john hawks weblog

paleoanthropology, genetics and evolution

dispersal

  • Across the waters

    Thu, 2013-03-14 00:28 -- John Hawks

    Japanese tsunami debris has been arriving on the northwest coast of the United States, carrying exotic Asian marine species along for the ride. Earth magazine takes the opportunity to tell a broader story about long-distance dispersal by rafting: "Setting sail on unknown seas: The past, present and future of species rafting". The evolution of primates included at least two major rafting dispersals, into South America and onto Madagascar:

    Perhaps the most famous example of rafting is the colonization of the island of Madagascar across 400 kilometers of open water from Africa. Madagascar appears to have been an island for at least 120 million years. Genetic studies suggest that animals began arriving about 60 million years ago. Geologic evidence for land bridges or island chains during this window has never been found, leaving rafting as the most likely explanation.

    “The rafting hypothesis has been well explored; it’s really been a process of elimination,” says Ann Yoder, an evolutionary anthropologist at the Duke Lemur Center in Durham, N.C. “It’s kind of crazy to imagine lemurs clinging to vegetation and rafting across the Mozambique Channel,” she says. “But time and time again, it really seems to be the best fit for the data.”

    It's the kind of stuff that inspired long-dead theories of sunken continents -- in this case, Lemuria.

    Many people have discussed shorter-distance rafting among present and past Mediterranean islands to explain the dispersal of Miocene primates, most notably Oreopithecus. By the time hominins show up and begin dispersing to islands (first Flores, more than a million years ago), rafting was probably deliberate.

  • Neandertal anti-defamation files, 17

    Tue, 2013-01-01 17:30 -- John Hawks

    Let no one say that I'm an uncritical voice about the many advantages of releasing preprints. They do have their downsides. Lack of editing is one.

    Here's a passage from a new preprint from Peter Waddell and Xi Tan, "New g%AIC, g%AICc, g%BIC, and Power Divergence Fit Statistics Expose Mating between Modern Humans, Neanderthals and other Archaics":

    The apparent lack of Denisovan alleles on the X chromosome suggested that some of these archaic interbreeding events were male biased, that is archaic males mating with modern females (Waddell, 2011). This was formerly dubbed the “archaic Ron Jeremy” hypothesis, after the well-known American thespian. Formerly known, because a journal editor has recently urged us to alter our manuscript, to avoid confusion with a “Ron Jeremy Event”, which they referenced to the Urban Dictionary. The new synonymy is the “lecherous archaic man” hypothesis.

    I'll return to the argument in the paper later, I just wanted to consider the question of Neandertal similarity to well-known thespians. This is a followup to another preprint from last 2011, which addressed the question of male-biased gene flow into the ancestry of Papua New Guinea from Denisovan peoples ("Homo denisova, Correspondence Spectral Analysis, Finite Sites Reticulate Hierarchical Coalescent Models and the Ron Jeremy Hypothesis"). From that preprint:

    While the origin of the unusual features of the NSYFHP pattern is just a hypothesis at this stage, it is testable and deserves a name, so we call it the “Ron Jeremy hypothesis” (after the accomplished American thespian Ron Jeremy, who is adroit at debauching modern young women, whose father’s might well call him a Neanderthal or a Denisovan, and who looks remarkably like reconstructions of these archaic humans in museums, including being very big boned).

    Big boned.

    Similarly, we may refer to the low frequency of the NSYFHP on the X chromosome as “Ron’s Grandfather hypothesis” which is the mixing of the Denisovan lineage with an even more ancient hominid lineage due to a male biased infusion.

    Obviously we badly, badly need a better system of terminology to discuss the relationships of archaic human groups, including MSA and earlier Africans, which we now understand to have been subject to recurrent gene flow. Male-biased gene flow has often happened in human groups, sometimes due to warfare or the dominance of elites, sometimes as a simple function of greater male dispersal. Male-biased gene flow also appears to characterize orangutan population history, but not chimpanzees, so it depends on species-specific aspects of population structure and dispersal strategies.

    We unfortunately have a 150-year history of looking at Neandertals, and secondarily at other archaic human groups, as strange evolutionary dead-ends. When faced with the evidence that these ancient people are among our ancestors, some scientists have turned first to the idea that mating among ancient people was exotic and strange. Hence the "Ron Jeremy" angle.

