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If some of us have Neanderthal genes, are Neanderthals us? David Winter Jun 08

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I got a little bit starry eyed writing about the Neanderthal genome the other day. I chose to retrace the arc of scientific progress that links the initial description of Neanderthal man as something different than modern humans to the point reached last month, where we are able to tag some of those differences to a single gene. Most of the news stories about the Neanderthal genome focused not on the genes that made us different from them, but a small percentage of the genome that reinforced the continuity been them and us. Genetic evidence that Neanderthals interbred with the ancestors of some modern humans. The revelation of these ancient assignations has caused some quite sensible people to say some quite silly things about what species are and what Neanderthals were. So, perhaps I can compliment my slightly hazy earlier piece with a more hardheaded take on why Neanderthals remain a species unto themselves.

Let’s start with the evidence that Neanderthals interbred with the ancestors of modern humans. Modern humans (Homo sapiens) arose in Africa about two hundred thousand years ago, all modern human populations outside of Africa descend from a relatively small number of migrants who left that continent between eighty and fifty thousand years ago. When those migrants first left Africa and entered the Middle East they would have met other humans. The ancestors of the Neanderthal had moved out of Africa and established themselves in Europe and Central Asia thousands of years before. Until now we haven’t known which of the four ‘F’s (fighting, fleeing, feeding or reproduction) followed that first contact, the Neanderthal genome has given us a clue.

When you compare individual DNA bases that are variable within modern human genomes to the corresponding sequences in the Neanderthal genome you find that non-African sequences match the Neanderthal sequence slightly (but significantly) more often than African sequences do. It’s possible that this pattern is an artifact of our poor sampling of African genomic diversity (that observant nerd Christie does a good job of explaining how here) but for the sake of argument let’s take it for granted that his pattern is the result of ancient interbreeding. The authors of the paper describing the Neanderthal genome estimate people with no recent African ancestry inherited between one and four percent of their genome from Neanderthals. That number is the same for Papuan and East Asian populations as it is for Europeans despite Neanderthals having lived alongside Europeans for thousands of years, suggesting any interbreeding that contributed to modern human genomes was limited to that first period of contact.

This is where the problems start. Having heard the news that Neanderthals and some of our ancestors might have once swapped genes some people remember that nice easy test of species-status from high-school biology. Something like “if two animals can interbreed then they’re part the same species.” So, are we Neanderthals; or are Neanderthals us? No. In fact, the Neanderthal genome serves to highlight some the mistakes we commonly make when start trying to define species.

Biologists have spent a lot of time arguing about just what a species is and how can delimit species from the creatures that we study, too often we’ve forgotten that those are two different arguments. DeLene from Wild Muse has a thoughtful overview of some of the factors that contribute to the “species problem” in her review of Jody Hey’s book on the same topic. You should read her piece because the species problem really is a fascinating philosophical question, but I think most of the fights that erupt around competing definitions of species come from a failure to understand that defining species and organising critters into species are two different tasks. We’ve been studying speciation, the process by which new species arise, for a while now and we’ve developed a pretty good idea of how it works. Two populations stop interbreeding with each other, during that period of “reproductive isolation” genetic changes in one population can’t effect the other so natural selection and random changes (called genetic drift) change each population independently. Species are populations which are on independent evolutionary trajectories.

Reproductive isolation drives the independence that is at the heart of what species are, but it’s not the sine qua non of a species. James Mallet from University College London has made a special study of hybridisation, and he reckons 10% of animal species and a whopping 25% of plants interbreed with other species from time to time. As molecular tools have been applied to non-model organisms it’s become increasingly clear that the “species barrier” is more porous than we’d thought, and species can maintain their independence even in the face of the occasional injection of genes from other species.(If you’re interested in the wider question, I’ve written a bit on the species problem here. The short version is we should see competing “species concepts” as operational tools that might be used to help delimit species, but not as definitions).

Now, think about the results from Neanderthal genome. Most sequences in that genome are separated from their human counterpart by a split that happened over five hundred thousand years ago. There is pretty good evidence that Neanderthals and the ancestors of non-Africans interbred when they met each other in the Middle East about four hundred and fifty thousand years after that initial split. That gene flow had the potential to homogenise the two populations into one, but it didn’t. Each lineage maintained its identity. For the twenty or so thousand years that Neanderthals continued to exist they retained identifiable morphological traits. There are fossils in Europe that some argue show a mixture of characters, but any interbreeding in that continent left no mark on modern European genomes, which have no more Neanderthal DNA than Papuan and Chinese genomes do. At the same time, the authors didn’t detect any flow of modern human genes into Neanderthal genomes (so it’s not a case of of modern humans swamping Neanderthal populations and erasing any trace of genetic admixture in the process). The available evidence seems to point o Neanderthals and modern humans as separately evolving populations, and a little bit of gene flow between them wasn’t enough to upset that pattern.

