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Posts Tagged evolution

Chimps are our closest relatives… but not for all of our genes David Winter Mar 15

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Ladies and genetlemen, we have the gorilla genome. You reaction to this news is probably determined by what you do for a living. If you write the headlines for major news services you will convince yourself that this result will, in some utterly undefined way, teach us about what it is to be human. Just about everyone else will develop a case of  Yet-Another-Genome Syndrome. The gorilla is, by my count, the 51st animal to be added to the full-genome club and the last of the great apes (joining humans, chimps and orangutans). More to the point, the publication of a new genome sequence doesn’t, by itself, tell us all that much. The real achievement in a “genome of x” paper is the creation of a resource that scientists will continue to work from for decades. The analysis that comes with it is really just a first pass.

But there was one very cool result to come from the analysis of the gorilla genome. About 15% of our genes are more closely related to their counterparts in gorillas than they are to the same genes in chimps.

That sounds suprising. People are always going on about how humans and chimps are ninety-nine-point-some-magic-number percent identical, and there are exactly two scientists in the world who think chimps are not our closest relatives (Grehan and Schwartz, 2009 doi: 10.1111/j.1365-2699.2009.02141.x). Have we been wrong? And how can 15% of a genome show one pattern while the rest shows another?

To understand what’s going on, we need to remember where species come from. Species start forming when populations stop sharing genes which other. When genetic changes in one population can’t filter through to another, those two populations are capable of evolving apart from each other and so can become distinct and take on the various characters that we use to tell species apart. So, new species only become different as they start to evolve apart, but they start of with a more or less random sampling of the genes in the ancestral population from which they descend. If we want to understand what’s going with the gorilla genome, we need to understand the history of those genes.

In most populations at least some genes come in distinct “flavors” (technically called alleles) . So, for instance  we all have a gene called MC1R, but some of have an MC1R allele that is associated with red hair, and others have alleles that usually lead to dark hair. We inherit  our genes from our parents, so each allele has a history that stretches back through time. If we look at modern populations we can use genetic differences between alleles to reconstruct that evolutionary history. Here’s a simplified history of four alleles, in a very small population (if you re-trace the lineages you see they fit the tree to the right):

So, what happens when a population with different alleles starts to diverge into new species:

The genetic lineages will keep on evolving down through the new tree, but now lineages will never cross the barriers to gene flow that are driving speciation. Often, the genetic lineages in the ancestral population will “sort” in such a way that when you trace the genetic lineages within a species back you arive at a member of that species (not an individual from the ancestral population). In that case, the genetic relationships (which we’ll call “gene trees) will be the same as relationships between species (”species trees”):
But population genetic theory tells us we won’t always get such a simple pattern. For recent or repeated and rapid speciation processes there might not be time for the genetic lineages to sort. The gene tree can be different from the species tree:

Exactly this process has happened with the gorilla genome. The genetic lineages hadn’t sorted before the human-chimp split so some of our genes are more closely related to gorilla ones than chimps ones.  This phenomenon might tell us something about the evolution of the great apes . The time that it takes for lineages to sort is proportional to the population size of the organisms through which the lineages are evolving. Processes that effectively limit the population size (like natural selection, which results from relatively few individuals contributing to the next generation) might leave a pattern in the way lineages have sorted.  The authors of the gorilla genome paper use this prediction to search for and find areas of the gorilla genome that may have been subject to strong selection after the population went its own way.

So called “incomplete lineage sorting” is a problem for people like me who aim to reconstruct the evolutionary history of species using genetic data. Although we’ve always known this problem existed, we’ve only recently been able to extend population genetics theory to actually infer the history of species for gene trees even when those gene trees are unsorted. It’s important we have these methods, because it’s actually predicted that most genetic lineages will be unsorted for about 1 million years after speciation starts – often all we have are unsorted genes and it’s nice to be able to extract some information from them.

The Gorilla Genome paper is

 Scally, A., Dutheil, J. Y., Hillier, L. W. et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature, 483, 169-175 doi:10.1038/nature10842

The Tree of Diversification (or why the March of Progress is wrong) David Winter Feb 22

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I’m giving a big talk next week – a departmental seminar. It’s the first time I’ve had more than 15 minutes to talk about my research, so this talk will be a little more discursive that my usual.

I study speciation, how new species come into being, and one of the things that I want to emphasise is that speciation hasn’t really entered into the broader understanding of what evolution is.Take the one image that describes evolution in modern society:


The March of Progress, Rudolph F. Zallinger. From Time Life’s book Early Man.

The so called “march of progress” has been used to describe the origin of our species thousands upon thousands of times. But it never happened. Only a few of the species depicted are potential ancestors for humans and many of them were contemporaries to each other (as the original diagram makes clear) so can hardly be different steps along a single evolutionary path. 
To try show what really happened, I’ve redrawn “March of Progress” into the “tree of diversification” – trying to show how the species depicted above relate to each other (parts of this tree are very much up for debate, by the way). Bear in mind, I’m only including the species that are represented in the original graphic, if we were to include all the fossil ape species we know about the tree would be much bushier):


Silhouettes are CC BY-SA by José-Manuel Benitos this image is released under the same license. 