  • Carnivores and early Homo

    Tue, 2012-04-24 10:27 -- John Hawks

    Ann Gibbons reports on a recent conference investigating the interaction of climate change and Plio-Pleistocene human evolution "Where's the beef? Early humans took it." I like her description of Lars Werdelin's work:

    After comparing fossils of 78 species of carnivores that lived during five different periods of time between 3.5 million years ago (when large carnivores were at their peak) and 1.5 million years ago, Werdelin found that all but six of 29 species of large carnivores (animals that weighed more than 21.5 kilos) had gone extinct in that time. Moreover, the mass extinction began just before H. erectus appeared in the fossil record 1.9 million years ago. He also found that the community of carnivores alive 2.5 million to 2 million years ago ate a much broader range of food—with species within a community filling a wider range of dietary niches. By 1.5 million years ago, just hypercarnivores that ate only meat, such as lions and leopards, had survived while omnivores that scavenged and ate a wider range of foods, like civets, had disappeared. "Even I was surprised by the dramatic drop," Werdelin says.

    It will be interesting to see more details of this work as it is published. The picture described here seems fairly different from Werdelin's 2005 paper with Margaret Lewis [1], in which they concluded there was no evidence of a turnover pulse of carnivore species between 3 million and 2 million years ago. In that paper, they did note that the present carnivore community is dominated by species that have no Pliocene record in Africa. It's not clear how much of this turnover resulted from dispersals of carnivores into Africa from Eurasia, and how much was in situ origins of new genera. That paper was focused on the role of herbivore species turnover on the carnivore community, showing that the two records do not match each other.

    With the present focus on hominins as potential competitors, maybe the expansion in scope to a greater number of omnivores made the difference to the analysis. On the other hand, it's hard to see how recent carnivores can be purer meat-eaters than extinct sabretooths like Megantereon. Lewis and Werdelin's 2007 book chapter [2] (in a Springer volume with no access for me, naturally) does link the origin of Homo erectus 1.8 million years ago to carnivore turnover.

    While the appearance of stone tools at 2.6 Ma has no apparent effect upon carnivorans, the appearance of Homo ergaster after 1.8 Ma may have been at least partly responsible for the decrease in the carnivoran origination rate and the increase in the extinction rate at this time. The behavior of H. ergaster, climate change, and concomitant changes in prey species richness may have caused carnivoran species richness to drop precipitously after 1.5 Ma. In this situation, even effective kleptoparasitism by H. ergaster may have been enough to drive local populations of carnivorans that overlapped with hominins in dietary resources to extinction. Possibly as a result, the modern guild, which evolved within the last few hundred thousand years, is composed primarily of generalists.

    We should probably add to the picture the evidence for dispersal into and out of Africa, which is unclear at the moment for carnivores [3]. If humans had an important effect on the carnivore guild, we should expect codispersal of some carnivore genera with humans in the Early Pleistocene. It's possible that such codispersal did occur into Eurasia, but first appearance dates are not the greatest evidence to build such a hypothesis.

    On that note, there are some incredible carnivore materials from Malapa that may really add to the picture of carnivore-hominin relations. The first of these were published last fall by Brian Kuhn and colleagues, including Werdelin [4]. It will be exciting to see more of this work come out, as I'm sure that the preservation of a wide array of carnivore materials is really shifting how we can think about the relative diets and ecological roles of these species. It's another case where paleontologists can now leverage the vast record of time covered in East Africa by applying the detailed information from the exceptionally preserved Malapa deposit.

    UPDATE (2012-04-25): Adam Van Arsdale writes that Dmanisi provides even more evidence about carnivore-human interactions: "Early Homo and the carnivore guild".

    The Dmanisi fauna in general, including the carnivores, are only just beginning to be more widely published. A 2011 paper by Hemmer and colleagues discusses a possible large cheetah-like carnivore found at the site. This 2010 paper by Sotnikova and Rook looks at Canid evolution in Eurasia more broadly, but discusses the abundant Canid material from Dmanisi in some depth.

    Kate Wong gives some more information about Werdelin's presentation: "Rise of Humans 2 Million Years Ago Doomed Large Carnivores".


    References

    1. Werdelin L, Lewis ME. Plio-Pleistocene Carnivora of eastern Africa: species richness and turnover patterns. Zoological Journal of the Linnean Society. 2005;144(2):121 - 144.
    2. Lewis ME, Werdelin L. Patterns of Change in the Plio-Pleistocene Carnivorans of Eastern Africa: Implications for Hominin Evolution. In: Bobe R, Alemseged Z, Behrensmeyer AK Hominin Environments in the East African Pliocene: An Assessment of the Faunal Evidence. Hominin Environments in the East African Pliocene: An Assessment of the Faunal Evidence. Dordrecht: Springer Netherlands; 2007. pp. 77 - 105.
    3. O'Regan HJ, Turner A, Bishop LC, Elton S, Lamb AL. Hominins without fellow travellers? First appearances and inferred dispersals of Afro-Eurasian large-mammals in the Plio-Pleistocene. Quaternary Science Reviews. 2011;30(11-12):1343 - 1352.
    4. Kuhn BF, Werdelin L, Hartstone-Rose A, Lacruz RS, Berger LR. Carnivoran remains from the Malapa hominin site, South Africa. PloS one. 2011;6(11):e26940.
  • Y chronology awry

    Wed, 2011-08-24 09:57 -- John Hawks

    Dienekes links to and discusses a current paper by George Busby and colleagues [1] on the Y chromosome chronology for the settlement of Europe: "Back to the drawing board for R-M269 (Busby et al. 2011)." The main idea is that microsatellite loci on the Y chromosome have made up the majority of our information about biogeography using this marker, but the rate of mutational changes of these loci has been badly misapplied:

    A bad clock is not useless: it gives you some information about time. Moreover, you can often use several to iron out the inaccuracy of any single one of them.