I should stress, by saying H. neanderthalensis and H. sapiens are different species we aren’t saying very much about how different Neanderthals were from us. Species are not defined by a degree of difference, or an essence that was missing in Neanderthals but is present in us, they’re just another human population that was moving in a different direction (and eventually extinction). If some of us do have Neanderthal genes, then it only goes to show how fuzzy the line between our species and the rest of the biological world is.

Green RE, and many, many others (2010). A draft sequence of the Neandertal genome. Science (New York, N.Y.), 328 (5979), 710-22 PMID: 20448178

James Mallet’s bit on the frequency of hybridisation is taken form here:

Mallet, J. (2005). Hybridization as an invasion of the genome Trends in Ecology & Evolution, 20 (5), 229-237 DOI: 10.1016/j.tree.2005.02.010

The ideas about species and species delimitation presented above are pretty similar to Kevin de Quieroz’s take:

De Queiroz, K. (2007). Species Concepts and Species Delimitation Systematic Biology, 56 (6), 879-886 DOI: 10.1080/10635150701701083

Sunday Spinelesness – One for the arachnophobes? David Winter Jun 06

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It occurs to me that some readers might be put off by my affection for spiders. I’d be interested to see which creature, the wasp or the spider, you find yourself cheering for at the end of this post. Let’s introuduce them. First, the large black hunting wasp Priocnemis monachus emerging from its burrow in one of the steps on our garden path (I messed up the focus, but nature has a way of refusing to re-pose):

pomp1

And the creature the black hunting wasp has been hunting, one of the native tunnelwebs Porrhothele antipodiana:

spider1

Po. antipodiana is pretty cool spider, it’s one of very few that are capable of eating snails. Snails usually avoid the attentions of ground dwelling spiders by being too slimy to get a hold off and being able to retract into their shell. Po. antipodiana get’s around those defenses by hooking its fangs into the snail’s body and holding on while the snail struggles, produces tonnes of mucus and finally succumbs to the spider. A couple of months ago I gave a talk to a local school who wanted someone to help their study of invertebrate lifestyles and one of the kids told me that he’d seen a tunnelweb eating a snail. The budding naturalist didn’t seem at all proud when I told him that he’d observed a behaviour that was only recognised by scientist 30 years ago. I guess 30 years seems an impossibly long time when your 10!

If this particular spider looks a bit bedraggled it’s because it has already been anesthetised by the wasp. Pr. monachus is a member of the family Pompilidae which, like the ichneumonidae that featured here last week, use the living bodies of other arthropods as incubators to grow their young. While most of the ichneumonidae use caterpillars to grow their larvae the pompilids specialise in spiders (which has earned them the name spider wasps). There are ten described species of spider wasp in New Zealand, each targeting a range of spider species. Pr. monachus the largest of our spider wasps, and by choosing Po. antipodiana to provision her nest this one has taken on of New Zealand’s largest spiders:

Pomp3

Pr. monachus follows the typical pompilid nesting behavior, which means they go hunting before they set up their nest. As I watched these two the wasp would drag the spider a few centimetres then drop it and scurry back up the step and into its nest for a few seconds before returning to the spider, checking it was still incapacitated (and giving it another sting if it showed a fight) and repositioning it again. I don’t know how much of that behavior was down to the wasp setting up its nest and how much was the wasp struggling with having bitten off more than it could drag up the sheer surface of the step it built its nest in.

Pomp5

The wasp was definitely seemed to be having a hard time hefting the spider up the step. I spent about half an hour watching her grab and the spiders legs, its spinnerets or its even its head while clinging to the sheer face of the concrete step. In the end, it started raining and I decided I should probably do something else with the rest of my weekend so I left her to her work. I came back about an hour later and both spider and wasp were gone. I don’t know if the wasp gave up; or if it achieved its Herculean task and the spider’s body is, even now, nourishing the next generation of these impressive wasps.

Pomp4

Sunday Spinelessness – Attack of the Killer Sponge! David Winter May 23

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ResearchBlogging.org
Chondrocladia turbiformis, a ruthless carnivore hauled from bottom of the sea off new New Zealand by NIWA scientists, has been named among the top ten new species described last year. This abyssal predator isn’t a kraken, a plesiosaur that time forgot or even an improbable (but awesome) hybrid. It’s a sponge.

