john hawks weblog

paleoanthropology, genetics and evolution

domestication

  • Rapid adaptation to captivity in salmon

    Wed, 2011-12-21 13:15 -- John Hawks

    I just want to note this study by Mark Christie and colleagues [1] because it is such a clear demonstration of powerful selection working on standing variants in association with domestication. Rachel Newer has a good description of the study in the New York Times Green blog. Here's the study's abstract:

    We used a multigenerational pedigree analysis to demonstrate that domestication selection can explain the precipitous decline in fitness observed in hatchery steelhead released into the Hood River in Oregon. After returning from the ocean, wild-born and first-generation hatchery fish were used as broodstock in the hatchery, and their offspring were released into the wild as smolts. First-generation hatchery fish had nearly double the lifetime reproductive success (measured as the number of returning adult offspring) when spawned in captivity compared with wild fish spawned under identical conditions, which is a clear demonstration of adaptation to captivity. We also documented a tradeoff among the wild-born broodstock: Those with the greatest fitness in a captive environment produced offspring that performed the worst in the wild. Specifically, captive-born individuals with five (the median) or more returning siblings (i.e., offspring of successful broodstock) averaged 0.62 returning offspring in the wild, whereas captive-born individuals with less than five siblings averaged 2.05 returning offspring in the wild. These results demonstrate that a single generation in captivity can result in a substantial response to selection on traits that are beneficial in captivity but severely maladaptive in the wild.

    We have few cases of new or recent domestication, so this kind of experiment is hard to do in other contexts. Also, in this case the selection is "natural-looking", imposed by the captive environment in some way, instead of directly applied by culling undesirable individuals. In most cases of mammal domestication, the wild relatives are either now vanishingly rare, or have been potentially influenced by introgression from the domesticated population. But I think it's reasonable to hypothesize that the additive variation in behavioral traits in wild populations is large enough to have allowed early mammalian domesticates like dogs and horses to adapt to captivity almost as fast as the salmon. Notice that the key element here is high reproduction in captivity, and in the salmon that trait covaries negatively with success in the wild.

    Domestication may not have been a "hump" that humans brought wild animal populations over; it may have been a valley that trapped once-wild animals into dependence on humans.

    References

    1. Christie MR, Marine ML, French RA, and Blouin MS. 2011. Genetic adaptation to captivity can occur in a single generation. Proceedings of the National Academy of Sciences of the United States of America.
    Tags: 
    domestication
    rapid evolution
    natural selection
    fish
    non-primate

  • Potato sack race

    Fri, 2011-10-28 14:30 -- John Hawks

    Smithsonian magazine has a very nice article by Charles C. Mann, "How the Potato Changed the World", focusing on the effects of the Columbian exchange on Europe.

    “For the first time in the history of western Europe, a definitive solution had been found to the food problem,” the Belgian historian Christian Vandenbroeke concluded in the 1970s. By the end of the 18th century, potatoes had become in much of Europe what they were in the Andes—a staple. Roughly 40 percent of the Irish ate no solid food other than potatoes; the figure was between 10 percent and 30 percent in the Netherlands, Belgium, Prussia and perhaps Poland. Routine famine almost disappeared in potato country, a 2,000-mile band that stretched from Ireland in the west to Russia’s Ural Mountains in the east. At long last, the continent could produce its own dinner.

    When I toured through the Altai this summer, I was impressed at the healthy potato patch outside nearly every house. How unlikely it seems that this American crop should have become a central part of people's lives in some of the most remote parts of Central Asia.

    Tags: 
    agriculture
    domestication
    diet
    history
    America
    Europe

  • Mailbag: Dogs in Chauvet

    Sat, 2011-06-25 11:25 -- John Hawks
    Love your blog, which I stumbled across while googling for more detail on the wolf tracks in Chauvet Cave. Have been fascinated by this stuff since 1st grade, did fieldwork in high school & college, and now wish I hadn't let the dryness of academia drive me away from anthro back in Ann Arbor (not Wolpoff's fault). I still read around though; loved your take on the Clovis Comet Crap (what suckers the media are), though obviously impact events play a major evolutionary role.

    So anyhow, back to my question. Recently saw Herzog's documentary on the art in Chauvet. Having dabbled in caving during a Peace Corps Guatemala stint, I find it extremely unlikely that a wolf is going to be walking around deep in a pitch black cave by himself. To me this is potentially strong evidence if not downright proof of domestication, but I'm looking for more specifics on track layout (esp. in relation to those human child tracks) and actual location/depth within the cave (to ascertain feasibility of wild vs domesticated access). Do you have anything more on this, or could you point me towards same? Much obliged, tlc

    Thanks for the kind words!

