenophores (comb jellies) because, as the original paper (Just et al., reference and link below) noted, they lack features present in other similar phyla (my emphasis in this original quote):

Dendrogramma shares a number of similarities in general body organisation with the two phyla, Ctenophora and Cnidaria, but cannot be placed inside any of these as they are recognised currently. We can state with considerable certainty that the organisms do not possess cnidocytes, tentacles, marginal pore openings for the radiating canals, ring canal, sense organs in the form of e.g., statocysts or the rhopalia of Scyphozoa and Cubozoa, or colloblasts, ctenes, or an apical organ as seen in Ctenophora. No cilia have been located. We have not found evidence that the specimens may represent torn-off parts of colonial Siphonophora (e.g., gastrozooids). Neither have we observed any traces of gonads, which may indicate immaturity or seasonal changes. No biological information on Dendrogramma is available.

DNA data, which would have been very useful, weren’t available for these specimens as they were collected in 1986 and fixed in formalin, which destroys DNA. While the authors didn’t name a new phylum, they suggested that these two species were indeed representatives of a new phylum, and that caused a lot of excitement. (New phyla aren’t often described.)

However, a 2015 expedition, whose results are described in a new paper in Current Biology (O’Hara et al., reference and free link below), produced RNA that could be sequenced. And that RNA shows that Dendrogramma isn’t a new phylum at all, but a siphonophore. Siphonophores are well known, an order that falls in the class Hydrozoa, itself in the phylum Cnidaria. Siphonophores are a bizarre group consisting of specialized individual animals that band together as a group to form a “superorganism”; the most familiar member is the Portuguese man of war, and here’s another, the pelagic (free swimming) siphonophore Marrus orthocanna:

800px-Marrus_orthocanna_crop-1

As the new paper notes:

Siphonophores are bizarre pelagic colonial cnidarians in the class Hydrozoa. They are complex elongate or spherical organisms with specialised locomotive and feeding zooids, and a net of tentacles that can be extended to catch prey or attach to the seafloor. There are 175 described species, living in a range of habitats from the sea surface (e.g., Physalia physalis, the Portuguese Man O’War) to the deep-sea. Larger, more delicate species have been found mainly in the non-turbulent mesopelagic (300–1000 m) or bathypelagic zones (1000–3000 m).

The RNA analysis places Dendrogramma (probably just one species, not two), firmly in the siphonophores: it’s the red species in the phylogny below.

1-s2.0-S0960982216304055-gr1
(From the paper): Dendrogramma in the tree of animal life. Dendrogramma bracts showing the (A) ‘discoides’ and (B) ‘enigmatica’ morphologies (scale bar = 10 mm). (C) Simplified phylogenomic tree of the Metazoa, predominantly derived from Whelan et al. 2015 [3], showing the position of Dendrogramma. Bootstrap values are 100% unless otherwise indicated.
Finally, the authors hypothesize that the “animal” Dendrogramma in the first picture above is really part of a more complex colony, and that the discoid things with stalks are cormidial bracts. The figure below shows those bracts in an entire siphonophore:

Screen Shot 2016-06-08 at 6.45.23 AM
Reference here.

So, move along folks, nothing more to see here. It’s just the usual advance of science, when we can better identify a bizarre form using DNA—or in this case, RNA. The earlier speculations that Dendrogramma may be a living remnant of the bizarre Ediacaran fauna that went extinct about 540 million years ago is no longer tenable.

h/t: Matthew Cobb, Casey Dunn

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REFERENCES:

Just, J., R. M. Kristensen, and J. Olesen. 2014. Dendrogramma, New Genus, with Two New Non-Bilaterian Species from the Marine Bathyal of Southeastern Australia (Animalia, Metazoa incertae sedis) – with Similarities to Some Medusoids from the Precambrian Ediacara. PLOS One DOI: 10.1371/journal.pone.0102976

O’Hara, T. D. et al. 2016. Dendrogramma is a siphonophore. Current Biol. 26: R457-458.

The best interactive tree of life ever!

