Human Phylogeography

February 23, 2019 • 11:33 am

by Greg Mayer

For the spring semester, my colleague Dave Rogers and I are teaching a seminar class entitled “Human Phylogeography.” Phylogeography is the study of the history of the genetic variation, and of genetic lineages, within a species (or closely related group of species), and in the seminar we are looking at the phylogeography of human populations. DNA sequencing now allows a fine scale mapping of the distribution of genetic variation within and among populations, and, remarkably, the ability to sequence ancient DNA from fossil remains (including Neanderthals). The seminar is based primarily on a close reading of David Reich’s (2018) Who We Are and How We Got Here (published by OUP in the UK).

A Krapina, Croatia, Neanderthal woman, photo by Jerry.

Although rarely under that rubric, human phylogeography has been a frequent topic of discussion here at WEIT, by Jerry, Matthew, and myself, including our several discussions of Neanderthals (or Neandertals) and Denisovans. So it may be of interest for WEIT readers to follow along. Below the fold I’ve placed the course syllabus, which includes the readings, and links to many newspaper articles of interest, and online postings, including many here at WEIT, and also from John Hawks Weblog, a site we’ve recommended on a number of occasions when discussing human evolution. (The newspaper links appear as images; just click to go to the story.) We just finished our third meeting, and I’ve been quite impressed by the students’ discussion and writing. We’re fortunate to have some students from anthropology or with some anthro background.

Please read along with us, or browse what seems interesting below. If you have questions or comments, post them here, and I’ll be looking in.

Continue reading “Human Phylogeography”

What were the first animals?

October 31, 2018 • 11:45 am

by Matthew Cobb

I’ve just finished making a BBC World Service radio programme about the first animals. Anyone, anywhere in the world, can listen to it (it’s only 28 minutes long!) – you just have to register with the BBC (free, rapid and cost- and spam-free). Click on the pic to go to the BBC website:

The programme deals with two different ways that researchers are studying this question – by looking at fossils, and at DNA. In both cases I interview researchers and – in the case of the Ediacara – get to handle some fossils. I also ate some 600 million year embryos at Bristol University (to see what they tasted like, obviously), but we didn’t include that in the programme. . .

The fossil data relate to what are called the Ediacaran biota – strange fossils from before the Cambrian, around 570 million years ago. The fossils are very hard to interpret – they don’t look like much alive today – but an amazing technique for analysing cholesterol molecules in the rock, so organic molecules preserved for all that time, has confirmed that Dickinsonia, the thing in the picture above, was an animal. Other techniques involve looking at large numbers of Ediacaran fossils and seeing how their distribution relates to those of modern animals. All the data suggest that some of the Ediacaran weirdos were indeed animals, although we cannot know if they are the ancestors of any animal alive today.

The DNA data focuses on a different question, which DNA can answer – which of the groups of animals alive today was the first to branch off the tree of life? Traditionally there has been a straightforward answer to this: sponges, which are nerveless and tissueless. But 10 years ago comparative genomic studies dropped a bombshell – they suggested that the first group to branch off were the ctenophores or comb jellies. This has caused a huge row because it would mean either that nerves evolved twice – once in the ctenophores, and once in our ancestors, after the nerveless sponges branched off – or that the huge sponge group somehow lost the genes for producing nerves.

Many biologists (myself included) don’t like either of these options, and prefer the sponges as the first model, but the data are persistent. Or are they? I spoke to experts on both sides of this argument, which has caused quite a hoo-haa in the zoological community for the past decade.

Anyway, go ahead and have a listen – download it and listen to it on public transport or while you are exercising. NB: I made the programme with ace producer Andrew Luck-Baker.

If you are a teacher, especially if you teach animal evolution, please get your students to listen to it.

A new phylum of very weird sea creatures

September 7, 2014 • 6:57 am

Read some biology today; it’s good for you!

It’s not often that a new animal phylum has been described, but a new paper in PLoS ONE apparently does just that, basing the phylum on two enigmatic species, dredged up from the deep sea, that can’t be placed in any existing phylum. This may add one more to the 35 phyla that already exist (see the list here, and please look. It’s nice to review the major divisions of life.)

The paper is by Jean Just et al. (all authors are from the Natural History Museum of Denmark at the University of Copenhagen), and the reference and pdf, which is free, are below.

What we have is something that looks like a cnidarian (jellyfish, corals, and sea anemones) or a ctenophore, but with a stalk. (Some cnidaria do have a stalk). But it has features that keep it from being placed in the phyla Cnidaria or Ctenophora.  Its placement on the tree of life is further complicated by two things: we don’t really know where some major groups fit on the tree of life already (see below), and we don’t have any DNA or molecular data from this group to see what it’s most closely related to, or whether it’s an outgroup (a more distant ancestor) to all metazoans (multicellular animals).

The problem is that these creatures, which I’ll show shortly, were dredged up off of Victoria, Australia in 1986 from 400-1000 meters down. They were then fixed in formalin and later transferred to 80% ethanol. I’m no molecular biologist, but I think that would pretty much destroy the DNA, preventing any molecular analysis. And the samples are now old, shrunken a bit and degraded, and so some features may be effaced.

