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Sunday Spinelessness – Speciation by magic David Winter Sep 18

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For someone that writes about evolution, I don’t spend much of my time talking about the ‘debate’ that surrounds that topic. That’s probably an artifact of living in a county that doesn’t allow people who are so confused about the world that they think the bible is a biology textbook to acquire any political power. But it’s also because debating whether evolution happened, a fact that no serious biologists has debated since Darwin’s generation and is further confirmed with each new DNA sequence, is so utterly and spectacularly boring when you compare it with some of the real debates with evolutionary biology. So here’s a little something on one debate, and the land snail shells that help swing it a little towards one side.

Some of the most contentious debates within evolutionary biology are to do with how new species arise (a process we call speciation). For instance, it’s not clear how much ecology* matters when it comes to speciation. Some authors argue that speciation and ecological adaptation are usually seperate processes – the second making species distinct only after speciation has separated them. Others argue that ecological adaptation can itself be an important part of the speciation process and maybe even be enough to drive species apart.

Like many ideas in evolution, this debate goes back to Darwin’s time. People who really ought to know better will sometimes tell you that, despite its name, The Origin of Species doesn’t have a theory of speciation. You should tell those people to read Chapter 4. Darwin did have a theory of speciation, and it explicitly placed ecological competition between newly formed species as the key to driving species apart from each other. We’ve learned a few things about biology since Darwin’s time, and it turns out his verbal arguments don’t hold up to mathematically rigorous models of the ones genes work in populations. Natural selection can’t push a population apart more quickly than genetic recombination (the mixing of genes that happens in each generation) pulls it back together. So, species can’t arise soley from selection. In fact, the modern conception of speciation revolves around the flow of genes between populations. If a population isn’t sharing genes with others it’s free to evolve independantly and take on the properties that make species distinct.

Although people have talking about gene flow with regard to speciation since Darwin’s time, Ernst Mayr is probably the person most associated with establishing this idea among evolutionary biologists. Mayr took the importance of ‘reproductive isolation’ to its logical extremes – arguing lack of gene flow was not just a pattern that created species but actually the definition of a species (I disagree) and that speciation almost exclusively occured because of geographical barriers that keep populations apart from each other (leaving no room for selection).

But the gene-flow conception of speciation still leaves a tiny bit of room for selection as a driver of speciation. For instance, imagine a trait that could, at once, be subject to ecological competition and prevent gene flow between members that don’t share the trait. Then selection would be acting to keep diverging species away form each other at the same time as adapting them to their habitat. Sergey Gavrilets, a theoretical evolutioanry biologist, called models of speciation that rely on these sort of quirks “magic trait” models, partly to represent some scepticsm that such traits could exist in the wild. But empiricists have known for a long time that these sorts of traits really are out there. For instance, many plant eating insects only mate on their host-plant. So, if two diverging species are adapting to particular hosts plants, that same adaptation process will be preventing them from mating with each other. Other examples of these magic traits include body size in fish, beak size in birds, wing colouration in butterflies and, now, shell characters in land snails.

Snails can be left- or right-handed. Or, at least, the sprial of a snail’s shell can turn clockwise (making a right-handed or dextral spiral) or anti-clockwise (a left-handed or sinistral spiral) and the direction of spiraling is decided by a single gene (inherited from the mother, suggesting in may be an imprinted gene as snail’s don’t have sex chromosomes) . Most species are predominately right-handed and very few individuals within a species don’t match the predominant spiraling direction (I only know of one exception to this rule). In fact, I’ve spent more time than most people looking at snails, and I’ve never seen a left-handed one (trust me, I check!). There’s a very good reason one individuals within one species are predominately of one spiraling direction – left-handed land snails have great trouble mating with right-handed ones. Land snails are all hermaphrodites and they mate by lining up extending their gentals through a pore on the ‘spiral side’ of their body (if you aren’t invert-phobic, there are plenty of photographs of this process here). But mirror-image snails, espacially those with relatively flat shells, struggle to line up in this way, and when they do their shells bump into each other. For this reason, ‘mirror’ snails (which do arise in populations all the time) struggle to reproduce and leave few descendants.