    Unfortunately, better estimation through averaging of bad estimators works only in one case: when the estimators are unbiased.

    The inclusion of some fast-mutating STR loci tends to make all estimates too young. The paper finds that this problem is general, affecting most commonly-used datasets.

    Our analysis confirms that this phenomenon is not specific to the R-M269 haplogroup nor to methods using ASD. Figure 4b shows that STRs with high D produce larger estimates of T. What is clear is that estimates of T implicitly depend on the STRs that are selected to make this inference. Using BATWING on an HGDP population for which 65 Y-STRs are available, we have shown that the median estimate of TMRCA can differ by over five times when STRs are selected on the basis of the expected duration of linearity (electronic supplementary material, figure S4). While researchers take into account STR mutation rates when estimating divergence time with ASD, commonly used STRs do not have the specific attributes that allow linearity to be assumed further into the past. The majority of haplogroup dates based on such sets of STRs may therefore have been systematically underestimated.

    One weakness of the study is that its reliance on geographic patterns of the haplotypes depends on the assumption that they have evolved neutrally relative to each other. Selection might radically affect this pattern.


    References

  • Quote: Fisher on the limits of diffusion

    Thu, 2009-09-17 22:16 -- John Hawks

    R. A. Fisher and Sewall Wright introduced diffusion approximation methods into genetics; Fisher (1937) was the first to consider spatial disperal using a reaction-diffusion model. I found this quote a useful expression of his acknowledgment of the limits of the model:

    The use of the analogy of physical diffusion will only be satisfactory when the distances of dispersion in a single generation are small compared with the length of the wave. In reality diffusion is a complex process, compounded often of the diffusion of gametes, and that of larvae, in addition to adult forms; a more exact treatment than that supplied by a simple coefficient would involve the interaction of these components, and the stages at which the selective advantage was enjoyed. So far as it is applicable, the analogy of physical diffusion, therefore, greatly simplifies the problem (355-356).

    The paper has no references.

  • Quote: Peter Turchin on the "bugbear" of randomness

    Sun, 2009-08-30 16:18 -- John Hawks

    I'll probably have some more material on quantitative analysis of dispersal in the few days. Here's a quote from Peter Turchin (1998:17-18):

    Of course, we do not know that animals truly move at random, like flipping coins to decide whether to turn right or left. Each individual could be a perfect automaton, rigidly reacting to environmental cues and its internatl states in accordance with some set of behavioral rules. However, even if this were true, we might still choose to model behavior of such animals stochastically, because we would not have the perfect knowledge of all the deterministic rules driving these animals. Even if we did, we might not want to include them all in our dispersal model, since such a model would have an enormous number of parameters and would require a very accurate representation of all environmental "micro-cues." The point is that randomness is a modeling convention. Because it is impractical, and not even helpful, to attempt to model individual movement deterministically, we use a more parsimonious probabilistic model.

    I'm pausing the quote to point out my boldface. It has become computationally feasible in the last few years to model enormously complicated scenarios with individuals acting pseudo-deterministically. The most popular use of such modeling is to try to constrain dispersal models by some geographic conditions, such as local habitat richness, rainfall, or altitude (see also, "One model, hold the extra parameters"). Of course, animals really do disperse in ways that depend on such geographic parameters. The question is whether any datasets are sufficient to test models involving so many parameters.

    This approach is aptly termed behavioral minimalism (Lima and Zollner 1996). In essence, we adopt a thermodynamic approach: the behavior of individuals is erratic, or irregular, but the redistibution process at the population level has many regular features. There is a direct analogy with with thermodynamic theory. The motion of each gas molecule is chaotic and essentially unpredictable, and can only be described probabilistically. When dealing with large numbers of molecules, however, the laws at the aggregate level are for all intents and purposes deterministic. Similarly, the problem of biological dispersal can be treated by starting with a probabilistic description of individual movements (in other words, formulating the problem as a random walk), and then approximating the redistribution process of the ensemble of individuals with a deterministic equation, diffusion.