I think that when you look at it this way it becomes clear that if we want to understand how the organisms depicted in the most famous icon of evoluton came to be we need to focus not just on how changes occur in one lineage, but on how new lineage form and become capable of changing in their own directions. At the moment there are probably 10 million species on earth, and just how they got to be here is surely one of the biggest questions that biology asks us. Speciation and diversification ought to be central to the way we think about evolution.

Sunday Spinelessness – The first animals (modern analogs) David Winter Jul 03

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The last time I tried to work out what the first animals might have looked like I decided fossils probably weren’t much help. So, today I’m going stop looking back into the depths of time, and see if any modern creatures might provide clues as how animals got their start in life.

Remember from the last post, the major challenge for ideas about the origin of animals is explaining how a group of single celled organisms, each with their own evolutionary interests, can join together to create a mutli-cellular creature in which almost all of the cells can never reproduce in their own right. Our glance at earliest animal fossils record showed us that the resolution of this record just isn’t fine enough for us to isolate the first cells to go in for this sort of arrangement, but there are a wealth of modern organisms that seem to have gone some way down this road, and they provide useful models for us to study.

Let’s start by looking at the closest living relatives of animals the choanoflagellates:


(photo is CC 3.0 from Choano-wiki (really!) user Mark J. Dayel)

Choanoflagellates are a widespread a diverse group of single-celled creatures that live in the ocean as well as freshwater. At first glance it might seem a stretch to propose a relationship between these ten micrometre long cells and animals, but there is good reason to believe the relationship is real. Choanoflagellates, with their characteristic ‘collar’ around the tip of the cell body and the the flagellum extending from it are almost identical to a class of cells called choanocytes found in sponges. In fact, the two cells work in exactly the same way – the flagellum pushes water and nutrients into the cell body through collar were than are digested or, in the case of sponges, moved from one cell to another. By comparing molecular sequences, biologists have confirmed the choanoflagelletes are close relatives to animals, and also established they aren’t simply a lineage discended of a sponge1 that gave up the multi-cellular lifestyle

The shared anatomy and feeding methods of sponge cells and choanoflagelletes gives us a clue as to how animals might have evolved. If a sponge is a bunch of cells that are held together by proteins that feeds using choanocytles, could the first animals have evolved from choanoflagellates that formed colonies? You don’t have to imagine too hard here, because there are modern choanoflagellates that do just that:

In fact, colonial behaviour appears to have evolved multiple times within the choanoflagellates. This behaviour might crop up so often because even the solitary species have a wealth or sticky proteins that they use to trap bacteria and other food items in their collars. However it arises, colonial behaviour is obviously worthwhile for some choanoflagellates because they been doing it for millions of years, either forming spheres like the Sphaeroeca shown above, clusters like Protero below or as small groups sitting on a stalk like Proteospongia 2

Colonial choanoflagellates might well have been the first step on the road to true mulit-cellularity, but an agglomeration of cells each doing well out of their association with each other is still a long way from the specialisation we see in modern animals. Thankfully, there are organisms out there that give us a glimpse as to what the next step might have looked like. And some of them are stunningly beautiful:

B0007761 Colony of <span class=
(photo is CC 2.0 from Wellcome Images)

The sphere you see above us an alga called Volvox that makes blurs the line between a colony of single celled organisms and a multi-cellular life form. Of course, algae are only very distantly related to animals, but we are looking for models of how simple multi-cellular life might work, and Volvox is interesting because it’s a very simple organism that has a clear distinction between reproductive cells and the rest of the organism. The closest realtives of these beautiful creatures are single celled algae called Chlamydomonas. Most of the time Chlamydomonas are free swimming cells, propelled about in search of sunlight for photosynthesis by two flagella:

When it comes time for them to divide they draw their flagella in and begin a series of cell-divisions, keeping between two and eight daughter cells within the ‘old’ cell wall before they burst out and get back to the swimming lifestyle

Volvox has ditched this two-stage life cycle, instead, the individual (or colony if you’d rather) simultaneously contains reproductive and ’swimming’ cells. That dotted sphere is made up of thousands of cells very similar to swimming Chlamydomonas each connected in an extra-cellular matrix of proteins and carbohydrates. Importantly, those outer cells don’t divide. Reproduction is down to a set of immobile cells within the sphere, called gonidia. Each gonidia can go through a set of programmed cell divisions that create all the cells that make up a new Volvox individual. Volvox is probably the simplest example of an organism that displays a division of labour between ‘body cells’ (in this case the swimming cells that move the individual around) and reproductive ones. As I said, algae are not closely related to animals, but the larvae of some sponges seem in some ways analogous to an individual Volvox. Like all sedentary animals, sponges have larvae that can move, and in sponge larvae that movement comes courtesy of a set of ciliated cells that form the lower portion of the larva:

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A glass model of a sponge larvae, photo provided by Welsh Museum

So, between Volvox and sponge larvae we have an idea of what a very simple free swimming animal with specialised cell types might look like. But how might that division of labour between different cell types have evolved? Now we really are heading into some murky waters. Animal multi-cellularity happened once, at least 600 millions ago. Obviously any answer we offer as to why this happened is going to be at best a tentative explanation, but I’ve always like an idea developed by New Zealand evolutionary biologist Paul Rainey (and not just because he has been the head of a Centre for Research Excellence of which I’m a member!)

