domestication

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 [5] 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 [27]. 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)

References:

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

Read Nick Wade's article about Siberian rat breeding experiments. Two strains of rat: one tame and one aggressive. Now they're screening their genomes to see what's up.

"The ferocious rats cannot be handled," Mr. Albert said. "They will not tolerate it. They go totally crazy if you try to pick them up."

When the aggressive rats have to be moved, Mr. Albert places two cages side by side with the doors open and lets the rats change cages by themselves. He is taking care that they do not escape to the sewers of Leipzig, he said.

Well, those might be some nasty rats, but odds are they wouldn't do too well in a natural sewer. Their Siberian rat cages protect them just as much as their tame relatives; their alleles probably are already present in the wild population, and the pattern of selection on them almost certainly wouldn't change just because of their release.

(I know what you're thinking. The rats from NiMH were entirely different! They had some kind of special pharmaceutical alteration.)

The article covers Belyaev's experiments, which are best known for the tame foxes:

The experiment did not become widely known outside Russia until 1999, when Dr. Trut published an article in American Scientist. She reported that after 40 years of the experiment, and the breeding of 45,000 foxes, a group of animals had emerged that were as tame and as eager to please as a dog.

As Belyaev had predicted, other changes appeared along with the tameness, even though they had not been selected for. The tame silver foxes had begun to show white patches on their fur, floppy ears, rolled tails and smaller skulls.

Sure, the founding of the breeding population would have gotten a few rare alleles by chance, but we're really talking about the selection of alleles that are mostly already fairly common in wild foxes (common enough to get into a small sample of them, anyway). So this breeding experiment has concentrated a few alleles that are generally present into a single group where they are always coexpressed.

Anyway, nobody ever seems to talk about the other colony of "vicious" foxes. The article covers a few surprising correlates of tameness, like the ability to follow gaze. But what are the surprising correlates of aggressiveness? Are these foxes and rats sociopaths?

The root question is whether humans domesticated themselves, and therefore have some of the same genetic changes as these domesticated rats and foxes. But then, the rats and foxes haven't so much undergone genetic changes as simple enrichment of alleles that are already common. Which means that they may have unusual phenotypes as a result of these alleles being coincident at high frequencies, but those alleles already are doing something in normal, wild (and mostly solitary) animals. This doesn't mean that the tame phenotype should already exist -- even if all these alleles are independently common, if there are enough of them they may never all be present in any single wild individual.

So the interesting question is why these alleles that permit domestication in combination should already be common. Do they all contribute to variant behavioral strategies -- such as a proper balance of fear, aggression, tolerance, and sociality? Are they all in selective balance? They aren't all present because they make animals tame, at least, not if tame animals are naturally rare. But each has some advantage on the wild genetic background, or they wouldn't persist as common functional variants.

And if these genes did change in identifiable ways during human evolution, well then, what started the process? It is easy to imagine sociality evolving in parallel in humans and domesticated animals -- at least in certain respects -- but widespread changes in systems that are often found in selective balances would be sort of surprising. With domesticated animals there is a huge fitness cost to aggression. Is that really true of people?

It's a great topic, and a great story. Considering how much money there is in beef, it seems like it would be a small investment to raise 40,000 bison, or pronghorn, or eland, or any number of other wild animals to select for tameness. Maybe Ted Turner could do it.

A study of pig mtDNA sequences by Greger Larson and colleagues in Science establishes that domesticated pigs originated in multiple geographic locations from different ancient wild boar populations.

The study shows that wild boars have a strong mtDNA association with their geographic locations, with an apparent origin in Island Southeast Asia. The authors contrast this with other domesticated animals, whose wild relatives do not give as good an opportunity for testing the origin of domesticated forms:

The wild progenitors of many Eurasian domesticates are either extinct [e.g., the aurochs (8) and the wild horse (10)] or have little or no phylogeographic structure [e.g., the wolf (11)]. Consequently, the broad distribution of surviving wild boar populations across the Old World provides a unique opportunity to analyze the origins of modern domestic lineages. Previous studies (3, 12) have identified three divergent clusters of Sus scrofa mitochondrial sequences, one Asian clade and two European groups, of which one consists solely of Italian wild boar. Both the Asian and European groups contain domestic breeds, yet molecular clock estimates indicate the split between the two groups significantly predates evidence for pig domestication, which suggests independent domestication events in each area from divergent wild boar lineages (3, 12).

They find that European pig breeds (excluding those with recent cross-breeding with Asian pigs) are related almost exclusively to European wild boar lineages, with little or no input from Near Eastern boars. The authors conclude that this is consistent with a domestication of European pigs within central Europe, perhaps Germany. They argue that Neolithic peoples entering Europe from West Asia either did not bring pigs with them, or that any pigs of Near Eastern origin ultimately did not become progenitors of European breeds. They also argue that the structure of the data exclude the alternative hypothesis, that European wild boars are largely derived from feral populations of pigs with origins elsewhere.

Additional pigs from other regions appear to provide evidence of several other domestication events in other areas. This includes India, Southeast Asia, possibly Italy, and China.

Also, the study finds that neither Celebes wild boars nor Taiwanese wild boars are related to those in New Guinea, Melanesia, or Polynesia, which they take as evidence against the idea that Polynesian human dispersal was a rapid movement of people out of Taiwan. There is no clear origin for the pigs from the Polynesian dispersal from extant wild boar lineages, which they suggest may indicate that a now-extinct lineage of Wallacean boars may have served as the origin, or that a longer-term human domestication of pigs from elsewhere in Island Southeast Asia may have occurred.

References:

Larson G. et al. 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307(5715):1618-1621. Science Online