    Pat Shipman has written about this topic quite a lot lately, she has a book out on the history of human-animal interactions. Last year she wrote about Aurignacian-era dog domestication evidence (I linked here):

    http://johnhawks.net/weblog/reviews/archaeology/upper/europe/dog-domesti...

    And I cited some of the original research here:

    http://johnhawks.net/node/1686

    The main impediment to accepting a very early domestication is the genetics; as modern dog breeds don't seem to have such a distant ancestor. But that may be due to recent gene flow among breeds and subsequent selection after domestication. At the very least, domestication was clearly early enough that dogs accompanied people to the Americas before 12,000 years ago.

    Tags: 
    wolves
    domestication
    dogs

  • Divergent MHC alleles in domesticated sheep

    Sun, 2010-11-28 09:47 -- John Hawks

    I know, what an exciting headline!

    I've written quite a bit about the origins of domesticated cattle and introgression among the species of wild cattle giving rise to the current pattern of genetic diversity. I'm keeping track of that area because the process of domestication and subsequent interaction of domesticates with their wild relatives provide one kind of natural model for the interaction of ancient human groups such as the Neanderthals. We used these examples in our 2006 paper [1].

    Cattle have been a convenient example because there has been a lot of genetic work on them, and they have multiple wild species that diverged early in the Pleistocene. But other domesticates are also intense targets of sequencing and genome discovery, and as we understand more about their variation, we are beginning to find interesting patterns. Going through my notes today I found an interesting paper on sheep MHC polymorphisms [2]:

    Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep

    Highly polymorphic genes with central roles in lymphocyte mediated immune surveillance are grouped together in the major histocompatibility complex (MHC) in higher vertebrates. Generally, across vertebrate species the class II MHC DRA gene is highly conserved with only limited allelic variation. Here however, we provide evidence of trans-species polymorphism at the DRA locus in domestic sheep (Ovis aries). We describe variation at the Ovar-DRA locus that is far in excess of anything described in other vertebrate species. The divergent DRA allele (Ovar-DRA*0201) differs from the sheep reference sequences by 20 nucleotides, 12 of which appear non-synonymous. Furthermore, DRA*0201 is paired with an equally divergent DRB1 allele (Ovar-DRB1*0901), which is consistent with an independent evolutionary history for the DR sub-region within this MHC haplotype. No recombination was observed between the divergent DRA and B genes in a range of breeds and typical levels of MHC class II DR protein expression were detected at the surface of leukocyte populations obtained from animals homozygous for the DRA*0201, DRB1*0901 haplotype. Bayesian phylogenetic analysis groups Ovar-DRA*0201 with DRA sequences derived from species within the Oryx and Alcelaphus genera rather than clustering with other ovine and caprine DRA alleles. Tests for Darwinian selection identified 10 positively selected sites on the branch leading to Ovar-DRA*0201, three of which are predicted to be associated with the binding of peptide antigen. As the Ovis, Oryx and Alcelaphus genera have not shared a common ancestor for over 30 million years, the DRA*0201 and DRB1*0901 allelic pair is likely to be of ancient origin and present in the founding population from which all contemporary domestic sheep breeds are derived. The conservation of the integrity of this unusual DR allelic pair suggests some selective advantage which is likely to be associated with the presentation of pathogen antigen to T-cells and the induction of protective immunity.

    That probably deserves more thought and explanation that I can give it right now. As the authors point out in the paper, sheep domestication was a complicated process:

    The complex origin of domestic sheep is apparent from the presence of at least five distinct mitochondrial lineages [20], some of which cannot be traced to a wild ancestor [24], [25]. This diversity is likely to originate from geographically isolated subspecies of wild sheep that have hybridised as a result of human migrations over the 8–10 millennia since the initial domestication events in the Near East and Asia [26]–[28]. Frequent hybridization events are likely to have occurred between domesticated and local wild populations providing the high levels of MHC diversity evident in present day domestic populations as well as a degree of resistance to endemic disease and adaptation to local environmental conditions [29].

    Their interpretation of an ancient selective balance, retained in domesticated sheep from very distant common ancestors with oryx, probably is the most likely scenario. But I think this provides a nice example of how difficult it is to tell ancient balanced polymorphisms apart from relatively recent hybridization. That's a problem that we continue to face with interpreting human and Neandertal genetic variation.