Rainey is an experimental evolutionary biologist, taking advantage of the speed at which miroogranisms reproduce to answer questions those of us that wander about in the field couldn’t even begin to ask. One of his experiments involved growing bacteria in a stable environment, which reliably procudes mutants that are rather charmingly called “wrinkly spreaders”. The wrinkly spreaders form mat-like colonies on the top of the tubes that they live in:

To be part of that mat each cell has to pay a small cost in the form proteins that stick the cells together, but that cost is more than repaid by the fact only cells in that mat can access oxygen from the barrier between the fluid in the cell and air above it. For this reason wrinkly spreaders soon take over the population in the tubes. Natural selection acts on individuals, not colonies, and very often selection acting on cells within the mat will lead to its destruction. Cells within the mat can take advantage of their neighbours by not producing the adhesive proteins that hold the mat together while still enjoying the benefit of being within it. In time, the small advantage these mutant cells gain by not paying the price in adhesive proteins will be enough to see them out compete their neighbours. But, of course, once such ‘cheating’ cells predominate the mat won’t be able to sustain itself and it will fall apart.

Here’s were is gets really interesting. Each mat seems like an evolutionary dead end, because the mats themselves can’t reproduce (a prerequisite for evolution by natural selection) – when the mat falls apart the cells fall into the oxygen-free zone and die. But ‘cheating’ cells can reproduce and they can leave the mat and, most remarkably, because there are so many cells in a population that, in time, it’s likely one of them will mutate back to the co-operative wrinkly spreader type. Now stand back and think about the big picture here. You have a larger stationary structure, the mat, that can give rise to small, mobile cells (the cheaters) that can each go on to establish a new large structure. That sounds very similar to a larval-adult life cycle, or even the distinction between body cells and reproductive cells that we are trying to explain. Since the ‘cheater’ cells probably arise by mutations that break existing genes, the switch between cheater and wrinkly spreader could, in time, be controlled by gene expression rather than by waiting for mutations.

Of course, I’m not trying to argue that animals evolved from wrinkly spreaders specifically, or even this sort of pattern generally. The really neat idea in Rainey’s description of the dynamics of wrinkly spreaders is the way the cohesive nature of multi-cellular organisms might have evolved from competition rather than co-operation. Hundreds of co-operative systems have been identified within colonies and populations of single celled organisms and all of them are prone to sabotage by cheaters, so it’s definitely something to think about, but, like all the ideas in this field, it is speculative and may turn out to be wrong.

So, modern organisms can give us a few clues as to animals might have got their start. Colonial choanoflagellates are an example of how simple colonies that feed in the same way as modern sponges could form. Volvox is an example of a very simple organism that has a distinction between reproductive and body cells and Rainey’s wrinkly spreading bacteria show us one possible route to how that distinction would arise in the first place. In this peice of really presumed that the first animals fed in much they way modern sponges do, but not everyone thinks is the case. Next week I’ll turn to genes, genomes and the family trees we can estimate from them to explain some of the slightly more outre ideas about the origin of animals.

1 I really wanted to call this post “To be descended of a sponge“, but I called the first “The first animals” so I guess I’m stuck with it for the series

2 The world’s number one protist fan, Psi Wavefunction, would like it to be known that the Proteospongia species you might read about that is meant to have specialised cell types similar to a sponge’s ameboid cells probably doesn’t exist (being recorded in error a in the 1880s and not seen since)

Lots of references today:
Choanoflagellate biologists have their own wiki, and it’s pretty cool

The free online version of Molecular Biology of the Cell has a section on the evolution of multi-cellularity including Volvox as does Scitable, Nature’s education website.

Paul Rainey’s ideas are more thoroughly explained in:

Rainey, Paul B. 2007. “Unity from conflict.” Nature 446 (7136): 616. doi:10.1038/446616a.

Sunday Spinelessness – The first animals (fossils) David Winter Jun 19

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I see that Prime is playing a documentary by David Attenborough on the origin of the animals. One of my favourite people talking about one of my favourite topics is motivation enough to dust off one of the many posts in The Atavisms massive “drafts” folder….

You and I are connected. Trace our lineages back long enough and we are guaranteed to find a shared ancestor. In fact, we are each connected to all of life on earth. Every cell in your body can trace its existence back through an unbroken chain of cell division and DNA replication to the origin of life. The same is true of every creature on earth, so, in a very real sense you are connected to all life on this planet.

Animals are a bit weird though. Every piece of DNA in your body is the latest link in chain that goes back to the origin of life, but most of your cells can’t continue that chain. Very early on in our development, there is a fundamental distinction between the cells that make our germline (and will go on to make sperms and eggs) and those that make our bodies (the so called somatic cells). It seems natural to us for some of our cells to have no chance of leaving descendants that outlive us. But how the transition from singled celled organisms, each with a chance of reproducing, to multi-celled creatures in which most cells on reproduce ‘by proxy’ happened is one of the most fascinating questions in biology. So, how did animals evolve?

What is an animal?

Before we can ask how animals came about, we have to know just what makes animals different from other types of life. If you studied biology at school you may remember that animals are “heterotrophs” – that is they eat food rather than make their own. Lots of singled-celled animals are heterotrophs, but almost all animals are multicellular (some very strange single-celled parasites called Myxozoa appear to have evolved from multicellular ancestors). All animals are capable of moving, at some stage in their lives. There are plenty of animals that spend their whole adult life on one spot, but they all have larval forms that can get about under their own steam. Finally, animals are the only group of organisms to go through a “blastula” stage in development, and the only creatures to use collagen to hold themselves together. Since these characters are all unique to animals, and found in all branches of the animal family tree, we’d expect the common ancestor that unites all animals to share them.