    The effective scale of stochastic versus deterministic processes is important. I'm chiefly interested in the dispersal of adaptive genes in human populations, for which the deterministic approximation may be considered to have become more and more relevant over time, as the population sizes of regional populations grew. Still, the present pattern in many cases may reflect the stochasticity of populations from earlier time periods, when they were smaller. And formerly important deterministic processes, such as the adoption of agriculture, may no longer be directly observable. So how do we model variance?

    The thermodynamic approach to dispersal does not have to assume that the movement of each "particle" is completely random. The important feature of this approach is that we can control the degree of realism in the model. Environmental factors that have strong effects on movement can be included explicitly in the model, while other factors that have weak effects (or about which we have no information) are included in the stochastic component.

    This would incorporate the geographic modeling approaches mentioned above -- deterministic processes related to spatial variance of habitat or dispersal potential. But then the important step must be to find a minimal deterministic model to account for the data, and then test it with other observations -- such as more extensive genetic sampling, archaeological information, or historical documentation.

    References:

    Turchin P. 1998. Quantitative Analysis of Movement. Sinauer, Sunderland MA.

  • Spatial variation and near-fixed selected alleles

    Thu, 2009-06-11 14:39 -- John Hawks

    I couple of people have asked me about a new paper in PLoS Genetics by Graham Coop and colleagues, titled, "The role of geography in human adaptation." The paper is open access, and while the details of genetic measures and simulations can be hard to follow, I think it's a great example of the way recent work on selection and human diversity has been structured.

    I'll just expand on a few of the topics in the paper, and discuss how they relate to the previous findings about the number and age of selected variants in human populations.

    Here's the paper's abstract:

    Various observations argue for a role of adaptation in recent human evolution, including results from genome-wide studies and analyses of selection signals at candidate genes. Here, we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme FST values across the whole genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.

    The paper looks for "nearly fixed" genetic differences between populations, and finds relatively few of them. That's relatively well-known; the FST-based test has been done on fewer populations with similar results (e.g., Williamson et al. 2007; Barreiro et al. 2008). This paper has the HGDP panel, which includes many more populations, and therefore is able to add geographic resolution to these older results. They find that the geographic distribution of near-fixed alleles is clinal; there aren't strong boundaries delimiting the geographic distributions of most apparently selected alleles. That means that the same demographic forces affecting neutral genetic variation have also affected recently selected alleles.

    Is that surprising? As we pointed out in our 2007 paper, the recent demographic history of human populations has included a lot of population growth. This means that the number of adaptive mutations should have increased during the last 10,000--20,000 years. High-FST selected alleles can only reflect selected mutations that are older than this (old enough to reach near fixation in one population), or are extraordinarily strong. A few mutations are exceptionally strong in their selective advantages -- SLC24A5 and lactase persistence seem to be examples. But as long as adaptive mutations are intrinsically rare, very few of them could have occurred in the small populations of 20,000 years ago or earlier, even if many happened in the large populations of the Holocene. So I think the new paper actually reinforces the interpretation of acceleration. The pattern we're seeing today with new mutations just can't be a feature of human evolution before around 20,000 years ago.

    If selection is affected by demographic processes, does that mean that it is "weak"? Clearly, "weak" is a matter of scale. Adaptive genes disperse through a spatially structured population very slowly, even if they confer very large fitness advantages. That means that their dispersal is highly dependent upon demographic conditions, such as the disproportionate growth of some populations or occasional long-distance gene flow. Locally, an allele may rapidly increase under selection, but that effect may have little influence on the evolution of distant populations.

    We see that pattern with genes known to be under strong selection in humans, like the ones that help some people resist malaria. Sickle cell, hemoglobin C and E, alpha- and beta-thalassemia, ovalocytosis, G6PD deficiency all have restricted geographic ranges that parallel the clinal pattern of neutral genes. There is an important difference: the patterns of these genes diverge in areas where malaria risk changes rapidly with geography (like coastal versus inland areas of Mediterranean Europe), and some of them have wide geographic distributions compared to their young haplotype ages (like sickle cell). But even in the latter cases, most are too rare to elevate the FST of surrounding SNP markers. Malaria adaptations are a tremendous example of the way that demographic conditions limit strong selection.

    Africa versus other populations

    Derived alleles are expected to have lower frequencies on average than ancestral alleles. So if a population has a bias toward higher-frequency derived alleles, that may be evidence against neutral evolution. The paper finds that this bias is greater in non-African populations than within Africa:

    The overall genic enrichment is present in all three population comparisons, and each tail seems to be similarly enriched for high- FST genic SNPs. However, the number of derived alleles in each tail does differ substantially and is biased towards derived alleles outside Africa and especially in east Asia. Thus, the statistical evidence for enrichment of events inside Africa is weaker than for the other two populations (we return to this point later).