What we have are two species placed in a new genus, Dendrogramma, which the authors consider members of a new phylum as well, though they didn’t formally name one in this paper—probably because the placement of these creatures is uncertain.  Two species were named. Here’s the first, Dendrogramma enigmatica:

Screen Shot 2014-09-06 at 12.55.41 PM

Like the other speciers, it has a flattened disc with a notch in it, a stalk (so it was attached to the substrate), and a mouth-like opening that leads into an “gastrovascular” canal in the stalk that also feeds into the radiating canals in the disc. The tissue types were not examined, so we can’t draw homologies between the types of layers and those of other metazoans.  Here’s the other species, Dendrogramma discoides:

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And both species together. You can see from the scale (1 mm) that they were very small (10 mm = 1 cm, and there are 2.54 cm per inch).

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Because of the stalk and the inflexible disc, these things were probably unable to swim but attached to rocks or the sea floor. Given their mouthlike opening, the authors suggest that “they fed on microorganisms, perhaps trapped by mucus from the specialized lobes surrounding the mouth opening.”

Why aren’t they members of existing phyla like cnidarians and ctenophores? Because they lack features found in those phyla. As the authors say (my emphasis):

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.

Given the absence of DNA data or complex characters that might help us decide where these things fit in the tree of life, the authors can only speculate. One big problem is that we don’t really know where the major phyla of multicellular animals fit on the tree. For example, some biologists claim, based on both molecular and morphological data, that the “outgroup” (the most unrelated phylum) to all metazoa is the Porifera (sponges). Others (and the authors of this paper take this position) claim that the outgroup is really Ctenophora (which, based on morphology alone, I would have thought were more closely related to the cnidarians, as biologists once thought [they’re really distantly related groups, though]). So here’s the phylogeny presented in the paper, showing cetophores as the outgroup to other metazoans (including the Bilateria, the group of phyla that includes all bilaterally symmetrical animals, including us:

Screen Shot 2014-09-06 at 12.56.24 PM

To hedge their bets, the authors have also included ctenophores within other groups, as its placement is uncertain. They’ve put Dendrogramma as either an outgroup to all other phyla, or perhaps more closely related to the ctenophores or cnidarians. We just don’t know yet.

Molecular evidence could potentially resolve the placement of all these groups, and, frankly, I’m surprised that we haven’t settled the issue. For Dendrogramma we clearly need fresh material to get DNA (the authors plead for someone to get more specimens), but we could get plenty of DNA from the other species.  Either that hasn’t been done (which I strongly doubt), or the lineages diverged so long ago that DNA evidence is inadequate to settle the question of, say, whether sponges or ctenophores are the outgroup.  Perhaps some reader can explain to us why this major issue remains unsettled.

I noticed that the discs of these species resemble some creatures described from the Ediacaran fauna (also called the “Vendian fauna”), a group that lived from about 580 million years ago to about 545 million years ago, when the “Cambrian explosion” occurred and Ediacaran animals (if they were animals!) disappeared. (For pictures of various weird Ediacaran creatures, see here.)

My friend Latha Menon, who is not only the trade science editor at Oxford University Press (and editor of the British edition of WEIT) but also a Ph.D. candidate at Oxford’s Department of Earth Sciences, would know more about this, as she works on discs that strongly resemble these, but lived hundreds of millions of years ago. I therefore asked her to relate the new finding to the old group, as they could be related. Her answer is below, along with references. As you can see, she’s a very good writer, and I’m grateful for her input on this issue.

by Latha Menon

The discovery of Dendrogramma from the deep sea off Australia has undoubtedly caused a frisson of excitement among researchers on early life. A living fossil? An Ediacaran that has been surviving quietly in bathyal regions for several hundred million years? Let’s not get carried away, but it is an intriguing find.

When Reginald Sprigg discovered, in the 1940s, a set of strange impressions, many of discoidal forms, preserved on surfaces of the sandstone and quartzite of the Ediacara Hills, South Australia,  he called them “medusoids”. Further work by Martin Glaessner and Mary Wade in the late ’60s continued to describe the various discoidal forms as medusoids, while frondose forms such as Rangea were considered to be Pennatulaceans (sea pens), and Dickinsonia was thought to be an annelid. Since then, Ediacaran macrofossils have been found all over the world, including spectacular fossil assemblages from the White Sea coast in Russia, the Nama Group, Namibia, Lantian and Miaohe Formations in South China,  and the remarkable “E surface” at Mistaken Point, Newfoundland (see e.g. Fedonkin et al., 2007). The biota gave its name to the Ediacaran Period (635-541 Ma) ratified in 2004, and the fossils themselves appear from about 579 Ma (perhaps earlier), soon after the Gaskiers glaciation, the last of several widespread glaciations, and stretch up to the Cambrian boundary. Close to the boundary, the earliest biomineralized forms, the “small shelly fossils” appear, along with intense burrowing activity (bioturbation), and the Ediacarans, as far as we know, disappear, perhaps in an extinction. So what were the Ediacarans?