So how to we reconstruct this ur-animal? This is one of those exciting fields of science where a whole suite of different tools and methods need be used to try and arrive at a clear picture The events that we are talking about happened around 600 million years ago, there are lots of different ways to try an peer back to that time, but as we’ll see, each of them has their own strengths and weaknesses. Over the next couple of weeks I’m going to look at evidence for different methods and see if we can’t pull together a consensus view of what the first animals might have been like.

Fossils

If you want to know what animals looked like 600 million years ago, you’d think the obvious place to look was 600 million year old rocks. There used to be a real problem here. Until the 1950s the fossil record seemed to have a very abrupt start in rocks from the Cambrian period (around 540 million years ago). Cambrian rocks had plenty of fully developed animals, while earlier formations seemed to have no fossils at all. The problem of life seeming to arrive fully-formed in the Cambrian period has come to be known as Darwin’s Dilemma. In Chapter 10 of The Origin (p308) Darwin talks about it (in a characteristic style that has been abused by creationists who seemed to think Darwin didn’t believe his one theories). First he acknowledges the problem, and grants that it could be used to argue against the evolutionary origin of life

To the question why we do not find rich fossiliferous deposits belonging to these assumed earliest periods prior to the Cambrian system, I can give no satisfactory answer… The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained.

So Darwin was happy to admit, at least at the time that he was writing, that there was no clear reason why pre-Cambrian rocks had no fossils and this lack of fossils was a mark against his theory. But, he goes on to offer a particular explanation for why pre-Cambrian rocks might be fossil free even if their were many pre-Cambrian creatures (which, as far as I can tell turned out to be wrong) and a more general reason to be skeptical about claims that rested on a lack of fossil evidence. Darwin argued that the evidence geologists had so far uncovered was only a thin slice of the full history of earth, in fact it was like:

A history of the world imperfectly kept and written in a changing dialect. Of this history we possess the last volume alone, relating only to two or three countries. Of this volume, only here and there a short chapter has been preserved, and of each page, only here and there a few lines. Each word of the slowly-changing language, more or less different in the successive chapters, may represent the forms of life, which are entombed in our consecutive formations, and which falsely appear to have been abruptly introduced. On this view the difficulties above discussed are greatly diminished or even disappear.

When we view fossils not as a complete record of life on earth, but as a few snapshots of different periods, the apparently sudden appearance of animals in the fossil record becomes less of a problem.

But Darwin was right, simply saying the fossil record was incomplete might be perfectly reasonable, but it wasn’t the satisfactory answer he would have wanted. Darwin’s Dilemma lacked that answer until the 1950s and the discovery of Charnia A frond-like impression in a rock discovered by a school boy in England was the first fossil to confirmed to exist in pre-Cambrian rocks.


The first pre-Cambrian fossil, holotype of the genus Charnia. CC2.5 from wiki-commons user Smith609

People had found things that looked like fossils in old rocks before, but they were dismissed or ignored either because the impression were presumed to be of an non-organic origin or because the dates of the rocks were disputed. Charina was different, the impression is clearly biological, and the rocks from which it was collected had been dated by the British Geological Survey. Once Charnia has been established as something real and something pre-Cambrian, people got a bit more serious aobut older fossils. In time an entire community of large creatures were discovered, what we now called the Ediacaran bioata

Though the Ediacarans were morphologically diverse, but there were made up from repeats of some pretty simple patterns. Charnia had is fronds growing from a rib Ediacaria left disc-like fossils and Dickinsonia was a flat oval made of tubular sections (which probably inflated like an air mattress)

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Life in the &&<span class=

Above: A Dickinsonia fossil. Below A reconstruction of an Ediacaran ocean (with way too much light!)

It’s hard to say quite what the Ediacarans were. The rocks they are preserved in were formed at the bottom of deep oceans, so it’s clear they were heterotrophs (because photosynthesis wouldn’t work down there). The fronds like Charnia must have been filter feeders (or “absorbers” feeding by osmosis) while the surface spreaders like Dickinsonia also left trace fossils, suggesting they dragged themselves across the sea floor. It’s not clear if there were any predators in these systems (leading some to call the time the “Garden of Ediacara”). So, the Ediacarans were heterotrophs, they could move and they were obviously multicellular – it seems like they must be animals. But placing them into the tree of life we’ve created by looking at modern animals has proved extremely difficult. When it was discovered Charnia was thought to be like a modern sea pen (a cniderian) but recent evidence evidence suggests that interpretation was wrong. Some researchers, most notably Adolf Seilacher, have argued that the Edicarans don’t fit easily within modern animals because most of them aren’t very closely related to them. In this view, most of the Ediacaran biota form a distinct group, which seperatley arrived at the idea of being large, multicellular heterotrophs. Others have argued that particular fossils fit into existing groups; Kimberella as a mollusc, or, more sketchily Vernanimalcula as an early Bilaterian.

