Category Archives: evolution

A limerick for Darwin’s 200th

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Thursday is, of course, the 200th anniversary of Charles Darwin’s birth. To kick off a week of commemorations, symposia, and nerdy parties, I humbly submit a limerick:

The vicar, one Quite Reverend Darwin
Considered, whilst penning each sermon,
How he might have advanced,
Had he taken that chance
To go with the Beagle a-voyagin’.

(It is widely considered that Darwin, had he not taken an interest in natural history, would’ve ended up as a clergyman; see David Quamman’s excellent pocket biography, The Reluctant Mr. Darwin.)

Draft Neanderthal genome next week

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ResearchBlogging.orgNature News reports that the first complete genome sequence for a Neanderthal will be released, appropriately enough, on next Thursday, the 12th of February, and the 200th anniversary of Charles Darwin’s birth. It’s the same group at the Max Planck Institute that released the first million bases of Neanderthal nuclear and mitochondrial DNA sequence [$-a] back in 2006. As in the earlier work, the new data were collected with a “454” next-generation DNA sequencer.

The earlier publication, which I just read this week as part of a reading group focused on next-generation sequencing technology, was more like a stunt than a groundbreaking result in evolutionary genetics. The actual results were two new estimates of the human/Neanderthal divergence times (basically confirming earlier estimates), and a coalescent estimate of the effective population size of the common ancestor, neither of which would be worth a whole paper, let alone a letter to Nature.

But it was pretty awesome just as a stunt – at every step of the analysis, the authors did some clever error checking by comparing the Neanderthal sequence to human and chimpanzee genomes, and they came up with actual nuclear sequence data from a freaking Neanderthal. Ahem. The collection of an entire Neanderthal genome is a big deal as a stunt, but I’ll look forward to seeing what new insight into human evolution comes out of it.

Reference

R.E. Green, J.Krause, S.E. Ptak, A.W. Briggs, M.T. Ronan, J.F. Simons, L. Du, M. Egholm, J.M. Rothberg, M. Paunovic, S. Pääbo (2006). Analysis of one million base pairs of Neanderthal DNA Nature, 444 (7117), 330-6 DOI: 10.1038/nature05336

Arrested development, and reproductive incompatibility, from duplicate genes

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ResearchBlogging.orgSpeciation isn’t something that evolution sets out to do – it just sort of happens. One day, a species colonizes two sides of a river, say, migration across the river drops off, and then a few million years of genetic drift later, there are two species where once there was one. The question is, what’s the final genetic change that makes the accident of speciation irrevocable?

A paper in this week’s Science pinpoints exactly that change. Bikard and coauthors report that, in the little flowering plant Arabidopsis thaliana (the plant world’s answer to white lab mice and Drosophila fruit flies), it only takes one duplicated gene to finalize speciation [$-a]. It’s a clear-cut case of a classic speciation scenario, Bateson–Dobzhansky–Muller incompatibility.


Arabidopsis thaliana
Photo by tico bassie.

It all comes down to gene duplication, which I’ve discussed before in the context of the trouble it gives to genetic analysis. Making copies of an entire genome is an error-prone process, and sometimes a whole gene gets duplicated twice. If that extra copy is inherited, it means that the carrier has redundant coding for whatever the original gene does – so now one copy can mutate without affecting its carrier’s fitness. Often this just results in loss of function for the mutating copy – sometimes it leads to new gene functions. In Arabidopsis, it’s lead to reproductive incompatibility between two strains of the plant that took different evolutionary paths.

Bikard et al. noticed that, when they crossed two strains of Arabidopsis, the resulting seeds didn’t include every possible combination of the parental strains’ genes – and a few seeds grew short, not-quite-healthy looking roots when germinated. Some of the hybrid seeds just died in mid-development. With a lot more controlled crosses, the authors narrowed the candidate genes down to a pair that normally work together in synthesizing the essential amino acid histidine. Each of the two parental strains had working copies of the two genes – but when you crossed them, sometimes the seeds couldn’t produce histidine, and so they snuffed it.

This looked like the above-mentioned (and awkwardly named) Bateson-Dobzhansky-Muller incompatibility [$-a], which is an old idea about how populations evolve reproductive incompatibilities to become separate species. Under B-D-M incompatibility, a new gene evolves in one population that doesn’t work if it interacts with genes from the other. Imagine if Windows users didn’t have to share documents with Mac users: as the two operating systems went through multiple redesigns and their respective versions of Microsoft Office(TM) were revised to keep up, it might no longer be possible to read a Mac-written Word document on a Windows machine.