It may come as some surprise that a sponge can be a carnivore, or even that sponges are animals. Sedentary as they are, sponges tick all the boxes for inclusion in the kingdom Anamalia. They eat other organisms to make energy and build their body (differentiating them form plants and algae), they have cells enclosed by membranes (not cell walls like plants and fungi) and they are truly multi-cellular, with specialised cell-types (which sets them apart from protists). On the other hand, sponges are pretty unusual animals. Sponges have no nervous system, no gut, not circulatory system and their cells don’t form tissues. The relative simplicity of sponges helps us to understand the evolutionary history of animals, by plotting some of the characteristics of modern animals onto a phylogeny we can see what order those characters evolved in:

How the sponges relate to other animals. The protostomes and deuterostomes differ from each other in in fate of the blastopore, the first opening to form during embryonic development. In protostomes it becomes the mouth, indeuterostomes it becomes the anus.

So, sponges are useful in trying to understand the evolution of animals. But we shouldn’t view modern species as steps along a path toward more complex animals. Sponges are amazing creatures in their own right, for a start they’re the only animals that don’t have a mouth. Most sponges feed by drawing water into the their body through pores and absorbing bacteria and small algae from that water with specialized cells on the inner surface of their bodies. The cells of the inner surface have two sets of projections to help them with this task. The tail-like flagella which beat together to get water flowing over the absorbing cells and the hair-like micro-villi which increase the cells surface area and make them more efficient absorbers (the guts of more complex animals play the same trick on a larger scale). Most sponges further increase the efficiency of this process by taking the form, and the function, of a chimney. The tubular forms are help together by a mesh of small calcium carbonate structures called spicules.

Filter feeding works well in relatively nutrient-rich shallow waters, but scientists have pulled odd looking sponges up from the bottom of the ocean. Some of those sponges still had the characteristic sponge filter feeding system, but others had lost it all together. Quite how these strange sponges were getting by in the dark and unproductive abyss without even the normal sponge feeding system remained a mystery until 1995 when French researchers found a relative of the deep sea sponges in a relatively shallow submarine cave. Abestopluma hypoa gave scientists their first chance to observe these sponges, and what they saw was amazing: it was a carnivore. In life A. hypoa projects a set of filaments into the water. Those filaments are covered in tiny spicules which act like Velcro (that’s the author’s own simile) grabbing passing crustaceans and holding them in place. It takes a while for the sponge to get its meal, cells make contact with prey within an hour but the actual ingestion follows a period of cell growth and movement which completely covers the animal after a day. It takes another couple of days to completely digest the crustacean.

Since that first discovery scientists have discovered many more carnivorous sponges, with a surprisingly large number coming from sea mounts off New Zealand and in the Southern Ocean. The topic of today’s post (I knew I’d get to it eventually…), Chondrocladia turbiformis, is one of the newest killer sponges, and it looks a bit like a mushroom:


The Chondrocladia are a bit of a special case among the carinovore-sponges because they have retained the rudiments of their filter feeding system. They don’t appear to use it to supplement their diet, rather it’s been re-purposed to inflate a balloon like structure the sponge uses to help capture prey. (For a stunning example of this structure in a live sponge see the photo that illustrates Olivia Judson’s article here.). But the thing that really distinguishes C. turbiformis from the already amazing carnivorous sponges are its spicules:


Beautiful as they are, those symmetrical curved claws in D and E are run of the mill for Chondrocladia. The spinning top spicules in G and H are something quite different. It was only through the description of C. turbiformis and a related species C. tasminae that it became apparent these spicules, with have been named trochirhabds, are present in some modern Chondrocladia species. It’s not extactly clear what these cool little spiclues are doing in modern Chondrocladia but they give us a clue to the history of carnivorous sponges. Spicules just like the trochirhabds described from C. turbiformis have been found in marine sediments from the Jurassic period. It appears the carnivorous sponges that it took us until 1995 to learn about have been living in the oceans for at least 150 million years.

The rest of the this years top ten – including bombardier worms, amphibious sea slugs and giant web building spiders – can be found here.