It’s very hard to come down on one side or another here. If the Ediacarans really are early animals, then when we look at them we are looking at the first twigs of what would go on to form the mighty branching tree of animal life. We shouldn’t expect those first twigs, all those years ago, to contain the traits that would go on to define animal groups. On the other hand, the fossil record is so fragmentary, and gap between out time an theirs so great, placing any particular early fossil into a modern takes a bit of leap. It seems likely some of the creatures preserved in Ediacaran rocks are closely related to animals, and some others are experiments in multicellular life that burnt out. (For what it’s worth, this guy thinks the are all lichens). Whatever the Ediacarans were, they left the scene, replaced rapidly in the fossil record by the Cambrian fauna. The amazing diversity that arose in the so called Cambrian explosion is worth more than blog post by itself, but it’s not really relevant to the question at hand, reconstructing the first animals.

I should include a little discussion on some of the claims to “first animal fossil” you might have read in headlines. “Firsts” are important in paleontology, and they’re a sure fire way to get your work into a good journal, but the further back we go the more circumstantial the evidence becomes. Some very old rocks have biological chemicals that are as far as we know only produced by modern animals. That is circumstational evidence for the presence of animals in those periods, but when the rocks are hundreds of millions of years older than the oldest known animals, it seems like good evidence that some animal-ancestors could make those chemicals too. Similarly, there are very old trace fossils (tracks left behind by crawling creatures), but we know modern single-celled eukaryotes are capable of producing similar tracks, so they don’t provide water tight evidence for the presence of animals in the sediments that have been preserved.

So, fossils seem to leave us with as many questions as answers. The patchiness of the record means we can’t be sure the Ediacarans were early animals, the earlier “animal” fossils are sketchy at best and the Cambrian fauna (wonderful as it is) is just too late to tell us about the origins of animals. Next week, I’ll see if modern organisms can’t help up understand how ancient animals might have got their start, but now I’m going to tune in to David Attenborough and see how much we agree with each other… (8:30, Prime TV)

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)

Flash Fiction David Winter Nov 10

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A friend of mine send me a link to New Scientist’s Flash Fiction competition. The idea is pretty simple, write a super-short (350 words) story on the way the world might have been if some now disproved scientific theory turned out to be true. Get an entry in and it might be published in New Scientist and, much more excitingly, Neill-Freaking-Gaiman might read whatever crazy idea you came up with.

Three hundred and fifty words is about a prefect word count for my schedule at the moment (although it does take quite a long time to write something that short) so I’ve been working on a couple of ideas. You can only submit one story to the competition, so here’s the one that I deemed too silly to send in. (There are bonus points for anyone who can explain why this wouldn’t work even if recapitulation theory did turn out to be true)

***

FOR IMMEDIATE RELEASE June 25, 2014

Researchers Recreate Human Ancestors

  • Bipedalism nothing new
  • First animals sponge-like
  • New tools create ethical dilemmas

An historic series of publications presented in PLoS Biology today detail how scientists have recreated stages of our species’ evolutionary history for the first time. Researchers took advantage of new technologies and the fact organisms recapitulate their evolutionary history during their embryological development. By arresting development of an embryo at an early stage and “knocking out” genes inferred to have arisen at different times in humanity’s evolution researchers recovered the developmental program of two human ancestors.

Etienne Meckle, the head of the Human Ancestor Project (HAP), expressed his amazement at the achievement.

“ 150 years ago – when Ernst Haeckel presented the modern version of recapitulation theory – Darwin’s ideas of evolution were new, we didn’t know what a gene was and we didn’t understand embryology at all. Now, two human lifetimes after his work we’ve used his theory to recreate two of our ancestors”

The creatures so far created by the HAP had been separated by 600 million years. By halting development of a human embryo after four days, and removing the effects of all genes not shared by all animals, scientists created a simple filter-feeding animal. This early animal is similar to a modern sponge, and supports the long held theory that the first animals were sponge-like.

The second of the team’s creation is bound to prove more controversial. Merca is a 3 foot tall ape, thought to similar to the last shared common ancestor of modern apes and not seen on earth for 32 million years. She walks on two feet, a trait once thought to be unique to modern humans.

Scientific controversy aside these results have fueled a wider ethical debate, summarized by a comment by BioEthaciser121 on the PloS Biology website:

“Science has delivered us the ability to bring intelligent animals into a world they can’t possibly be prepared for. Society now needs to decide if we want to do that.”

Both recreated ancestors are on display at the National Zoo in Washington, DC.

Ka Pai Kakariki David Winter Oct 14

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New Zealand has spoken, the kākāriki is our newest Bird of the Year. It took a late surge to push the slender parrot past the other main contender for the prize, the pukeko, but in the end the kākāriki won a clear majority and it’s time for the nation to celebrate these endangered birds.

New Zealanders are rightly proud about some of the weirder creatures that call our islands home. Our native wrens, frogs, tuatara, large parrots and kiwi are all examples of ancient lineages found in New Zealand and nowhere else in the world. These species, and our geological origins, have formed part of New Zealand’s creation myth – a country that went its own way 85 million years ago and has been doing its own thing ever since. The kākāriki don’t fit in that narrative. Instead, theses parrots connect New Zealand’s biota to the Pacfic and serve to highlight the way the recent geological and climatic history of our islands has shaped the creatures we share them with.