    In general, populations outside Africa have a genome-wide bias toward higher frequencies of derived alleles. The causes of that bias aren't clear -- ascertainment may account for some of the bias but cannot account for all of it; it's possible that early demographic events may explain some of the bias but the pattern isn't obvious.

    The FST-based tests of neutrality are most powerful when a new allele has swept several rare mutations with it to near-fixation. Rare mutations tend to be derived ones. So the power of the test depends on how many rare mutations there are to start with, and what their frequencies are in other populations that didn't have the same selected allele.

    It's one of many issues that make finding selection in African populations slightly different from elsewhere. I think that Africans have undergone as much, and very possibly more, selection by new adaptive mutations as other populations. But our 2007 work suggested that the modal age of the selection we ascertain in Africa may be older than in other regions. That would be consistent with demographic history, since Late Pleistocene African populations were larger than others. But it's possible that genome-wide features like faster LD decay, higher heterozygosity, and more ancestral versus derived variants may also influence our estimates of the timing and number of selected alleles in Africa.

    Polygenic adaptation

    Toward the end of the paper, the authors discuss the pattern of local adaptation in a more general sense. Why should there be relatively few near-fixed genetic differences between populations, if human ecological changes suggest that local adaptation should have been a powerful force in our recent evolution? One possibility is acceleration -- most of the variants are too recent to have reached near-fixation in any single population.

    But the authors mention another possible influence that we've also been thinking about: epistatic interactions among new variants. For example, lots of skin pigmentation loci are known to have been under recent selection, but only a couple of them have reached near-fixation in any population. The rest are at lower frequencies. Since these alleles all affect the same phenotype, they're subject to diminishing returns. As one lighter-pigment allele becomes common, it reduces the strength of selection on the others. The population doesn't have to fix for any of them; in fact, selection probably cannot drive more than one or two up to fixation since the rest of them compete with each other.

    Over the very long term, this situation would be sorted out. A handful of loci that optimize skin pigmentation might ultimately go to high frequencies or fixation, for some alleles the costs may exceed the benefits and they will disappear. Others, relatively neutral to each other, may fix by drift. But the "very long term" is a span of hundreds of thousands of generations. Here we're talking about a few hundred generations at most. So human populations aren't anywhere near an optimum, they're in a transient where epistatic interactions may be quite important.

    Greg Cochran and I have been discussing this idea for some time. We call it the "Stooge effect". Think of the Three Stooges all trying to run through a door at the same time and getting stuck in the middle. That's what these genes are doing -- all of them are competing to respond to selection, but each is slowed by the presence of the others.

    It's not a new idea -- Frank Livingstone used to talk about this general concept with different malaria adaptations. What's new is the increasing evidence that humans are really in a transient with a lot of genes out of equilibrium. It's very possible that for some phenotypes, standing variation has been an epistatic block on the selection of new mutations. For others, the emergence of some new mutations has limited the trajectory of selection on others.

    Conclusion

    All in all, I think this paper is a nice contribution to our understanding of the pattern and rate of recent positive selection in human populations. Certainly, the HGDP sample will continue to be a very informative addition to our understanding of spatial dynamics in ancient humans. The addition of the new HapMap v.3 samples may be even more important, because these represent further regions with roughly the same discovery power as the initial three HapMap samples. And of course, we have the 1000 Genomes sample coming up, adding significant potential for discovering rarer selected variants.

    References:

    Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, et al. 2009. The Role of Geography in Human Adaptation. PLoS Genet 5(6): e1000500. doi:10.1371/journal.pgen.1000500

  • Ant magnetism

    Wed, 2009-05-20 18:21 -- John Hawks

    Strike "compass" off the list of human inventions not shared with ants:

    "The incorporation of minerals probably starts as soon as ants start getting in touch with soil," she added, explaining to Discovery News that her team found ultra fine-grained crystals of magnetic magnetite, maghemite, hematite, goethite, and aluminum silicates in ant antennae. These particles could make a "biological compass needle" that drives ant GPS.

    I for one welcome our magnetic myrmelords.

  • Simulations bubbling like a stew

    Thu, 2009-04-16 11:40 -- John Hawks

    Peter Turchin writes very effectively about quantitative modeling and analytical methods in biology. So every so often I like to post an illuminative quote. Here's his description of maximum likelihood estimation, from Quantitative Analysis of Movement:

    Simpler, more direct analyses may make unwarranted assumptions, but they are better at revealing important patterns in the data, and their results can suggest what variables and functional forms to use in the modeling of data. Eventually, however, direct methods of analysis get beyond the bounds of their competence. The general approach discussed in this section can in principle estimate parameters of any model, given infinite amounts of informative data and infinite computer power.