The direction in which a snail’s shell coils also has ecological implications. Animals that specialise in eating snails have adapted to attacking right-handed shells. So, for instance, Pareas snakes always attack from the left and have lopsided jaws that help them work the snail out of the shell:

As you might imagine, these adaptations mean the snakes are less able to attack left-handed snails. If death by snake is a big risk in a snail population, then left-handed snails, while still having a hard time when it comes to mating, will be at a distinct ecological advantage. So the direction of snail’s coil could be subject to ecological selection, and it definitely presents a potential barrier to gene flow. But to be a magic trait it needs to be doing both of these things at the same time.

The Japanese land snail genus Satsuma provides a natural experiment to test this idea. Satsuma snails come in left- and right-handed forms and some populations share their homes with the snake eating Pareas iwasakii snakes. Masaki Hoso and his colleagues (Hoso et al 2010, http://dx.doi.org/10.1038/ncomms1133) looked at the distribution of left- and right-handed Satsuma species and their relationships with each other.

From this data they concluded that sinistral Satsuma species have evolved multiple times and almost always in regions that are currently home to snail-eating snakes. So shell shape really does seem like a magic trait here – left handed shells get an ecological advantage that allows them to survive and it also prevents them from sharing genes with right handed snails.

So Satsuma snails are another example of magic traits in the wild. But I think they are an opportunity to understand a bit more about speciation. The hardest thing about studying speciation is separating the differences that cause speciation with those that arise once species stop sharing genes. In the case of Satsuma we know a change one gene caused speciation so any other traits that differentiate left- and right-handed snails living along side each other happened after the fact. The number of left-right species pairs, and the different ages of the lineages they represent gives us a unique chance to understand the how interactions between newly formed species shape their futures.

Surely that’s infinitely more interesting that another round of the evolution-creation controversy?


You should also check odd Ed Yong’s take on this study, which is predictably excellent.

*I’m sorry to do this, because I don’t want to be one of tiresome people who complain about the way language changes, but the science of  ecology is something quite different from what’s fast becoming the modern definition of the word. Ecology is the study of the way organisms interact with each other and their environment and (as far as I can tell) mainly involves counting a lot of things then doing some clever statistics on the resulting numbers. It’s not (directly) about conservation or sustainability and it’s certainly not an idea invented by advertisers who worked out adding ‘eco-’ to a products name and putting it in a plain box allowed them to sell it at twice the price.

3 tweets David Winter May 20

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Let’s see if Storify stories can be embedded in blogger (if not, I guess you’ll have to read it here)

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

The Origin of Species and the origin of species David Winter Dec 31

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2009 was the double celebration for evolutionary biologists, In February we markerd the 200th anniversary of Charles Darwin’s birth and in November we celberated the 150th anniversary of That Book’s publication. Somehow I’ve managed to go the whole year without dedicating a post to Darwin’s ideas about speciation. Which is odd because I’ve spent quite a lot of thinking about, talking about and even writing about Darwin this year. So here, with about seven hours of 2009 left are a few of my thougts on Darwin and speciation.

Darwin’s book was called The Origin of Species but I’m sure that most of the tributes you’ve read to Darwin and his book this year will have focused on how he proved evolution had happened and provided natural selection as the mechanism required to explain modern organisms in that framework – the fact and the theory of evolution . Missing among the descriptions of the events that shaped Darwin’s thinking and the thousands of strands of evidence he wove to form his thesis will have been an answer to the question the title of the books seems to ask – where do new species come from. In fact, there is a prevailing view in evolutionary biology that for all his triumphs Darwin didn’t quite understand species and as a result The Origin failed to provide a theory of speciatoin. I don’t think it’s quite that simple.

To know what someone thinks about speciation you need to know what they think about species.