When we say kākāriki we are actually talking about three species of small parrot, each native to New Zealand. There had been considerable debate among ornithologists about whether the different forms, which are most easily differentiated by the colour of a patch of feathers on their forehead, really represent different species rather than variants of a single species. In 2001 Wee Ming Boon, then a PhD student at Victoria University in Wellington provided the answer. Molecular data showed that each of these forms are distinct from each other.

orange-crowned parakeet (kakariki) Kākāriki
Kakariki on Matiu Somes

The orange, yellow and red fronted kākāriki all CC 2.0 thanks to John Sullivan, Tim Williams and Peter Hodge

When Europeans first arrived in New Zealand all the kākāriki species were relatively common in beech forests. So much so that when the beech failed to set enough seed for the parrot populations they would invade the settler’s farms and orchids. Robert Fulton, speaking to the members of the Otago Insitute in 1907, noted how the birds which had been “shot in their thousands” only thirty years before had all but disappeared. (The Otago Witness also recorded Dr Fulton’s sentiment that the way Kererū were slaughtered in the province put Otago-ites on “the same level as the Spanish and the Mexicans“) . Today all three species are endangered, deforestation and the introduction of mammalian predators like the stoat being a much more to blame than early orchardists. The yellow fronted species is still relatively widespread, whereas the red fronted is extinct on the mainland and the orange fronted is restricted to few small pockets of beech forest in the South Island and there may be as few as 50 birds left.

All three species are in the genus Cyanoramphus, which has representatives stretching from Raiatea in the Society Islands all the way down to Macquarie Island in the sub-antarctic. The same sort of molecular evidence that was sued to establish species status for the various kākāriki can be used to establish relationships between them and their Pacific cousins. The New Zealand species are most closely related to a species from New Caledonia. Using a molecular clock analysis, Boon and colleagues could show that modern populations of kākāriki on New Zealand and the Chatham Islands descend from a single invasion of our country from the Pacific, most likely from New Caledonia, within the last five hundred thousand years. Interestingly, the three New Zealand species split even more recently than that. It seems seems populations of kakariki become isolated within pockets of beech forests that survived the last ice age. Seperated in this way, populations would become become independently evolving lineages, which in turn can come species.

It might seem that recent arrivals like the kākāriki aren’t quite as uniquely New Zealand a group of birds as those ancient and odd birds like the kakapo and the kiwi. But, as we’ve been able to apply molecular tools to more and more of the plants and animals we share our islands with it’s become increasing clear that recent arrivals far out number the old timers. In fact, in many ways the kākāriki is a perfect example of the way life has evolved in New Zealand . It’s been here for only a short while, but in that time the turbulent geological and climatic history has shaped these birds in a unique way. So, apart from being very handsome parrots indeed, the kākāriki are worthy holders of the title of Bird of the Year. Now let’s just make sure we get to keep some of these birds in our forests!

Sunday Spinelessness – Throwing pesky males off the scent David Winter Sep 19

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ResearchBlogging.org

We often think about evolution as a competition, but it’s not always clear who the competitors are. While popular accounts of evolution often talk about species competing for survival, Darwin saw evolutionary change as the result of individual’s struggle for existence and Richard Dawkins recast individuals as proxies in a battle between genes. A new paper from Kerstin Johannesson and her colleagues at the University of Gothenburg highlights another ongoing competition which explains a good deal of biology: the battle of the sexes.

In sexually reproducing species, the costs of making the next generation often fall unevenly on males and females. Take the rough periwinkle, Littorina saxatilis for an example.

Periwinkles are snails that live in the harsh zone between the sea and the shore on rocky beaches. Life in the inter-tidal means a periwinkle can expect to spent some if its day underwater, some high and dry, and be buffeted by waves the rest of the time. Female L. saxatilis have tweaked the typical marine snail lifecycle in response to their harsh habitats. Instead of laying a lot of eggs which hatch as tiny swimming plankton, L. saxatilis females retain a relatively few eggs within their shells. Safely stowed by their mothers, the young snails can develop to such a size that they are able to look after themselves once they hatch. Which is all well and good, but the maternal care displayed by these periwinkles means males have very different interests than females when it comes to mating. From a male’s point of view more is always better, since every mating will increase the number of offspring he will sire. For females it’s a different story, they can only retain so many eggs so only need so many matings to maximise the number of offspring they will produce.

In my little sketch of this sexual conflict I’ve suggested females actually decrease the number of offspring they produce with each mating after some optimal point. That’s with good reason, as mating almost always comes at some cost. The examples from species with sexual conflicts can be gruesome; male bedbugs exclusively inseminate females by puncturing their abdomen with a hypodermic penis, some male water striders will attract the attention of predators unitl would-be mates yield to their advances, and ducks, well, Carl Zimmer has said enough about the ducks. There doesn’t seem to be anything quite as unsavoury going on with these snails, but Joannesson and colleagues were able to show mating still comes at a cost. Inter-tidal creatures are always at risk of being washed off their rocks. Enough rough periwinkle lives have been lost to the waves that all around the world L. saxatilis populations have evolved into two distinct morphological types, a form with a large muscular foot capable of tightly gripping rocks dominates low on the shore while a less muscular form lives higher on the beach. Since a mating couple presents twice as much surface area to an incoming wave, you might expect mating increases the chance a periwinkle gets swept from the rocks. To test this idea researchers got crafty. Literally. They broke out the hot glue guns and stuck empty shells on to females and saw what happened. They showed that periwinkles sporting an extra shell were more likely to fall off a platform dragged underwater in a laboratory tank and less likely to survive in the wild.