    The basic approach is to construct a detailed simulation model (better even, a series of models) and fit it to the data using nonlinear estimation techniques. Jon Schnute colorfully describes a detailed simulation as a "stew" of calculations from which observable quantities (to be compared with the actual data) bubble up to the surface (quoted from Hilborn and Mangel 1997). Nonlinear estimation is the process of adjusting the parameters of the stew (adding more or less salt, increasing or decreasing temperature, etc.) until the stuff that bubbles up resembles the actual data the best. The crudest approach is to change parameters in the simulation by the method of trail [sic] and error and to compare the simulation results to data by eye. A more refined approach is to use some quantitative measure of goodness of fit and a nonlinear minimization routine to search for the best fit automatically (Turchin 1998:295).

    The quote has some relevance to yesterday's discussion of the Neandertal population structure paper. I'm philosophically reluctant to turn to simulations until I exhaust my analytical options. This is a matter of trusting myself -- if I really had a lot of confidence in my ability to choose the right assumptions to underlie my simulations, I might turn to them first. But assumptions are tricky. Analytical models have their own assumptions, but those have the advantage of transparency -- I didn't pick them, they are fundamental to the models.

    Still, in some cases it doesn't take long to exhaust the analytical options. So we let the observable quantities "bubble to the surface" of simulations.

  • Weed species (part 1)

    Mon, 2008-07-07 20:26 -- John Hawks

    This is the first in a series of essays titled, "Practical Evolution." Here are links to the whole series and the series introduction. I've decided to break the articles up into two parts, so that a full essay will appear in two successive weeks. So if you enjoy the current installment, by all means come back on Friday, when I will follow the threads of dispersal by way of an obnoxious animal pest right back to hominids.

    Dandelion seeds

    Probably the most well-known weed species in America is the one growing so prolifically in my yard: the dandelion. Any kid can tell you why dandelions spread so quickly: Their seeds are carried by the wind.

    But for all their blowing of the puff-heads, as Goodwin calls them, my kids haven't noticed what seems so obvious to me. Dandelions are almost indestructible. Pull them up and their leaves will dry, but the flowers on the dead-looking plants continue to develop seeds and puff out. Leave just a little of the taproot in the ground, and new leaves will sprout hydra-like from all directions. Gretchen drenched a goodly portion of our sidewalk dandelions last year with boiling water, wilting the leaves like spinach. Some of them really died. The rest sprouted right back.

    Even when we're talking about dainty little parasol-like seeds, much depends on the size of the whole package. The part that looks like a "seed," a botanist calls an achene, which is technically a kind of fruit. The sunflower seeds that teenagers spit at softball games are fruits, too, but don't try telling that to their mothers. The dandelion's parachute, or pappus, is connected to the achene by one long shaft. A large, massive achene will tend to fall faster and won't blow very far except in a very strong wind. Sunflowers and coneflowers go for the big achene strategy, which the winter-resident birds really appreciate come January. Dandelions go the opposite way: small achene, big pappus. That's why weedy coneflowers are only a problem within five feet of my perennial beds, while weedy dandelions are in every disturbed field in the country.

    Barkley Sound, Broken Island group

    Barkley Sound, Broken Islands group

    A remarkable botanical field study has been carried out over the last twenty-seven years by Martin Cody, in Barkley Sound, British Columbia. In 1981, Cody began keeping track of the plants on a few of the small islands that dot the Sound. After a few years, the study had changed into something grander than a simple plant census: Cody's 2006 book on the subject begins, "This is a book about a field study that just grew and grew." For more than twenty years, Cody and his students have counted plants on hundreds of tiny islands, most under a few hundred square meters in size. Many of these islands are so small that a species may disappear from them entirely, only to be re-established later by new colonists. With his careful censuses, Cody could determine when populations were newly founded, and when they became locally extinct.

    By 1996, Cody had amassed information about weedy plants that had colonized dozens of the tiny islands of Barkley Sound. These plants all originally had come from Europe, including dandelions, their close relative cat's-ear (Hypochaeris radicata), wall lettuce (Mycelis (Lactuca) muralis), and woodland groundsel (Senecio sylvaticus). That means that all the plants are recent colonists, and they have all been carried to the islands by the wind, each using similar seed packages that include an achene and pappus.

    What makes a successful colonist? The first seeds to reach one of these tiny islands have done an exceptional thing: Wind has carried them across a large body of water to reach a tiny speck of virgin soil. Only the tiniest achenes tend to make this unlikely journey, and only if their parachutes are big enough to carry them.

    Cody and his student, Jacob Overton, took some of these seeds from both island and mainland populations and embarked on a series of experiments. First, they set a stopwatch and dropped the seeds to see how fast they fell. The results of this seed drop were pretty much the same as when kids tie little parachutes onto green army men. Generally, the bigger the parachute, the slower the descent. But if the achene is small enough, even a very small pappus may be enough to keep it aloft. The key is the ratio: the volume of the pappus compared to that of the achene.