Vacelet, J., Boury-Esnault, N., Fiala-Medioni, A., & Fisher, C. (1995). A methanotrophic carnivorous sponge Nature, 377 (6547), 296-296 DOI: 10.1038/377296a0

Jean Vacelet,, Michelle Kelly, & Monika Schlacher-Hoenlinger (2009). Two new species of Chondrocladia (Demospongiae: Cladorhizidae) with a new spicule type from the deep south Pacific, and a discussion of the genus Meliiderma Zootaxa (2073), 57-68

Sunday Spinelessness – You don’t know the trouble you’re in David Winter May 16

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A scene from the garden. On the left, the New Zealand Praying Mantis Orthodera novaezealandiae. On the right, a hover-fly that doesn’t know how much trouble it’s in.

Trouble

(for those interested in the final result: the hover-fly flew off; the mantis lunged, but missed)

Memorialising my own folly David Winter May 05

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I’m usually a pretty cautious kind of a guy. I might be physically incapable of proofreading but I at least think these posts through and make sure I’m not committing any grave errors of science before I hit the publish button. Usually.

A couple of weeks ago I made fun of Garth George because he underestimated New Zealand’s carbon emissions by some staggering amount. It turns I overestimated the degree of Garth George’s underestimate. Or to put it another way, I screwed up that maths. Garth George is still spectacularly wrong, out by a factor of 375 000, but I had said he was out by about eight times more than that. In putting the graphics together I’d written down the inverse of George’s error (about 2.75 millionths, or 2.75 x 10-6) to help me calculate the sizes for each triangle and when it came time to write up the post I mistook my notes, reading 2.75 x 106 or 2.75 million.

That’s not an excuse, it should have been obvious to me, as someone who passed 3rd from maths, that 3.7 x108 couldn’t be millions of times bigger than 1 x103 and in writing the post I should have caught it. It’s all very embarrassing, but if you are going to make fun of people you have to be prepared to be treated in the same way. So, in that spirit, here’s the magnitude of my error plotted for all to see:

And the worst bit, Garth George is still among the wrongest people in history but not quite on the same level as the Young Earth Creationists (and will no doubt be overtaken by Bill Gates at some stage, if he really said that thing they say he said):

Any physical science types reading this post might want to make a joke at the expense of biologists now, can I suggest this one:

A group of biologists and a group of mathematicians meet each other at a train station on their way to a conference on ecological modeling. The biologists each line up to buy a ticket, while a single mathematician collects a few coins from each his colleagues and buys a single ticket. Both groups board the train and before the biologists can ask what the mathematicians are up to one of them yells out that the conductor is on his way. The mathematicians leave on mass, cramming into one bathroom. The conductor arrives and clips the ticket of each biologist before knocking on the bathroom door and asking “tickets please”. The mathematicians slide their single ticket under the door, it gets clipped and the mathematicians get their train journey at a fraction of the cost the biologists paid.

The two groups run into each other again on the way home from the conference. This time the biologists are on to the game, so after exchanging a knowing wink with the mathematicians they send a representative off to get one ticket. But they are amazed to see the mathematicians don’t even bother with the single ticket that bought for the first journey. The biologists want to know what’s going on by the mathematicians stay tight lipped until their spy announces “conductor on his way”. The biologist scramble just as they’d seen the mathematicians do on the last trip, squeezing into a bathroom. In contrast, all but one of the mathematicians strolls down to the other bathroom in the train while the other approaches the biologists’ room, knocks on the door and asks “tickets please”.

(The moral of the story, biologists should think carefully before applying mathematical methods)

Sunday Spinelessness – A Nobel Prize Winning Insect David Winter Apr 04

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I think invertebrates are important. The 95% of animal species that don’t have a backbone are not simply the base of the animal kingdom’s pyramid, they are the little creatures that run the world. A third of the planet’s food production relies on honey bees, collembola and corpse-feeding insects turn dead tissue into living tissue and coral reefs can turn the nutrient-poor tropical seas into submarine rainforests. There are even a couple of invertebrate animals that have won the Nobel Prize.