L. saxatilis populations are often very dense (around 200 snails per square metre in this study) so females don’t have to go out of their way to provision their eggs with sperm and, given the cost of mating, it’s in their interest to dissuade males as much as possible. So how do they do it? In general, snails seek out other snails by following chemical cues in the trail of mucous they leave behind them. Periwinkles males in particular have been shown to follow female trails when they are on the lookout for a mate, so there must be some clue in the mucous that marks it as belonging to a female. To see how L. saxatilis males do at finding females the researchers collected populations of this species, and three other periwinkle species that live in much sparser populations on Swedish beaches. They then filmed these captive snails moving about in the laboratory and totaled up this distance each male covered in following female and male trails. By comparing L. saxatilis males’ tracking ability with males from these other species the researchers could isolate the effects of the sexual conflict in L. saxatalis . These other species have sparser populations and different mating systems, which mean females are less likely to achieve the optimal number of matings and sexual conflict is less likely to arise. Here’s what they found.

Each point in these charts is the result recorded from one male, the position of the point depends on this distance he covered following male trails (the y- or vertical axis) and the distance covered following female trails (the x- or horizontal axis). So, in the first chart the majority of males spend the majority of their time following female trails and one crawled to the beat of his own drum and followed male trails to the tune of 400 millimetres without showing the slightest interest in females at all. The same overall patter, males following female trails significantly more often than male trails, is repeated in each of the other species (charts ‘a’ through ‘c’) but not in L. saxatilis. Male L. saxatilis don’t seem to be able to pick male and female trails, even when a different population was subjected to the test (so it’s not a local effect in the Swedish snails) and when they were given an hour to get sniffing. So what’s going on? Are females deliberately putting pesky males of their scent, or do males in such a densely packed species just not have to bother with tracking females? As the authors point out, the latter seems unlikely since the males’ inability to pick female trails leads to an unusually large number of male-male couplings in the wild. Time spent tracking and mounting a male is time that could be spent in search of a female. So, even in a dense population, it’s in a males’ interest to be able to tell the difference between male and female trails. To put it to the test, the researchers ran one more test. This time the L. saxatilis males were observed among females from another species (the flat periwinkle L . fabalis). In this test, even with the species gap, the L. saxatilis males have no trouble picking out females:

So, given the chance, L. saxatilis males can find female trails but it seems female L. saxatilis aren’t giving them the chance. By smelling like males these females reduce the burden of unwanted matings and frequently set males up on accidental male-male couplings

Johannesson, K., Saltin, S., Duranovic, I., Havenhand, J., & Jonsson, P. (2010). Indiscriminate Males: Mating Behaviour of a Marine Snail Compromised by a Sexual Conflict? PLoS ONE, 5 (8) DOI: 10.1371/journal.pone.0012005

Sunday Spinelessness – Peripatus!!! David Winter Aug 15

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I really like Te Ara, the online New Zealand encyclopedia. I can’t begin to tell you how many of my posts here have been made better by the information and the illustrations at that website. Two events last week have made me like Te Ara even more. First, it now includes an article written by my Dad; and second the folks behind Te Ara’s twitter account replaced their profile picture with a peripatus (Onychophoran). Peripatus might just be the most wonderful animals that there are – nocturnal predators that crawl through leaf litter killing their prey after immobilising them with glue shot from their heads while still managing to look cute. They’ve also been the subject of some woolly evolutionary thinking, and New Zealand’s peripatus are the centre of one of country’s most interesting evolutionary debates. So, in honour of Te Ara’s fine taste in profile pictures, today’s post is all about our peripatus

Onychophora
Peripatoides sp. image is CC 2.0 from Flickr user Bruno C. Vellutni

I should probably start with the name. So called “walking worms” or “velvet worms” like the Perpatoides above all belong to the phylum Onychophora (the name refers to the claws on the end of each of those legs). In New Zealand we invariably call our species”peripatus” despite the fact that none of them have ever been considered to be part of the tropical genus Peripatus. I can’t quite work out how the name peripatus took hold in the public understanding of these creatures, but it hardly matters as long as we all know what we’re talking about. In fact, using peripatus as a common name in English makes for a nice congruence, since that name comes from Latin meaning “to walk about” and the Maori name for these creatures, ngaokeoke derives from the verb “to crawl”. And it’s fun to say (Stephen Jay Gould claimed he’d never written about onychophorans without mentioning how much he liked to hear the word peripatus).

As I mentioned above, peripatus spend their lives in leaf litter and rotting logs. A couple of years ago I spent a fair amount of my summer walking through forests pulling apart rotting logs looking for certain species of springtails. The springtails we were looking for were few and far between, so you did a lot more searching than finding, but looking through rotting logs always throws up interesting creatures. I couldn’t count the number of spiders, bizarre harvestmen, smart little native cockroaches, beetles, centipedes, millipedes and snails I found. But I remember each of the three times I encountered a peripatus. There is something very special about running into one of these creatures in their natural habitat, as they crawl away on legs almost identical to the ones that supported their (marine) ancestors 500 million years ago. But peripatus are more than “living fossils” (actually, nothing’s a living fossil, every creature on earth has been evolving for 3.8 billion years) almost everything about these animals is amazing.Their fleshy little legs work without a skeleton (inside our out) because their body is inflated with an incompressible liquid that muscles can work against, they shoot glue across (relatively) large distances to immobilse their prey, they have pretty complex brains and (among Australian species at least) complex social behaviours and for all their lack of morphological diversity they have a great variety of reproductive strategies. Most species are ovoviviparous, which means the young develop in eggs which are retained in the female where they hatch a little while before they are born. A few New Zealand an Australian species lay eggs which are supplied with yolk and left alone and others have gone in the other direction and taken eggs out the equation by giving birth to live young nourished by a placenta. All that and they remain, in the words of PsiWavefront “[really quite] adorable”