    Also the case illustrates how important is the mixture of different wild populations in the origin of domesticates. Even if a wild population makes up a very small fraction of the genetic heritage of the current domesticated species, one or more adaptive loci from that population may nevertheless be very important to the survival and success of the later species.

    Genes don't care where they came from, and their function is not irrevocably marked by their origin.

    References

    1. Hawks J, and Cochran G. 2006. Dynamics of Adaptive Introgression from Archaic to Modern Humans. PaleoAnthropology 2006:101–115.
    2. Ballingall KT, Rocchi MS, McKeever DJ, and Wright F. 2010. Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep. PLoS ONE [Internet] 5:e11402+. Available from: http://dx.doi.org/10.1371/journal.pone.0011402
    Tags: 
    immune
    domestication
    non-primate
    introgression

  • Ridded of rinderpest

    Fri, 2010-10-15 16:18 -- John Hawks

    Donald McNeil, Jr.::

    In only the second elimination of a disease in history, rinderpest — a virus that used to kill cattle and wildlife by the millions — has been declared wiped off the face of the earth.

    The last case was seen in Kenya in 2001. On Thursday, the United Nations Food and Agricultural Organization announced that it was dropping its field surveillance efforts because it was convinced the disease was gone.

    Two down, many more to go

    Tags: 
    non-primate
    disease
    health
    domestication

  • Mental mismatches

    Thu, 2010-09-23 08:30 -- John Hawks

    A Primate of Modern Aspect ("The sexuality wars, featuring apes") writes about some of the reactions to the new book, Sex at Dawn: The Prehistoric Origins of Modern Sexuality. As the subtitle suggests, the book is an account of human sexuality from the viewpoint of evolutionary psychology, written by Christopher Ryan and Cacilda Jethá. Ryan blogs at Sex at Dawn, I'm a frequent reader.

    Anyway, I loved this point about comparative studies:

    [F]or some reason, the only time primate sexuality gets any attention is when we turn it into a debate about how humans should be having sex.

    We never say, “Hey, those muriquis are too promiscuous. Don’t they know that all of their close evolutionary cousins are polygynous? If they just did what came naturally to them, they’d have a lot less psychological stress.” Or, “Those gibbons are so sexually repressed. If they just gave in to their natural predilection for promiscuity, I bet those nasty gibbons would have fewer territorial disputes and gibbon society would be much more peaceful.”

    Why worry about the "echoes" of psychic distress that may linger after the mating system changes? That's a very interesting point; there are unexplored assumptions here about the nature of adaptation and the structure of genetic causation of mental states. Clearly if major aspects of human social life change, we cannot expect people's minds to be perfectly optimized to the new regime. But what is the force of selection? What are the mental "rough spots" that differential fertility will ultimately iron out? How much "mismatch" between mental and social adaptations can persist?

    Primates may not be the best non-human model for such questions. Some domesticates have undergone social changes as great as humans, with strong selection against individuals who buck their human masters. But for many wild primates we may reasonably wonder, to what extent are social dynamics constrained by mental adaptations, and how quickly can mental lives shift under selection to fit a new social system?

    Tags: 
    sexual selection
    behavior
    domestication
    mating
    primates
    brain
    evolutionary psychology
    mind

  • The Aurignacian dogs

    Fri, 2010-05-14 14:37 -- John Hawks

    I didn't see this article when it came out but I ran across it this week: Pat Shipman writes about possible evidence for early dog domestication ("The Woof at the Door").

    Some of the earliest known art objects from Europe include the remarkable cave paintings of Chauvet Cave in France, the oldest of which were made 32,900 ± 490 years ago. None of the hundreds of glorious Chauvet paintings show wolves. However, the cave preserves something even more haunting: the footprints of a human child about four-and-a-half feet tall, as well as many footprints of large canids and bears.

    Michel-Alain Garcia of the Centre National de la Recherche Scientifique in Nanterre noticed in 1999 that one track of canid prints appears to accompany the child’s prints. These canid prints, unlike the others, have a shortened middle digit on the front paw: a characteristic of dogs. Garcia suggested that the child and dog might have explored the cave together. Charcoal from a torch the child carried is 26,000 years old.

    It's a nice article throughout, describing why some are convinced that dog domestication was Aurignacian or earlier in time. It would be interesting to see an update to the story in light of the recent description of dog and wolf genetics, that argued for a more recent domestication in the Near East. Personally I don't see a contradiction here, if we suppose that the population of dogs may have grown enormously with pastoralism in the Near East, drawing substantially upon local wolf populations. It's shaping up to be a complicated problem.