April 30, 2016 • 11:45 am

There’s a new, fractally constructed tree of life—with dates of the nodes—called OneZoom, and you must have a look at it. It was created by Dr. Yan Wong (who helped write The Ancestor’s Tale with Richard Dawkins) and Dr. James Rosindell; Luke Harmon contributed to the original idea.  The background and methods are explained on a page you can access by clicking on the magnifying glass at the lower right-hand corner of each searched page, or go here. It’s still a work in progress, and you can help the tree grow by sponsoring a leaf. The project is a charity, so your donations are tax free.

This just went up yesterday, and it’s already so extensive that, I’m told, if you printed the whole thing out it would be seven times larger than the solar system! I can’t vouch for that, but the fractal design is certainly impressive. Click on the screenshot below to get started, and remember these instructions:

Each leaf represents a different species and the branches show how they are related through evolution.

This tree of life is explored like you would a map, just zoom in to your area of interest to reveal further details.

To zoom you can use a touch screen (if you have one) or scroll up (zoom in) and down (zoom out) on your mouse or trackpad.

The search icon (second from the left) gives you an easy way to search or go straight to popular areas of the tree.

The location icon (third from the left) shows you which part of the tree of life you are looking at in the context of all life on earth.

If a leaf is coloured red this means the species it represents is known to be threatened with extinction.

Leaves with a dotted outline represent parts of the tree that are not filled out yet, if you sponsor one of the species in this part of the tree we will expand the tree to include your species.

Here’s one example you can use. Click to stop the zoom, and use your mouse or touchpad to get to clickable icons.

Screen Shot 2016-04-30 at 10.22.22 AM

For example, go to the mallard (here) to see the full capabilities of the system.

Finally, there’s a special version to accompany The Ancestor’s Tale, with all the common ancestors between Homo sapiens and other species numbered.

A species discovered on Flickr

August 15, 2012 • 1:53 pm

by Greg Mayer

A recent paper by Shaun Winterton, Hock Ping Guek, and Stephen Brooks describes a new species of lacewing (a type of insect in the order Neuroptera). There is nothing unusual in this– new species of animals, especially insects, are described all the time, and we have a few million more to go. What’s a bit unusual is how the species was recognized as new– a photograph of it was seen, more or less at random, by an entomologist while perusing Flickr.

sn-lacewing.jpg
One of the original photos of the new species. From ScienceShot http://news.sciencemag.org/sciencenow/2012/08/scienceshot-new-species-discover.html ; photo by Hock Ping Guek.

After recognizing the species as new, Winterton had Guek obtain another specimen, which was sent to Winterton for study; this specimen became the holotype for the new species.  A second specimen of the new species was found at the British Museum (Natural History) in London; this specimen is the paratype.

While quite a few new species are discovered during expeditions into the wild, many are also found in more prosaic circumstances, most often among sets of unidentified or misidentified specimens in museums (much like the paratype of the new lacewing). Many such undescribed species are already in museums. As a graduate student I recall seeing cabinets full of plaster-jacketed fossils in the basement of the Museum of Comparative Zoology, with labels like “Brazil 1936” (this was in the 80s), and I often wondered whether there might be any undescribed finds within. There’s a story I’ve heard, probably apocryphal, of a paleontologist who wrote a research grant proposing to fund an expedition to the basement of the British Museum, in order to examine the unsorted and unidentified specimens still awaiting study!

New species have also turned up in the pet trade. But my favorite example of a species discovered in an unusual place is the new species of lizard discovered by herpetologist Ngo Van Tri on his dinner plate (lizards- they’re not just for breakfast anymore); previous WEIT coverage here.