    Wall lettuce seedhead

    Seed head of wall lettuce (Mycelis muralis) with five achenes remaining

    There's nothing very surprising about this: The wind carries small seeds farther, particularly if they have big parachutes. Plants that bear this kind of seed have only a tiny chance of colonizing an island. But plants with big achenes and little parachutes may have no chance of colonizing new islands at all. So by sorting seeds, the wind and sea also sort the genes of the colonizing plants.

    Indeed, Cody and Overton found that new populations of these plants on islands produce the kind of seeds that occasionally skip across to new islands. For example, the youngest island populations of wall lettuce — less than four years old — have the tiniest achenes. Their parachutes are small, too, but they generate a lot of loft. If the seeds of mainland wall lettuce are like a green army man tied to a kleenex, the first island colonists are like a BB stuck to a postage stamp.

    Wall lettuce populations that manage to stick around on an island make a change. After ten years, they are producing achenes just as big as the mainland populations. But instead of big, fluffy parachutes, they grow smaller, stunted ones. Like green army men tied to smaller and smaller postage stamps, these seeds aren't made for dispersal. They drop fast, right next door to their parents.

    More dispersal is not always better, even if you're a weed. A windy day might carry your seeds far away, but what if you live on a tiny island? Your seeds will be carried right off into the ocean. Worse, even if you live on a large island in Barkley Sound, there may be only a small strip of good habitat. Too far toward the water and you're drowned by storm surges; too far inland and you have to compete with larger, more established plants. For these island weeds, the plants that disperse the least have more new seedlings.

    Cat's-ear

    Cat's-ear

    Adaptable as they are, dandelions have done a poor job colonizing these tiny islands. The best of these weed species have managed to invade one island in five. Dandelions are found on less than a fourth that many. Despite their fame for being windblown, dandelion seeds actually drop faster than the wispy seeds of the other species on these islands. The rare colonists that do reach an island tend to last less than two years.

    Their relative, cat's-ear, has done better. Since it carries its flowers higher, on branched stems, cat's-ear makes more headway into grassy areas away from the beach, giving it a bit more area to work with. As a result, its populations become extinct only a third as much turnover as dandelions. LIke the wall lettuce, the island cat's-ear populations are different from the mainland, sporting big achenes and small parachutes. Dropping their seeds nearby seems to make a big difference as to whether their populations will persist.

    Natural selection seems to have changed the island populations of both these weeds, favoring lower dispersal. But how do we know it is really selection on dispersal, and not just something about the islands affecting seed size?

    Woodland groundsel, another of the weedy asters on the islands, provides one natural experiment. Cody and Overton dropped dozens of groundsel seeds from twenty populations, and found that the sizes of achenes and pappus made no difference at all to the speed that the seeds drop to the ground. Small groundsel achenes drop just as fast as large ones, no less than if Galileo had dropped them from the Leaning Tower. Even if selection had favored faster drop times, woodland groundsel achenes and pappus volumes should not have changed. And in fact, Cody and Overton found that they didn't change: island populations of woodland groundsel have proportions almost exactly the same as the mainland.

    Another experiment has been carried out in the most unlikely location. Hawksbeards (genus Crepis), also relatives of the dandelion, are common weeds spread across the Old World and into North America. Like dandelions, the hawksbeard Crepis sancta can colonize urban habitat, including the tiny patches of bare ground that cities leave in sidewalks for trees to grow. These are the urban equivalent of the tiny islands in Barkley Sound: sometimes far apart, they are separated by stretches of inhospitable concrete. In Montpelier, France, during the last few years Pierre-Olivier Cheptou and his colleagues have performed the urban version of Martin Cody's work: counting plants and collecting seeds from the small hawksbeard colonies around the city. What it lacks in rugged charm, Montpelier makes up in record-keeping — knowing when the sidewalks were built, the researchers could work out the ages of different hawksbeard populations.

    Unlike dandelions, C. sancta produces two different kinds of seeds: one with the achene and pappus carried on the wind, and another with no pappus at all. These seeds without parachutes do not go far; they scatter near the mother plant. That makes them bad for colonizing new patches of ground, but really good for establishing a sustained presence in one patch.

    Compared to the rural C. sancta population, urban plants have more of the no-parachute seeds. These plants cast fewer seeds to the wind, and drop more on the ground to sprout nearby. Like the islands of Barkley Sound, these urban islands select for low dispersal.

    Cheptou and his coworkers were able to go farther than Cody and Overton: They planted the seeds from urban patches in a greenhouse alongside seeds from the rural areas outside of town. The urban/rural differences were still present in the greenhouse plants, showing that growing in a small patch is not enough to change the seeds. Instead, the differences are caused by differences in genes, the result of selection on the urban plants.