    Tags: 
    art
    Aurignacian
    dogs
    Upper Paleolithic
    domestication

  • A horse of a different color

    Sat, 2009-04-25 00:39 -- John Hawks

    I feel like I've been transported into the future to see what science will be like fifteen years from now:

    We successfully typed eight mutations in six genes (6) responsible for coat color variation for 89 [out of 152 tested; tables S1 to S5 (6)] ancient samples. To assess coat color variation of predomestic horses, we analyzed the bones of wild horses from the Late Pleistocene and Early Holocene found in Siberia, East and Central Europe, and the Iberian Peninsula. We found no variation in the Siberian and European Pleistocene horses, suggesting that these horses were bay or bay-dun in color.

    ...

    In contrast, a rapid and substantial increase in the number of coat colorations is found in both Siberia and East Europe beginning in the fifth millennium B.P. (Fig. 1 and figs. S1 and S2). Although the earliest chestnut allele (MC1R gene) was identified in a Romanian sample from the late seventh millennium B.P., chestnut horses were first observed in Siberia (fifth millenium B.P.). Their prevalence increased rapidly, reaching 28% during the Bronze Age.

    The whole paper is only a page long. Like, "Oh yeah, we just genotyped 89 horse skeletons from the Neolithic up to the Bronze Age, and here's how the process of selection on color patterns worked out."

    Couple of things --

    1. The pigment-altering mutations at these genes do not all show statistical signs of selection in contemporary samples of horses. But they aren't there in the ancient horses. That's the best evidence of selection you could possibly have. Message: tests of selection on contemporary samples are weak, particularly for loci with rare alleles or more than two alleles.

    2. The study shows how much you can learn with a moderate number of samples. The advantages working in this case: the genes responsible for pigmentation phenotypes are well-characterized, the number of loci is well-matched by the sample size; the study focuses on recovering SNPs instead of sequencing.

    UPDATE (2009-04-25): I looked at the statistical test of selection used in the paper with a little more detail. It comes from a paper by Jonathan Bollback, Thomas York and Rasmus Nielsen, published last year in Genetics. It's a very clever test. Assume a sample of genes taken from a population at some discrete set of times, t1, t2, t3, and so on. Under genetic drift, this series of frequencies approximates a random walk, with the size of deviations depending on the effective population size. Under constant directional selection, the random walk will be biased in a way that can be approximated by a diffusion model of selection.

    So if you have a big enough sample, you can estimate the relative contribution of stochastic (drift) effects and deterministic (directional selection) effects on the frequencies over time.

    In the current case, two alleles have sample sizes that are large enough, frequency changes that are large enough and constant enough in direction to show that drift is minor and selection is strong. For example, the chestnut variant goes from zero in the Neolithic to 65 percent in the Medieval time period, with every change a between time increments an increase. That's an allele with 44 copies (by my quick count) in all samples.

    Four alleles do not have such large changes (they are initially absent, but present in only four or fewer individuals in the later time intervals). There's only one copy of the SILV9 color variant mutation in the entire sample of archaeological horses. With a very small sample, the sampling variance will be larger than the stochastic effects of drift. So even if those few copies are exclusively in the latest time increments, the time series won't look unusual compared to drift.

    But what the test doesn't consider is the current frequency. Since this is known with much less sampling variance, we can compare the present frequency with the frequency summed across the older time intervals to get a more powerful test of neutrality. Also, the test assumes that selection is constant -- if selection had a stochastic element, varying over time, that would have the same impact on the sample as drift or sampling variance. That's why the absence of an allele in an ancient sample can be stronger evidence of selection than the fine-scaled record of change over time.

    Complicating matters is population structure. The coat color variants are not distributed evenly across the modern horse population; they are distributed into different breeds. The strong association of some color variants with breeds is, of course, evidence of its own that the color variants have been correlated with fitness under domestication. Now, whether this fitness association is a deliberate result of people liking colors (because they differentiate breeds, or look pretty, or whatever) or whether they arise incidentally (by linkage with other traits) isn't tested by these data. These functional aspects of selection provide another possible test of neutrality -- for example, in this case all the non-bay-black alleles increased over time, a bias that isn't consistent with chance.

    References:

    Bollback JP, York TL, Nielsen R. 2008. Estimation of 2Nes from temporal allele frequency data. Genetics 179:497-502. doi:10.1534/genetics.107.085019

    Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas A-S, Slatkin M, Hofreiter M. 2009. Coat color variation at the beginning of horse domestication. Science 324:485. doi:10.1126/science.1172750

    Tags: 
    genomics
    MC1R
    pigmentation
    domestication
    horses
    paleogenomics

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