Here, as Bikard et al. showed, one of the histidine-producing genes in Arabidopsis was accidentally duplicated – and one copy mutated into non-functionality. The catch is that, in the two partially incompatible strains, different copies went nonfunctional. So now, when the two lines are crossed, a small fraction of the seeds produced get nonfunctional copies of the duplicated gene. They die. And where once there were two strains of Arabidopsis thaliana, there’s something a little more like two separate species, all because of what boils down to the flip of a coin.

References

D. Bikard, D. Patel, C. Le Mette, V. Giorgi, C. Camilleri, M.J. Bennett, O. Loudet (2009). Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana Science, 323 (5914), 623-6 DOI: 10.1126/science.1165917

K. Bomblies, D Weigel (2007). Arabidopsis — a model genus for speciation Current Op. Genet. & Dev., 17 (6), 500-4 DOI: 10.1016/j.gde.2007.09.006

Blogging for Darwin, 12 February 2009

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I’ll be joining a long list of science blogs in commemorating Charles Darwin’s two hundredth birthday – only 23 more shopping days left! – as part of the Blog for Darwin blogswarm. (Not sure how I feel about the word “blogswarm,” but I like the concept!) Now: what to write about. There’s a nice list of suggested topics provided, and they only scratch the surface …

Stick insects not so excited about sex, apparently

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ResearchBlogging.orgStick insects in the genus Timema have evolved asexual reproduction on five different occasions in their evolutionary history, according to a new study in this month’s Evolution [$-a]. Why? Well, it turns out that from an evolutionary perspective, sex isn’t always a good thing.


A Timema walking stick.
Photo by WallMic.

The problem comes down to the mathematics of evolutionary fitness. Natural selection favors individuals who make more copies of their genes in the next generation – that’s the most basic definition of the “fittest” who survive. In most sexually reproducing organisms, each parent contributes half of the genes necessary to build each offspring. So for every two babies a parent makes with someone else, her genome is replicated once – half for each baby. Consider the possibilities if this parent can instead make a baby all by herself: for each baby, her entire genome is reproduced. That means that, all else being equal, an asexual critter has twice the fitness of a sexual one.

So it makes sense that asexual reproduction might pop up pretty frequently in the evolution of any group, let alone Timema – a mutant who gains the ability to reproduce asexually should be able to overrun a population of sexual competitors with ease. The question turns out to be not, why are some critters asexual? but why are any critters sexual?

One hypothesis is that sex helps in arms races against parasites, by shuffling genes to generate new combinations of defensive traits. This is called the Red Queen hypothesis because the parasite-host arms race recalls the Red Queen’s advice to Alice in Through the Looking Glass, that in looking-glass land, “It takes all the running you can do, to keep in the same place.” Population genetic studies have shown evidence of Red Queen dynamics in some species [$-a], but it’s not clear how widespread they are. Currently, more biologists favor the alternative hypothesis that sex is important in counteracting the Hill-Robertson effect, which prevents useful genes from spreading through a population if they are associated with damaging genes [$-a].

Under either hypothesis, sex is in some sense more useful in the long term than in the short term. That is, an asexual mutant can overrun a population faster than its offspring are killed by parasites or disadvantaged by the Hill-Robertson effect. This conflict should lead to a specific pattern: evolutionary lineages switch to asexuality rapidly if an asexual mutant arises, then die off when parasites or other hazards of natural selection catch up with them. This is what we see in Timema – several species have given up on sex, but all of them have recent sexual ancestors. Not only does giving up sex make life less exciting – it’s probably an evolutionary dead end.

References

M. Dybdahl, A. Storfer (2003). Parasite local adaptation: Red Queen versus Suicide King Trends in Ecology & Evolution, 18 (10), 523-30 DOI: 10.1016/S0169-5347(03)00223-4

P.D. Keightley, S.P. Otto (2006). Interference among deleterious mutations favours sex and recombination in finite populations Nature, 443 (7107), 89-92 DOI: 10.1038/nature05049

T. Schwander, B.J. Crespi (2009). Multiple direct transitions from sexual reproduction to apomictic parthenogenesis in Timema stick insects. Evolution, 63 (1), 84-103 DOI: 10.1111/j.1558-5646.2008.00524.x

Shrikes take their cues from the competition

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ResearchBlogging.orgOver evolutionary time, the easiest way to deal with a competitor is to do something different – if your competitor eats big seeds, say, it may be easier to start eating small seeds than to fight for the big ones. This idea goes all back to the Origin, wherein Darwin proposed that competition drives evolutionary diversification, with living things dividing up available resources into ever-finer slices as they scramble for shares:

Lighten any check, mitigate the destruction [of offspring] ever so little, and the number of the species will almost instantaneously increase to any amount. The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards by incessant blows, sometimes one wedge being struck, and then another with greater force.