TheFliesHaveEyes

Drosophila melanogaster has probably taught us more about genetics than any other animal on earth. In the wild D. melanogaster larvae develop on rotting fruit so, just like the flesh-flies that were featured here a couple of weeks ago, they are faced with the problem of having to complete their entire developmental program in the short period of time the fruit they are born in is a viable food source. Thanks to these environmental constraints, D. melanogaster has a very short life cycle. Under optimal conditions they can go from egg to adult in a week. This remarkable developmental haste means drosophilists can run genetic experiments that cover many generations in a few months, and they can run many replicates of these experiments because each of them takes up about this much space:

tubes

Drosophila has been kept in laboratories since the the turn of the 20th Century but T.H. Morgan was the first person to put Drosophila at the forefront of genetic research. Morgan was an embryologist by training and, like a lot of embryologists then and now, he became interested in a school of evolutionary thought called mutationism. As the name suggests, the mutationists argued that one-off mutations were the creative engine of evolution, relegating natural selection to weeding out maladaptive mutants. In order to test the creative power of mutation Morgan grew up generation after generation of Drosophila and bombarded them with anything he thought might mutate them; radium, salts, sugars, acids, bases and even centrifugal force. Two years of this mutational bombardment got Morgan nowhere, he could induce changes in his flies but none that would be stably passed on. In 1910 he found a single white eyed male.

There is a story, which I can’t find repeated by reliable sources, that holds that Morgan took the first white eyed male home with him in jar and slept with the jar next to his bed that night. I don’t know if that story is true but that one fly does have a treasured place in the history of genetics. By crossing it to normal eyed (what geneticists call “wild type”) females he was able to show that the genetic factor that made the fly’s eyes white was part of the sex determining chromosome. For the first time a gene had been shown to be reside on a chromosome. A few years later he showed that multiple genes are arranged in linear fashion along chromosomes by demonstrating crossing over between the white eye gene and another called rudimentary. At Otago second year geneticists repeat Morgan’s experiments, so this picture, sorting flies under a binocular microscope, will be familiar to anyone whose been through the program. (it will probably also bring back memories of escaped flies and a whiff of the (dilute) ether used to knock the files out…)

underthescope

Morgan was awarded the Nobel Prize in 1933, in 1948 Drosophila research got another Nobel, this time to Hermam Muller for showing X-ray radiation could induce mutations. Geneticists have continued to use Drosophila as a model organism, perhaps most usefully in untangling the genetic interactions that underly the development process. In 1980 Christiane Nüsslein-Volhard and Eric Wieschaus presented the results of a mutational screen; that is, they mutated Drosophila stocks at random and recorded the developmental phenotypes that resulted. Nüsslein-Volhard and Wieschaus identified 15 genes involved with the very early stages of development. In quick time Drosophilists mapped that those genes to chromosomes and worked out how their products combined to pattern a developing embryo. Nüsslein-Volhard and Wieschaus’ work laid the ground work for one of the most staggering findings of modern biology, almost all the genes that help shape the Drosophila embryo have counterparts in the human genome that play similar roles in our development. An insect can be a useful model for human development and disease genetics. Nüsslein-Volhard and Wieschaus were awarded the Nobel Prize in 1995, the third Nobel for work on Drosophila.

A big thanks to Sarah Morgan, one of Otago’s fly pushers, for the photos that illustrate this post. Sarah’s off to the US of A this week to show off her research at The Big Drosophila Meeting in Washington DC so she will probably have some less historical Drosophila science to talk about in the next little while…


Nüsslein-Volhard C, & Wieschaus E. (1980) Mutations affecting segment number and polarity in Drosophila. Nature, 287(5785), 795-801. PMID: 6776413

Rubin GM, & Lewis EB. (2000) A brief history of Drosophila’s contributions to genome research. Science, 287(5461), 2216-8. PMID: 10731135

Sunday Spinlessness – The Other Damsel David Winter Mar 28

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This week’s Sunday Spinelessness is dedicated to those people who wash up at this post after googling for “Austrolestes colensonis” only to be disappointed. At the time I wrote that post on our damselflies I didn’t have a photo of the the New Zealand Blue Damselfly, let me correct that now. A full body shot:

damsel2

And a close up:

damsel3

These photos were taken at Fensham Reserve in the Wairarapa. We walked through the bush there on a bright summer’s afternoon and every time we passed a break in the canopy we found a little flight of Austrolestes basking in the sun. The reflective wings were beautiful, but, as you’re about to see, not easily photographed:

damsel1

Does a forty thousand year old finger point to another human species? David Winter Mar 26

ResearchBlogging.org

DNA extracted from a 40 000 year old finger bone found in a cave in Siberia might be evidence for a previously unrecognized human species. Or it might not be. The bone, which comes from what New Zealanders call a “little finger”, Americans call a”pinky” and paleo-anthropologists call the “distal manual phalanx of the fifth digit”, was found in the Denisova cave, in a region of Siberia from which remains of members of both our own species (Homo sapiens) and Neanderthals (H. neanderthalensis) have previously been found. The mitochondrial DNA (mtDNA) sequences generated from the finger bone are distinct from both modern human sequences and from previously published neanderthal sequences, but inferring species boundaries is a tricky business and the mtDNA sequences are not, in and of themselves, proof that the finger belonged to a member of a third human species.