Practically, when a naturalist can unite two forms together by
others having intermediate characters, he treats the one as a
variety of the other, ranking the most common, but sometimes
the one first described, as the species, and the other as the
variety. But cases of great difficulty, which I will not here
enumerate, sometimes occur in deciding whether or not to rank
one form as a variety of another, even when they are closely
connected by intermediate links; nor will the commonly-assumed
hybrid nature of the intermediate links always remove the difficulty.

The Origin, p47

Darwin was the sort of person who could develop a world shattering theory, produce a body of data to support it then spent eight years looking at barnacles. Historians of science have spent a lot of ink trying to provide an explanation for “Darwin’s delay”. It may have been driven in part by an off-hand comment by his correspondent Hooker that only someone who has worked on the systematics of a group could hope to understand the nature of species or might just be a phenomenon all too familiar to modern systematists – a small project that grew out of control. Whatever the cause Darwin’s barnacle obsession (on visiting a friend’s house his son asked where his friends father “did his barnacles”) clearly shaped the way he thought about species. In numerous letters of the time, especially to Hooker, he remarks on the great deal of variation he finds within barnacles of a given species and the great trouble he finds in using that variation to define the limits of species. Partly as a result of his eight years spent dissecting barnacles Darwin came to see the variation within a species as the of the same sort as the variation that exists between species and, importantly, the difference between two varieties of a given species and two distinct species as one of degree not of kind. At the risk of boiling Darwin’s ideas down to the sort of diagram you might find in a powerpoint slide here’s a pictorial representation.

Darwin’s species concept makes the difference between species and “well marked” varieties an arbritary one. He even goes so far as to call varieties within a species “incipient species” and link the difference he noted in his barnacles, in organisms and under domestication and in organisms in the wild with the differences that seperate species and even higher orders

Hence I look at individual differences, though of small interest to the systematist, as of high importance for us, as being the first step towards such slight varieties as are barely thought worth recording in works on natural history. And I look at varieties which are in any degree more distinct and permanent, as steps leading to more strongly marked and more permanent varieties; and at these latter, as leading to sub-species, and to species.

The Origin, p51

It’s the fact that Darwin saw no fundamental difference between varieties and species that has lead many, notably Ernst Mayr, to conclude that he didn’t understand species and that The Origin was not a speciation book. I read it quite differently. To me it seems Darwin saw the term ‘species’ as something a systematist could apply to a group of organisms sometime after a process he called divergence (which we would now call speciation) has started to form discontinuities between them.

The big question then is what is the process that drives the discontinuities that make for species? The clearest answer to question comes in Chapter 4 of The Origin. Here is one example of Darwin’s ideas about the principle of divergence.

It has been experimentally proved, that if a plot of ground be sown with one species of grass, and a similar plot be sown with several distinct genera of grasses, a greater number of plants and a greater weight of dry herbage can be raised in the latter than in the former case. The same has been found to hold good when one variety and several mixed varieties of wheat have been sown on equal spaces of ground. Hence, if any one species of grass were to go on varying, and the varieties were continually selected which differed from each other in the same manner, though in a very slight degree, as do the distinct species and genera of grasses, a greater number of individual plants of this species, including its modified descendants, would succeed in living on the same piece of ground. And we know that each species and each variety of grass is annually sowing almost countless seeds; and is thus striving, as it may be said, to the utmost to increase in number. Consequently, in the course of many thousand generations, the most distinct varieties of any one species of grass would have the best chance of succeeding and of increasing in numbers, and thus of supplanting the less distinct varieties; and varieties, when rendered very distinct from each other, take the rank of species.

The Origin, p88

In typically prescient fashion Darwin took a proto-ecological view to the experimental evidence that plots sown with multiple plant species where more productive than monocultures. If the the mixed-species plot is doing better than the monoculture it must mean each species is taken advantage of different resources in that plot – what we’d now call distinct ecological niches. But then he took it yet further. What would happen if we let that monoculutre grow on for several generations. We know from his barnacles and from all the examples he listed in the previous chapters of The Origin that variants will arise. A very few of those variants will be able to make use of some of the resources that were previously going untapped. Over many generations natural selection would act – the most specialised forms would produce more seeds and produce more variants while forms intermediate between the ancestral species, not being masters of either niche, would be out competed and driven to extinction. Let this process continue long enough and you’d get first new varietes and finally, since they are just very distinct varietes, new species. Darwin provides his own diagram (the only one in the book) to describe this process and its phylogenetic implications but that is, in my supervisor’s words, “a rattly looking thing” so here’s one from me.