But what if competition can sometimes make competitors more like each other? A new study, published through PLoS ONE this week, shows that red-backed shrikes prefer to set up hunting territories in places where their competitors have already been hunting.


Photo by phenolog.

Shrikes are cute but vicious predators – they capture small prey and spear them on thorns or twigs for storage, or to indicate to a prospective mate what great hunters they are. Red-backed shrikes migrate from Africa to Eastern Europe for the summer mating season. When they arrive, male red-backed shrikes must establish a hunting territory with a nesting site, but they have to contend with the established territories of great gray shrikes, which live in the same area year-round, and eat the same kind of prey.

You might expect, then, that red-backed shrikes would establish nest sites well away from the impaled victims of great gray shrikes. In fact, as the paper’s authors show, red-backed shrikes are more likely to nest near great gray shrike caches. They don’t raid the competitors’ larders, but, the authors argue, understand the presence of a great gray shrike’s cache to mean there is plenty of prey nearby.

This could mean a number of things: perhaps great gray shrikes and red-backed shrikes prey on critters that are so abundant, it’s arguable that they’re not really competing. If that’s the case, it makes plenty of sense for red-backed shrikes to use great gray shrike caches as cues to find particularly good hunting grounds. Alternatively, red-backed shrikes settling near great gray shrike caches might shift their prey preferences to avoid competition – the presence of one type of prey may very well correlate with the abundance of many other types, so that the great gray shrike caches are only indirect indicators of prey abundance. Unfortunately, the current paper has no data comparing prey preferences of red-backed shrikes nesting nearby and away from great gray shrike caches, so there’s no way to test this hypothesis.

Still, this observation has significant implications for the way we think about species interactions across evolutionary time. If competitors can be drawn together as well as driven apart, maybe competition doesn’t contribute to diversification as much as we think it does.

Reference

M. Hromada, M. Antczak, T.J. Valone, P. Tryjanowski (2008). Settling decisions and heterospecific social information use in shrikes PLoS ONE, 3 (12) DOI: 10.1371/journal.pone.0003930

Natural selection at work

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Roger Alsing has written a genetic algorithm – a computer simulation of evolution via random mutation and “natural” selection – that recreates the Mona Lisa. It achieved a pretty good replica layering only 50 semi-transparent polygons of various colors, in just shy of a million generations. And it got pretty close in the first hundred thousand generations; a neat example of R. A. Fisher’s “geometric model” of evolution toward an optimum, in which evolutionary change slows as the distance to the optimum decreases.

Via kottke.org and BoingBoing.

(Considerable debate on the BoingBoing thread about whether this is “really” evolution, since there’s a preordained optimum – I’m going to to say that it is, in fact, evolution. Specifically, a single bout of adaptive, directional evolution towards “Mona Lisa”-ness. The equivalent of which happens all the time in nature, except that usually the selective optimum shifts from “Mona Lisa” to “Les Demoiselles D’Avignon” after a million years or so.)

Snail trails lead toward speciation

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ResearchBlogging.orgFinding a mate is at the top of just about every to-do list in the animal kingdom. This might involve following the smell of pheromones or triangulating the source of a mating call; in the snail Littorina saxatilis, it turns out to require tracking your beloved by the trail of her slime [$-a].

That’s according to a paper in the latest issue of Evolution, in which Kerstin Johannesson and coauthors took video of male and female snails to catch slime trail-following in action. And it occurred to them that slime-following could be a component of speciation in L. saxatilis. This particular snail comes in two forms, or “ecotypes”: a small one that lives in the crevices of exposed rock faces and a larger one that lives in quieter, sheltered pools. When Johannesson et al. presented male snails with slime trails from each ecotype, the males preferred to follow trails made by females of their own ecotype.

This is what’s called assortative mating – preferentially mating with similar individuals – and it’s usually thought of as a first step towards speciation. Whether L. saxatilis ever eventually evolves into two species is another question, though. The world is full of experiments in speciation, where adaptation to local conditions or difficulty moving between populations can cause a species to begin diverging. But it’s just as likely that the forces pushing a species apart will change or disappear, and diverging groups re-merge into a single interbreeding population. Part of the fun of studying the natural world is finding things like snail’s slime trail discrimination, and trying to figure out what will happen next.

Reference

K. Johannesson, J.N. Havenhand, P.R. Jonsson, M. Lindegarth, A. Sundin, J. Hollander (2008). Male discrimintation of female mucous trails permits assortative mating in a marine snail species Evolution, 62 (12), 3178-84 DOI: 10.1111/j.1558-5646.2008.00510.x

Earliest-known turtle had only half a shell

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ResearchBlogging.orgFresh in this week’s Nature: a newly-discovered fossil turtle, the oldest ever found, has a lower shell, but no upper one [$-a]. Odontochelys semitestacea, as it’s called, is a really neat potential transitional fossil – the ribs are flattened like butter knives, but not fused into an upper shell. Apparently, this is suggestive of the way in which the upper shell forms in embryonic modern turtles, and the authors are careful to point out that, in other respects, the fossil is clearly an adult.