A plush peripatus from Weird Bug Lady’s amazing Etsy shop

Peripatus have also fueled some slightly wonky evolutionary thinking, including perhaps the single stupidest idea to be published in a scientific journal – that insects like butterflies and wasps and beetles which have caterpillar-like larvae are the result of ancient hybridisation between caterpillar-like onychophorans and some flying insect. I don’t think that idea is likely to become widespread but it’s almost impossible to read about peripatus without coming across the idea that they form a “missing link” between the arthropods (animals with jointed limbs and exoskeletons like spiders, insects and crustaceans) and the annelids (earthworms, leeches and their relatives). There is probably no term that annoys me more than “missing link” – its continued use betrays the way we’ve failed to include what we know about evolution in the way we think about biology. By now we should know that links belong in chains and species belong in trees. More specifically, the term missing link comes from a theological idea called the Great Chain of Being or Scala Naturae which was meant to relate all of Creation in a giant hierarchy from God, who set it all in place, on down to mud with angels, kings, men, women (occasionally in that order) animals and plants filling the gaps. When natural historians brought up in the age of the Great Chain turned their eyes on the biological world they looked for creatures that could fill up the spaces, smoothly linking the “high” and the “low” animals. In that light you might see the stumpy little legs of onychophorans as filling the space between annelids (with segments but never true legs) and arthropods (with segments and specialised limbs associated with particular segments). Something like this:

But ever since Darwin we’ve known that animals weren’t created to fill a spot in a hierarchy. Rather, they’ve arisen in a branching pattern, with new lineages forming from the repeated splitting of older ones. Modern species aren’t links in an evolutionary chain, they are tips in an evolutionary tree. In this way evolution is actually a process that creates gaps – once a lineage splits each of the daughter lineages are free to evolve away from each. If anything the mixture of “worm-like” and “arthropod-like” character in peripatus might be evidence for shared ancestory between these groups (ie, all these groups descend from a segmented ancestor not shared by the un-segmented animals like molluscs) which would help us to understand the order in which those character evolved:

In the tree above the Onychophorans aren’t a link between arthropods and annelids, they are their own group with some degree of shared ancestory with each other group. As it happens, when you look at more characters (especially the nervous system, embryonic development and DNA) the apparent relationship between annelids and peripatus breaks down. The “worm-like” properties of the onychophorans are likely down to each group independently arriving at the same solution to problems arising from life as a tubular invertebrate or the maintenance of traits found in the ancestor of all animals and since modified in most lineages but not these ones. Here’s how we’d relate the four groups we’ve been looking at above given what we know today (”spiral cleavage” is a pattern of embryonic development shared by most lophotrochozoan animals):

On top of being a biological marvels, New Zealand’s peripatus might be able to tell us about our county’s geology. In fact, our peripatus might just be the only animals keeping New Zealand above water during the Oligicene. New Zealand got its geological start about 85 million years ago when the land that makes up our mini-continent split away from the super-continent Gondwana and for a long time it was considered likely that most of flora and fauna were on board when the split happened. That geological event and it’s biological ramifications have become something of a creation myth for New Zealanders, it suits our image as a a rugged and unique country forging its own way through the world. It just happens to be wrong. Or at least, it’s become increasingly clear that most of our flora and fauna are relatively recent arrivals (having been blown or rafted to our litltle islands) and some geologists have suggested the whole of New Zealand may have been underwater in the “Oligicence drowning” about 23 million years ago, an event that would have extinguished any Gondwanan refugees. Our peripatus form part of the debate because their relatives are found in Australia, South America and Africa – all formerly part of Gondwana – and as such provide us with the means to test the idea that our peripatus have been in New Zealand since New Zealand existed. Earlier this year Julia Allwood and colleagues presented a molecular clock study focusing on New Zealand and Australian onychophoran species. The molecular clock doesn’t tick as smoothly as a wristwatch, so good dating studies like Allwood et al’s almost always include large error bars. Nevertheless, they found that the oldest split between Australian and New Zealand genera was between 24.5 and 136.7 million years, with a point estimate just under 80 million years. It’s not quite and open and shut case, but it’s probably enough to make our peripatus the best candidate for a Gondwanan relict in New Zealand.

The trees and the chain use the following images:
Snail from Hadi Fooladi, Leech from PhatController, Onychophoran from Ant Boy and springtail from Cornell Mushroom Blog. All are licensed under Creative Commons 2.0 license (as is everything here that isn’t credited to someone else)

Allwood and colleagues’ paper is

Allwood, J., Gleeson, D., Mayer, G., Daniels, S., Beggs, J., & Buckley, T. (2010). Support for vicariant origins of the New Zealand Onychophora Journal of Biogeography, 37 (4), 669-681 DOI: 10.1111/j.1365-2699.2009.02233.x

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

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