Here’s the big figure from the paper, which was presented by Johannes Krause and colleagues in Nature yesterday. It’s a phylogenetic tree which relates the little finger’s mtDNA to H. sapiens and H. neanderthalensis sequences (click to see a high-resolution version):

The Denisnova sequence is red, Neanderthal sequences are in blue and modern humans are grey. So, the Denisova mtDNA forms a distinct lineage that isn’t represented in modern humans or in previously published Neanderthal sequences. By using the tree as the basis for molecular dating the researchers were able to estimate that Denisova lineage separated from other human mitochondrial lineages between 0.78 and 1.3 million years ago. The temporal context the molecular dating adds to the phylogenetic tree helps to us understand where this new mitochondrial lineage might fit into humanity’s family tree.

I’ve said before that most of our species’ history was played out in Africa, and, in fact, the same is true when we step up a taxonomic level and look at our genus. All the human species that have been found outside of Africa descend from migrants that moved out of that continent at some stage. Here’s a schematic representing some of the species in the wider human family tree and the timing of the migrations that moved them out of Africa.

How does the new evidence presented by Krausse et al. fit into that scheme? Perhaps the simplest interpretation is the the Denisova lineage represents a new species. The estimated age of the Denisova lineage makes it too young to have been carried out of Africa by the first wave of H. erectus migrants to leave Africa and apparently too old to have been inherited from the migrants that went on to form the Neanderthal lineage. If the Denisova sequence is something new then we’ll have to update our family tree, adding a new branch and a fourth migration out of Africa.

John Hawks thinks we should hold off on updating the family tree too qucikly. The Desinova specimen might be a Neanderthal. At first glance the tree presented by Krausse et al. seems to dispel that possibility since previously identified Neanderthal sequences are more closely related to modern human sequences than the new linaeage, but that tree is based entirely on mtDNA. The mitochondrial genome is inherited as if it was a single gene. We can often use trees estimated from a single gene (”gene trees”) as a proxy for species-level relationships (”species trees”) but, in fact, every gene in a population has its own history and there there are scenarios that can push a given gene tree away from underlying species tree. Perhaps the easiest way to visualise how you’d end up with mitochondrial lineages that diverged millions of years ago within a single species is to think about genetic lineages moving through a population while speciation happens. New species form when populations stop sharing genes with each other, in the diagram below the big black triangle represents a barrier to gene flow. What happens if multiple different gene lineages are present in the ancestral population at the time that this gene flow stops? Usually, given enough time, each species will “sort” into specific gene lineages that descend from just one of the lineages in the ancestral population, but it’s also possible for one (or both) species to maintain multiple lineages for some time. Such “incomplete lineage sorting” makes gene trees bad proxies for species trees and it’s just possible that something like this has happened in Neanderthals:

Perhaps by moving to the very Easterm edge of the Neanderthals range we’ve sampled for the first time a lineage that existed in that species for the whole time it was in Europe. Maybe, and Hawks surely knows a lot more about paleobiology than I do, but I don’t really buy it. It’s certainly possible for a species to harbour deeply divergent mitochondrial lineages, but the time it takes for gene-lineages to sort within a species is relative to the effect population size of that species. Neanderthals probably had a relatively small effective population size (and mtDNA definitely does, since only females pass it on and then in only one copy) making the retention of multiple lineages over hundreds of thousands of years seem like a long shot. As Hawkes argues, strong geographic structure in Neanderthal populations might have aided the retention of divergent genetic lineages against those odds, maybe the Denisova mitochondrial lineage was extinct in Western Europe but common in Central Asia? It’s possible, but I wouldn’t bet on it.

Finally, the Denisova sample might be our first look at H. erectus DNA. H. erectus remains have been recovered from China so it seems possible they were in Siberia too. As I’ve said, the molecular dating of the Denisova lineage probably makes it too young to be a descendant of the first wave of migration form Afirca (though, of course, there is some uncertainty associated with that dating), but it might be evidence of genetic exchange between African and the H. erectus diaspora. As we’ve come to understand the origin of our species we’ve realised that the simple “Out of Africa” model is just that, a model, and the true pattern is more complex. H. sapiens really did have its start in Africa and it really did push out into the rest of the world in the last 50 000 years or so, but during that expansion populations have continued to exchange genes. There’s no reason to believe that that H. erectus could not have done the same, perhaps the main thrust of the H. erectus expansion was 1.6-2 million years ago but genes continued to flow in and out of Africa for sometime after that.