After the rediscovery of the Mendelian genetics and the forging of the modern synthesis we’ve come to see that some of Darwin’s ideas about species and speciation are too simplistic. The verbal argument presented above in which new species are formed solely by natural selection doesn’t hold up to modern mathematical scrutiny – recombination between unlinked genes will break down the distinction between forms more quickly than selection can makes the difference. Modern models of speciation which come strong natural selection with assortative mating do produce new species and a number of emperical studies seem to suggest this has happened in the wild.

I find it very hard to marry the received wisdom that Darwin failed to understand the nature of species and provided on theory of speciation with the arguments Darwin presented in The Origin. When his species concept is viewed (as I think all such concepts should be) as a diagnostic tool rather than an essential definition then his is as good as any other. His theory of speciation as presented doesn’t hold up to our modern knowledge of genetics but the underlying process, selection driving ecological specialisation, forms one half of our modern models of speciation that don’t involve geographical isolation and those that involve secondary contact between incipient species.

Some answers on speciation David Winter Jun 26

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Alison at the BioBlog does a great job at bridging the gap between secondary school biology and and biological research at large. Today she has a couple of good questions from highschool students:

How do scientists know when a species finishes and a new one is formed?

Are there different species in between the formation of a new species or does a, for example, Homo habilis have a Homo erectus child?

Alison provides some good answers to the questions but I thought I’d add my own thoughts since species and speciation are at the heart of my PhD research. Before we can start to ask ‘when is a new species formed’ we need to know exactly what it is we mean by ‘species’. Sadly there is no simple answer to this question, at present there at least 26 different species concepts that have been put forward, all of which have supporters and most of which are incompatible with all the other ones. The shear volume of species concepts might suggest there isn’t a single answer to what a species is. In fact, I think most of these species concepts are not <i>definitions</i> of species so much as tools that scientists use to test for evidence of a much more simple definition of species. In evolutionary biology we know how species are formed, populations of a single species stop sharing genes from each other, this means changes each new population’s gene pool can’t feed into the gene pool of its sister population – each population now has its own evolutionary trajectory.

speciation as a process

In this scheme speciation is a process not an event. During the period in which populations are isolated from each other new mutations will occur in the each gene pool that change allele frequencies, make new morphological traits and new behaviours. It’s those characters that scientists use to decide when speciation has happened but they only start accruing once the speciation process has kicked off. So, for me at least, all those species concepts are actually different tools that scientists use to get at the question that Alison’s correspondant asked – how do we know when we have a new species – and all of them have the same underlying idea of what it is they’re testing for

speciation concepts as tool in species delimination

Different biologists might have good reasons to choose a particular species concept. If you are a field ecologist doing transects then you probably want to count each biological unit that inhabits a distinct niche so you should use the ecological species concept. My research is on speciation itself so I’m interested in determining the degree of isolation between putative species, to get at that question I’ve used all data I can get – phylogenetic, genotypic, morphological and ecological evidence.

Once you view speciation as process the second question answers itself. Asking does a Homo habilis have a Homo erectus child?” is kind of like asking “does a highschool student go to bed a child and wake up and adult?”. We can all agree that we started as children and grew to adults but drawing a sharp line between childhood and adulthood is impossible. It’s the same with species if H. habilis really was the ancestor of H. erectus then I’m sure the first generation to split with the ancestral stock would have been indistinguishable, its only during the speciation process that the H. erectus lineage will have picked up the traits that identify it as a species.

Since this is in relation to question from a highschool teacher I should probably add a little disclaimer, these are my thoughts on speciation (influenced especially by Kevin de Queiroz’s work) and do not necessarily represent any secondary school syllabus.

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