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 .
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 :
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 , some of which cannot be traced to a wild ancestor , . 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 –. 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 .
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.
- . Dynamics of Adaptive Introgression from Archaic to Modern Humans. PaleoAnthropology. 2006;2006:101–115.
- . Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep. PLoS ONE [Internet]. 2010;5:e11402+. Available from: http://dx.doi.org/10.1371/journal.pone.0011402
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
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?
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.
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.
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
Ancient DNA technology may make it possible to test some very interesting hypotheses about recent evolutionary change in human populations.
Meanwhile, several people are reporting the potential of DNA from museum specimens for testing hypotheses about ancient or extinct populations. Today's news includes a story introducing the term "museomics" -- otherwise known as the metagenomics of museum specimens, including the DNA of taxidermed specimens and their pathogens and commensal bacterial populations:
[Webb] Miller and his team used state-of-the-art DNA sequencing technology to analyze the hair of two preserved specimens: a female thylacine that died at the London Zoo in 1893, and a male brought to the National Zoo in 1902 that died three years later.
Although the two thylacines were continents apart, their mitochondrial DNA — a portion of the genome passed on via the maternal line — was nearly identical, illustrating the species' ultra-low genetic diversity around the turn of the 20th century.
Brandom Keim of Wired blogs that medieval parchment preserves enough DNA for analysis:
Initial tests showed that the animal skin pages contained enough intact DNA to make analysis worthwhile. So [Tim] Stinson and his brother Mike Stinson, a biologist at Southside Virginia Community College, skin samples taken from five pages of a 15th century French prayer book. Preserved mitochondrial DNA revealed that the pages came from two closely related calves.
Those results, said Stinson, are a proof of principle that it's possible to create a DNA database from manuscripts of known age and origin. Monastic paperwork tended to be dated, so DNA from those works could be cross-indexed with that of literary works from tomes of unknown provenance, producing a taxonomy of manuscript manufacture.
Sourcing manuscripts is pretty exciting to historians, no doubt, who must otherwise rely on indicators such as handwriting style and dialect.
But the results may be equally useful for understanding the processes of animal breeding in medieval Europe. Today's domesticated breeds are a remnant of a much larger diversity of local breeds that once existed. People bred animals both locally by selection and across large regions by introducing favored animals from long distances. Sometimes they favored diversity -- and considering the revival of interest in legacy breeds like Highland cattle.
As an example, today's European swine include a blend of genes from ancient European domesticates, and hogs introduced from China during the 18th and 19th centuries (Giuffra et al. 2000). That introgression probably caused some substantial improvements in the hog population, but has helped to reduce genetic variation and move the population from its medieval structure to a more homogenized gene pool.
Gregory Cochran and I gave a short description of the history of cattle domestication and ongoing gene flow in our 2006 paper about introgression (Hawks and Cochran 2006). With four original cattle species in different parts of Eurasia, and the possibility of continued gene flow among imported breeds as well as the original progenitor species of European cattle, the aurochs (still known in early medieval times), the population history of European breeds may harbor a lot of complexity during the last 1000 years. Finding the medieval distribution of today's genes -- even if the only result is a mitochondrial DNA distribution -- might help us understand the distribution in which favored traits originated and were selected.
Giuffra E, Kijas JMH, Amarger V, Carlborg Ö, Jeon J-T, Andersson L. 2000. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 154:1785-1791.
Hawks J, Cochran G. 2006. Dynamics of adaptive introgression from archaic to modern humans. PaleoAnthropology 2006:101-115.
I haven't seen this paper, so can't comment on the results, but the story is worth passing along:
An international team of scientists has just identified what they believe is the world's first known dog, which was a large and toothy canine that lived 31,700 years ago and subsisted on a diet of horse, musk ox and reindeer, according to a new study.
The discovery could push back the date for the earliest dog by 17,700 years, since the second oldest known dog, found in Russia, dates to 14,000 years ago.
Remains for the older prehistoric dog, which were excavated at Goyet Cave in Belgium, suggest to the researchers that the Aurignacian people of Europe from the Upper Paleolithic period first domesticated dogs.
It's very, very interesting if true, because it advances the story of subsistence differences between Neandertals and early Upper Paleolithic people. But I would have more confidence if the story quoted some zooarchaeologists whose work I know. I hadn't known about this:
Ancient, 26,000-year-old footprints made by a child and a dog at Chauvet Cave, France, support the pet notion. Torch wipes accompanying the prints indicate the child held a torch while navigating the dark corridors accompanied by a dog.
So why aren't there more skeletons? Hmmm...
New Scientist reports on the parallel evolution of Budweiser and Heineken:
Forced to produce their beer in the winter, brewers accidentally created conditions favouring the emergence of a hybrid yeast better suited to the cold. Researchers already knew that Saccharomyces pastorianus, now used to brew lager, is a hybrid produced through marriage between two yeast strains.
One was S. cerevisiae, the "brewer's yeast" on which the brewing industry is founded because it ferments sugars into alcohol so efficiently. The other was S. bayanus, a yeast strain seldom used alone in brewing because it ferments sugar into alcohol far less efficiently.
Now an analysis of the forensic ancestry of lager yeast has established that this same marriage happened independently at least twice, not once as previously thought, giving rise to two broad families of lager beer.
So, now you know. Oh, and this should be especially interesting if you've been following the Heineken storyline on Mad Men...
Bees, dogs, and cattle have all provided interesting evolutionary stories this week. Now it goes to the chickens: A study by Jonas Eriksson and colleagues finds that introgression from grey junglefowl contributed to the gene pool of domesticated chickens:
This study contradicts the assumption that the red junglefowl is the sole wild ancestor of the domestic chicken  and provides the first conclusive evidence that other species have contributed to the domestic chicken genome. We therefore propose that the taxonomy of the domestic chicken should be changed from Gallus gallus domesticus to Gallus domesticus to reflect the polyphyletic origin of chicken . The emerging technologies for total genome resequencing can be readily employed to determine if other parts of the chicken genome also originate from other species of junglefowls. Such regions are expected to be enriched for functionally important variants, like yellow skin, because neutral sequences should have been diluted out during the extensive back-crossing that must have taken place after introgression. It is possible that the introgression of yellow skin was facilitated by the fact that it resides on a microchromosome (only 6.4 Mb in size) with a high recombination rate, which reduces the amount of genetic material affected by linkage drag.
The need to reduce linkage to possibly disadvantageous genes around an introgressive allele is an important thing to consider, although breaking such an allele down to a 6 Mb block wouldn't take an terribly long time. The real question is why this trait in particular was brought into chickens -- whether it was linked to desirable pelage characters, or whether it may have had other advantages in survival or productivity under domestication.
These two species are not known to hybridize in the wild.
(via Blog Around the Clock)
(also Greg Laden)
Eriksson J, Larson G, Gunnarsson U, Bed'hom B, Tixier-Boichard M, Strömstedt L, Wright D, Jungerius A, Vereijken A, Randi E, Jensen P, Andersson L. 2008. Identification of the Yellow Skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet 4:e1000010. doi:10.1371/journal.pgen.1000010