So, there are three possibilities for the Denisova sample:

  1. It could be a new species,
  2. It could be an ancient mitochondrial lineage retained in eastern Neanderthal populations but lost elsewhere
  3. It could be the first H. erectus sequence.

We’ll need more genes (Krausse et al. report they are working on sequencing genes from the nuclear genome) or more complete specimens to know for sure but I’ll throw caution to the wind and say I think the first scenario to be the most likely and the second the least probable (remembering of course, that I’m not an anthropologist and these are pretty subjective estimates!). Perhaps I’m displaying some biases because I also think numbers one and three would be the cooler results. If either of those scenarios are true then we can add a third human species (alongside the Neanderthals and the ‘Hobbit’ H. floresiensis) that modern humans might have interacted with – it’s just so fascinating to imagine our ancestors living alongside other human species and how differently the world might have turned out if those other species had survived the few thousand years that separate us.

You should read Carl Zimmer’s post on the paper, he’s compiling expert opinions as they come to him. There’s also some more qualified comments via The Independent who made up for their poor news article on the story by having Chris Stringer from the Natural History Museum write a piece on it.
Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

Does a forty thousand year old finger point to another human species? David Winter Mar 26

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ResearchBlogging.org

DNA extracted from a 40 000 year old finger bone found in a cave in Siberia might be evidence for a previously unrecognized human species. Or it might not be. The bone, which comes from what New Zealanders call a “little finger”, Americans call a”pinky” and paleo-anthropologists call the “distal manual phalanx of the fifth digit”, was found in the Denisova cave, in a region of Siberia from which remains of members of both our own species (Homo sapiens) and Neanderthals (H. neanderthalensis) have previously been found. The mitochondrial DNA (mtDNA) sequences generated from the finger bone are distinct from both modern human sequences and from previously published neanderthal sequences, but inferring species boundaries is a tricky business and the mtDNA sequences are not, in and of themselves, proof that the finger belonged to a member of a third human species.

Here’s the big figure from the paper, which was presented by Johannes Krause and colleagues in Nature yesterday. It’s a phylogenetic tree which relates the little finger’s mtDNA to H. sapiens and H. neanderthalensis sequences (click to see a high-resolution version):

The Denisnova sequence is red, Neanderthal sequences are in blue and modern humans are grey. So, the Denisova mtDNA forms a distinct lineage that isn’t represented in modern humans or in previously published Neanderthal sequences. By using the tree as the basis for molecular dating the researchers were able to estimate that Denisova lineage separated from other human mitochondrial lineages between 0.78 and 1.3 million years ago. The temporal context the molecular dating adds to the phylogenetic tree helps to us understand where this new mitochondrial lineage might fit into humanity’s family tree.

I’ve said before that most of our species’ history was played out in Africa, and, in fact, the same is true when we step up a taxonomic level and look at our genus. All the human species that have been found outside of Africa descend from migrants that moved out of that continent at some stage. Here’s a schematic representing some of the species in the wider human family tree and the timing of the migrations that moved them out of Africa.

How does the new evidence presented by Krausse et al. fit into that scheme? Perhaps the simplest interpretation is the the Denisova lineage represents a new species. The estimated age of the Denisova lineage makes it too young to have been carried out of Africa by the first wave of H. erectus migrants to leave Africa and apparently too old to have been inherited from the migrants that went on to form the Neanderthal lineage. If the Denisova sequence is something new then we’ll have to update our family tree, adding a new branch and a fourth migration out of Africa.

John Hawks thinks we should hold off on updating the family tree too qucikly. The Desinova specimen might be a Neanderthal. At first glance the tree presented by Krausse et al. seems to dispel that possibility since previously identified Neanderthal sequences are more closely related to modern human sequences than the new linaeage, but that tree is based entirely on mtDNA. The mitochondrial genome is inherited as if it was a single gene. We can often use trees estimated from a single gene (”gene trees”) as a proxy for species-level relationships (”species trees”) but, in fact, every gene in a population has its own history and there there are scenarios that can push a given gene tree away from underlying species tree. Perhaps the easiest way to visualise how you’d end up with mitochondrial lineages that diverged millions of years ago within a single species is to think about genetic lineages moving through a population while speciation happens. New species form when populations stop sharing genes with each other, in the diagram below the big black triangle represents a barrier to gene flow. What happens if multiple different gene lineages are present in the ancestral population at the time that this gene flow stops? Usually, given enough time, each species will “sort” into specific gene lineages that descend from just one of the lineages in the ancestral population, but it’s also possible for one (or both) species to maintain multiple lineages for some time. Such “incomplete lineage sorting” makes gene trees bad proxies for species trees and it’s just possible that something like this has happened in Neanderthals:

Perhaps by moving to the very Easterm edge of the Neanderthals range we’ve sampled for the first time a lineage that existed in that species for the whole time it was in Europe. Maybe, and Hawks surely knows a lot more about paleobiology than I do, but I don’t really buy it. It’s certainly possible for a species to harbour deeply divergent mitochondrial lineages, but the time it takes for gene-lineages to sort within a species is relative to the effect population size of that species. Neanderthals probably had a relatively small effective population size (and mtDNA definitely does, since only females pass it on and then in only one copy) making the retention of multiple lineages over hundreds of thousands of years seem like a long shot. As Hawkes argues, strong geographic structure in Neanderthal populations might have aided the retention of divergent genetic lineages against those odds, maybe the Denisova mitochondrial lineage was extinct in Western Europe but common in Central Asia? It’s possible, but I wouldn’t bet on it.

Finally, the Denisova sample might be our first look at H. erectus DNA. H. erectus remains have been recovered from China so it seems possible they were in Siberia too. As I’ve said, the molecular dating of the Denisova lineage probably makes it too young to be a descendant of the first wave of migration form Afirca (though, of course, there is some uncertainty associated with that dating), but it might be evidence of genetic exchange between African and the H. erectus diaspora. As we’ve come to understand the origin of our species we’ve realised that the simple “Out of Africa” model is just that, a model, and the true pattern is more complex. H. sapiens really did have its start in Africa and it really did push out into the rest of the world in the last 50 000 years or so, but during that expansion populations have continued to exchange genes. There’s no reason to believe that that H. erectus could not have done the same, perhaps the main thrust of the H. erectus expansion was 1.6-2 million years ago but genes continued to flow in and out of Africa for sometime after that.

So, there are three possibilities for the Denisova sample:

  1. It could be a new species,
  2. It could be an ancient mitochondrial lineage retained in eastern Neanderthal populations but lost elsewhere
  3. It could be the first H. erectus sequence.

We’ll need more genes (Krausse et al. report they are working on sequencing genes from the nuclear genome) or more complete specimens to know for sure but I’ll throw caution to the wind and say I think the first scenario to be the most likely and the second the least probable (remembering of course, that I’m not an anthropologist and these are pretty subjective estimates!). Perhaps I’m displaying some biases because I also think numbers one and three would be the cooler results. If either of those scenarios are true then we can add a third human species (alongside the Neanderthals and the ‘Hobbit’ H. floresiensis) that modern humans might have interacted with – it’s just so fascinating to imagine our ancestors living alongside other human species and how differently the world might have turned out if those other species had survived the few thousand years that separate us.

You should read Carl Zimmer’s post on the paper, he’s compiling expert opinions as they come to him. There’s also some more qualified comments via The Independent who made up for their poor news article on the story by having Chris Stringer from the Natural History Museum write a piece on it.
Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

Sunday Spinlessness – Waste Not David Winter Mar 21

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Just a quick one today. A few weeks a go I used a picture of a male Cambridgea spider to spring off into a half-baked conversation on arachnophobia. That male had probably wandered into the warmth of our house after paying a visit to a female who has a web attached to the downpipe by our kitchen window:

cambridgea web

During the day the web’s owner hides in a retreat (in this case right behind the joint in the downpipe) but at night you can see a very impressive spider sitting under her web, waiting for some tasty morsel to get trapped. Cambridgea are really forests spiders, if you hunt around a decent piece of native forest and you are bound to find a similarly constructed, but much larger, web. In the forest expectant Cambridgea mothers obscure their egg cases with twigs and dried leaves. Apparently our kitchen wall did offer much camouflage when our Cambridgea mother

cammegg2

You really should click on that image and see the high-res version, it’s pretty cool. In order to grow, spiders have to cast off their rigid exoskeleton. You can see here our Cambridgea mother has used her discarded exoskeleton to help obscure her egg case!

The exoskeleton also gives you a clue as to how the spider has achieved its moult – the cephalothorax (the part of an arachnid body that includes the head and the thorax) is popped off and the spider pulls itself, legs and all, out through that gap. The last step of the process is photographed here.

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