The lacewing discovery on Flickr has attracted a fair amount of attention. For one of the best accounts, go to Guek’s website, and also this piece on Science‘s website, or this Mashable video :

h/t: Daphne

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Winterton, S.L., H.P. Guek, and S.J. Brooks. 2012. A charismatic new species of green lacewing discovered in Malaysia (Neuroptera, Chrysopidae):the confluence of citizen scientist, online image database and cybertaxonomy. Zookeys 214:1-11. (pdf)

Robert R. Sokal 1926-2012

May 1, 2012 • 11:11 am

by Greg Mayer

Robert R. Sokal,  Distinguished Professor Emeritus of Ecology and Evolution at the State University of New York at Stony Brook, died at the age of 86 on April 9. During his long career he made distinguished contributions to evolutionary biology, systematics, human population genetics, and statistics, and generations of biologists have learned the principles and practices of statistical inference from the textbook he wrote with Jim Rohlf, Biometry (first edition 1969; fourth edition 2011). It was my privilege to be a student of his as an undergraduate at Stony Brook.

Robert R. Sokal in 1964 (courtesy the late Robert R. Sokal, via Joe Felsenstein, from Panda's Thumb)

Mike Bell has written a fine summary of his career at the Stony Brook Ecology & Evolution website, and Joe Felsenstein also has memorialized him at Panda’s Thumb (read the comments there, too). His life story was just as, if not more, interesting than his scientific career. Born into a Jewish family in Vienna, his family fled the Nazis in 1939, and found refuge in Shanghai, China. There, he attended college, and met his future wife, Julie. They came to the United States after the war ended, and remained here. Their story, known in general terms to all at Stony Brook, was chronicled in the book Letzte Zuflucht Schanghai: Die Liebesgeschichte von Robert Reuven Sokal und Julie Chenchu Yang by Stefan Schomann (click on the title for pictures from their time in China).

He will be perhaps best remembered for his contributions to, and insistence on, rigorous, quantitative reasoning in all aspects of biology, and in helping to usher in the age of computer-based analysis of biological data. In systematics, he pioneered quantitative techniques in both phylogeny reconstruction and the assessment of similarities and differences. The latter, which he pioneered with P.H.A. Sneath, became known as numerical taxonomy. Sokal and Sneath argued that knowledge of phylogeny was not fundamental for the classificatory purposes of taxonomy, which they thought should be based on overall resemblance (an approach known as phenetics). This approach to systematics has not prevailed, but the methods developed have proved of great value throughout biology, including phylogenetics. Although he thought evolutionary considerations should not rule taxonomy, he was always devoted to the study of evolutionary questions, first in aphids, then weevils (a word he consciously strove to avoid saying, because of how it came out from a native German-speaker– something like “veevels”), then man, among other subjects. Ironically, it was some of his opponents in the taxonomic debate (the so-called transformed cladists) who seemed to lose interest in evolution, embracing a sort of Platonic idealism as the basis for what were supposedly phylogenetic methods.

At Stony Brook, he was a towering figure, always impeccably dressed in coat and tie, and with an Old World dignity and reserve, the latter reflected in the fact that, unlike all the other professors, he was known to graduate students as “Dr. Sokal”, until the students had gotten their Ph.D.’s.  (There was a weekly Friday afternoon social event called the “BS”, which initials might have various meanings; officially it was the “Beer Social”, but it was rumored that it had those initials so that graduate students could refer to “Bob Sokal” before getting their degrees.) He was also superbly disciplined: on a number of occasions, a hallway conversation with him ended as we approached the elevators, because he always took the six floors of stairs down, as it was a way to regularly exercise without an interruption in his other work. But he was witty, open to discussion, and generous with his time, even for an undergraduate.

For first year Ecology & Evolution (and some other) graduate students, his biometry class was, quite literally, a rite of passage: successful students were inducted in to the “Loyal Order of Normal Deviates”, whose hymn was “Freedom By Degrees”. I was fortunate to be able to take the class as an undergraduate in my senior year (fall 1978). The second edition of Biometry was in the works, and we received the revised text in xerox. As much for his accomplishments as a researcher, he should also be recognized for his accomplishments as a teacher, both in the classroom, and through his book, which I found to be perhaps the most readable self-teaching tool I have ever encountered. I have used it (or it’s shorter version, Introduction to Biostatistics or “Baby Biometry”) for 20 years, and plan to keep using it in future classes. But last week it was my sad duty to tell my class that they are the last to use it while Dr. Sokal was alive.