Nearly 70 years after Sprigg’s discovery, with many more fossil impressions, the affinities of the Ediacaran biota remain uncertain. Remember, that’s all we have – impressions (and in some cases, carbonaceous compressions) in the rocks. No skeletons; no biomineralized parts; and certainly no DNA. Molecular clocks provide little help so far back in time; results are notoriously varied and unreliable. Fossils really matter. And in spite of the limitations, a great deal of work has been done to glean information from the often exquisitely detailed impressions and the sedimentology of the surrounding rock, which indicates the setting in which they lived and died. As more evidence accumulated concerning morphology and sedimentary context, the early interpretations of medusoids, pennatulaceans, and annelids was increasingly questioned. Some may reach 30 cm and more in size, but were they necessarily early animals?  The late Dolf Seilacher proposed that these enigmatic forms represented a “failed experiment”.

Discoidal forms are particularly hard to interpret. Some simple forms may be pseudofossils formed by physical processes; others have been persuasively explained as microbial colonies (Grazhdankin and Gerdes, 2007).  Still, some possible affinities with familiar taxa have been suggested, with evidence put forward for bilaterian traces from about 555 Ma, and the claim that Kimberella may have been an early mollusc (Fedonkin & Waggoner, 1997). Our own group has found evidence in the early Ediacaran Avalon assemblage of Newfoundland for horizontal and vertical motion associated with a discoidal form (Liu et al., 2010; Menon et al., 2013), suggesting that some of these discs may indeed have been simple polyp-like forms. Two weeks ago, we published a paper describing Haootia quadriformis n. gen. n. sp. (Liu et al., 2014: – an extraordinary fossil impression that appears to indicate muscle bands, and bears a striking similarity to modern stalked jellyfish (Staurozoa). The idea that some of the Ediacaran discoidal forms may have been stem-group medusoids has made a big come-back.

And then we hear of Dendrogramma. The authors have referred it to Metazoa incertae sedis [“of unknown placement”]. The organism resembles cnidarians and ctenophores, but lacks the characters to establish a certain affinity with either group, though molecular analysis of further individuals might yet show that it belongs to one of these lineages (the existing specimens were damaged in preparation and not suitable for DNA analysis). Whether or not Dendrogramma turns out to represent a new phylum, it does seem to be a relatively primitive form, lacking cnidocytes, colloblasts, and other more sophisticated characters. From the discription, Dendrogramma appears to be a simple diploblastic animal with a disc showing a distinct pattern of gastrovascular branches and, in the case of one of the two species, D. discoides, a stalk with a possibly trilobed mouth-field. Various Ediacaran discoidal forms, particularly those from the diverse assemblages of South Australia and the White Sea, Russia, have trilobed structures within the disc, most obviously Tribrachidium. The authors point out the similarity of D. discoides with Albumares brunsae, and Anfesta stankovskii, as well as the less obviously trilobed Rugoconites from South Australia. There does appear to be a morphological similarity, particularly with the former two forms, both in the trilobed structure and in the pattern of radial ridges compared with the gastrovascular branching on the disc of Dendrogramma.

So can we conclude that Dendrogramma is a living Ediacaran? That’s almost certainly going too far. But it does seem quite possible that some of the trilobed Ediacaran discs may represent stem-group forms of such a lineage, lacking in such modern armoury as cnidocytes (for what would they sting?) and possessing a simple small mouth with no surrounding tentacles. As for all the other kinds of Ediacaran forms, even the many other discoidal forms, well, the work goes on.

Latha’s References:
Fedonkin, M.A., et al. (eds), 2007, The rise of animals: Evolution and diversification of the Kingdom Animalia: Baltimore, Maryland, Johns Hopkins University Press
Fedonkin, M.A., and Waggoner, B.M., 1997, The late Precambrian fossil Kimberella is a mollusc-like bilaterian organism: Nature, v. 388, p. 868–871
Glaessner, M.F., 1959, Precambrian Coelenterata from Australia, Africa and England: Nature, v. 183, p. 1472–1473
Glaessner, M.F., and Wade, M., 1966, The late Precambrian fossils from Ediacara, South Australia: Palaeontology, Vol 9 (4), pp. 599-628
Liu, A.G., McIlroy, D., and Brasier, M.D., 2010, First evidence for locomotion in the Ediacara biota from the 565 Ma Mistaken Point Formation, Newfoundland: Geology, v. 38, p. 123–126
Menon, L.R., McIlroy, D., and Brasier, M.D., 2013, Evidence for Cnidaria-like behaviour in ca. 560 Ma EdiacaranAspidella, Geology, v. 41, p. 895–898

Sprigg RC. 1947. Early Cambrian (?) jellyfishes from the Flinders ranges, South Australia: Trans. R. Soc. S. Aust. 71(Pt. 2):212–24

 

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REFERENCE TO THE NEW PAPER: 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