    What is more, they grew their own small patches of C. sancta, replicating the conditions of the urban plants. The seed heads of the real urban populations were the equal of those after 12 to 13 generations of selection on their fake urban patches. This rapid pace of selection on the urban plants matches that on the islands of Barkley Sound, where wall lettuce and cat's-ear repeatedly showed strongest changes after only a few generations.

    Cody and Overton 1996, Figure 1

    The cycle of founding new island populations and their subsequent extinction.

    Colonization is a filter: Only certain individuals may have the right combination of traits to cross a significant barrier and inhabit a new place. But the traits that enable individuals to make such crossings are not always very good for staying in the new place.

    For certain species, selection yields a complicated pattern. A plant that is a local failure may be a global success, as it casts its seeds to far-off places, a few of which may grow into significant new populations. Such high-dispersing plants may do very poorly as a new population grows, but may be the only ones with a chance to escape when local extinction looms. High-dispersing individuals are also the ones most likely to carry their genes from one population to another, providing the potential for adaptations across the species as a whole.

    Without dispersal, a species may become moribund, unable to change in the face of new challenges. At the extreme, this has been called "evolutionary suicide." Traits that are selected locally, because they enhance the reproduction of individuals in the species, may nevertheless doom the species as a whole by reducing adaptability to changing conditions. The cost of maintaining the ability to change is a constant unstable balance between dispersal and staying power.

    For the weeds of Barkley Sound, this unstable balance ultimately favors the colonizers. New island populations do not last long. The local selection in favor of lower dispersal helps them to persist for a time, but on the scale of centuries all of them will fail, only to be replaced by new colonists from elsewhere.

    Friday: We turn from plant parachutes to animal dispersal mechanisms. And by "mechanisms" I mean, "legs."

    Notes:

    I am indebted to George Cox, whose excellent Alien Species and Evolution: The Evolutionary Ecology of Exotic Plants, Animals, Microbes, and Interacting Native Species (2004) gives a good account of Cody and Overton's study of island weeds. I can't say enough good things about this book.

    Martin Cody's book, Plants on Islands: Diversity And Dynamics on a Continental Archipelago, gives an account of the history of his field project, as well as reviews of the many areas of ecology that it has helped to illuminate.

    Many readers may notice that there is another factor besides low dispersal potential by which selection might favor large achenes in these plant species. Larger seeds may be advantageous because, with more stored energy, they may tend to germinate more readily or grow more quickly, thus making them more competitive. In this circumstance, selection would pertain to energy allocation or reproductive effort, rather than dispersal. I'll be discussing that form of selection in a later essay. In the present cases, dispersal is indicated as the target of selection, but seed size and energy allocation may also be involved.

    If seed morphology makes so little difference to drop time in Senecio sylvaticus, you may wonder what maintains achene size and pappus volume in this species. At least, that's what I wondered. Without more information it is hard to say, but I would hypothesize that achene and pappus volume may be genetically correlated in a way that is hard to select for one and not the other. In the other species, the selection on achene size and pappus volume is apparently antagonistic -- larger achenes are favored at the same time as smaller pappus. If these two traits are strongly genetically correlated, it becomes harder to select for lower dispersal. It would also be worth investigating whether other traits besides these volumes may have evolved in the island populations.

    The rapid evolution of urban hawksbeard (Crepis sancta) was examined by Cheptou et al. (2008). Pierre-Olivier Cheptou has a webpage at CEFE, including a description of Crepis sancta as a model system.

    Photo credits:

    Dandelion seeds: Photo by Piccolo Namek, on Wikimedia. GPL license.

    Barkley Sound: Photo by Sam Wilson (BaylorBear78) on Flickr. Creative commons noncommercial share-alike license.

    Cat's-ear: Photo by Ian Boyd, on Flickr. Creative Commons noncommercial attribution license.

    Wall lettuce: Photo by Mollivan John, on Flickr. Creative Commons noncommercial attribution license.

    Colonization figure: Figure 1 from Cody and Overton, 1996.

    References:

    Cheptou, P-O, Carrue O, Souifed S, Cantarel A. 2008. Rapid evolution of seed dispersal in an urban environment in the weed Crepis sancta. Proc Nat Acad Sci USA 105:3796-3799. doi:10.1073/pnas.0708446105

    Cody ML. 2006. Plants on Islands: Diversity and Dynamics on a Continental Archipelago. University of California Press, Berkeley, CA.

    Cody ML, Overton JM, 1996. Short-term evolution of reduced dispersal in island plant populations. J Ecol 84:53-61.

    Cox G. 2004. Alien Species and Evolution. Island Press, Washington.

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