See that thing on its back? Its
ancestors may not have had one.
Photo by raceytay.

In an accompanying News and Views piece, Reisz and Head suggest that the lower half of a shell would be quite useful [$-a] if Odontochelys lived mostly in the water, where predators are more likely to attack from below than from above. They argue, though, that Odontochelys may not represent a transitional step between shell-less ancestors and full-shelled modern turtles, but a case of “secondary loss,” in which a full-shelled turtle took to the water and subsequently lost its unnecessary and cumbersome upper shell. I’m no turtle anatomist, but this sounds like a plausible alternative hypothesis. The only way to test it is is to dig up an even older turtle, and see what its shell looks like.

(See also coverage by All Things Considered, which is pretty good if unnecessarily snarky about the degree to which paleontologists specialize. It’s not like it’s that odd to think someone might build a career comparing birds’ beaks to turtles’ beaks.)

References

C. Li, X.-C. Wu, O. Rieppel, L.-T. Wang, L.-J. Zhao (2008). An ancestral turtle from the Late Triassic of southwestern China. Nature, 456 (7221), 497-501 DOI: 10.1038/nature07533

R.R. Reisz, J.J. Head (2008). Palaeontology: Turtle origins out to sea. Nature, 456 (7221), 450-1 DOI: 10.1038/456450a

Poison dart frogs can’t get too creative

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ResearchBlogging.orgBeing a poisonous animal isn’t much help if your predators don’t know about it. That’s why lots of poison-defended critters – monarch butterflies or poison dart frogs, for instance – advertise with bright “warning” colors. This is called aposematism. The idea is that predators will learn (or even evolve) to avoid bad-tasting, poisonous prey if they’re well-marked for future reference.

The trouble with aposematism, though, is that it requires giving up another, more common defensive color scheme: camouflage. If you’re a poisonous critter, and you evolve bright coloration for the first time, predators don’t yet know that you’re poisonous – but you’re really brightly colored and easy to see. How, then, does aposematism evolve from non-aposematic ancestors?


Photo by dbarronoss.

A new study on early release from Biology Letters suggests that it isn’t easy. The authors, Noonan and Comeault, set out to determine whether brightly-colored poison dart frogs are more likely to be attacked when they evolve new color patterns [$-a]. It’s possible that the frogs’ predators avoid all brightly-colored prey regardless of pattern, in which case new frog patterns would be just as good for predator deterrence as the old ones. But it’s also possible that predators only avoid patterns they’ve run across (and spat out) before – so that new, rare patterns would have all the disadvantages of giving up camouflage with none of the benefits of aposematism.

Noonan and Comeault performed an elegant behavioral experiment, setting out clay model frogs in an area where frogs of one color pattern predominate. One set of models matched the local color pattern, another was brightly colored but different from the local pattern, and a third was drab and camouflaged. Birds were much more likely to attack the “new” color pattern than either the “local” version or the drab one. This result is hard to understand at the first pass – if new color patterns are vulnerable to attack, how can aposematism evolve in the first place? The answer is, not by natural selection, but by genetic drift.

Genetic drift is a natural, mathematical consequence of finite populations: imagine a bag full of marbles, half of them black and half white. If you pull a sample of marbles from the bag, you expect them to be half black and half white on average (i.e., over many samples) – but any individual sample might have a very different frequency of white and black marbles, especially if it’s small. If the probability of picking a white marble from the bag is 0.5 (because half the marbles are white), then the probability of picking a sample of four white marbles is 0.5 × 0.5 × 0.5 × 0.5 = 0.0625. That’s a small probability, but not zero. Drift is a very real effect in the natural world, especially during the establishment of new local populations, when the population size is initially quite small.

The key to understanding Noonan and Comeault’s result is that aposematism is frequency dependent – it favors not the old pattern as such, but whatever bright color pattern is most common in the frog population. Birds attacked the “local” color pattern at a low rate, which suggests that they’re always re-learning which pattern to avoid. A new color pattern might be hard to establish within a population of frogs that look very different from it, but if a new pattern pops up in the course of establishing a new population, then – thanks to genetic drift – it may be common enough for predators to learn to avoid it.

Reference

B.P. Noonan, A.A. Comeault (2008). The role of predator selection on polymorphic aposematic poison frogs. Biology Letters DOI: 10.1098/rsbl.2008.0586