{credit}Agricultural Research Service via Wikipedia{/credit}

Understanding the genomic changes that occurred during the domestication of animals and plants by humans is important on many levels. Such insights can provide information about human history and our interactions with other species, as is the case with genetic studies of dog and cat domestication. These studies can also help us to improve crop plants (such as tomato) and livestock (such as cattle) for human consumption or other use. Finally, genetic studies on domestication can help to identify disease-causing mutations that have been selected for as a by product of selection for beneficial traits (for example, in cats and dogs).

Though humans have a huge influence on important traits in domesticated species, those species are still responding to natural selection during the domestication process, which in turn may affect traits important for agricultural purposes. Identifying genomic regions influenced by positive natural selection in domesticated animals  can lead to important insights into the biology of specific breeds.

In this respect, the pig is an excellent model to study. Humans domesticated pigs approximately 10,000 years ago in the Near East and China, but a relatively open method of keeping pigs allowed for continued interbreeding with wild boars for some time. In a study published this week in Nature Genetics, Lusheng Huang, Jun Ren and colleagues from Jiangxi Agricultural University sequenced the genomes of 69 diverse domestic and wild pigs in China to better understand their evolutionary history.

Pig sampling in China{credit}Lusheng Huang{/credit}

The study included pigs from 11 diverse breeds (and 3 populations of wild boar) within China in order to compare the adaptations in breeds from cold vs. hot areas. They identified over 700 genomic regions that showed evidence of selective sweeps. Many of the genes in these regions were involved in processes important for regulation of temperature during cold or heat stress, such as hair development, energy metabolism and blood circulation.

However, one of the most striking results was the identification of a large (~14Mb) sweep region on the X-chromosome. More than 94% of the single nucleotide polymorphisms (SNPs) in the 69 pig sample that had extreme allele frequency differences between North and South populations were located within the X-linked sweep region. All Northern Chinese samples showed a strong signature of selection in this region. Upon further analysis, the authors were able to determine that the most likely scenario, given their data, was that this region was introgressed from a now-extinct species of Sus. This region of the X-chromosome undergoes very little recombination. This fact, combined with the strong signal of positive selection in the region, meant the introgressed sequence remained mostly preserved for more than 8 million years.

We asked one of the study’s senior authors, Lusheng Huang, to tell us a little more about the work:

How did you collect the DNA samples from the pigs for your study? Were any of the samples difficult to get?

We collected DNA samples from 4,100 three-generation consangeneously unrelated pigs representing all 68 indigenous breeds that are distributed in 24 provinces of China. It took us four and half years to complete sample collections, Some native pigs lived in the high attitude regions (Yunnan, Guizhou, Sichuan and Tibet) were very hard to get. Afterwards, we constructed a DNA bank for Whole China indigenous pigs. As a pilot study, we first genotyped 520 unrelated pigs (no common ancestor within 3 generations) from 32 Chinese breeds for 60K SNPs in the Illumina porcine beadchip. Then, we selected 69 representative pigs from the 520 pigs according to their genetic relationships in the neighbor-joining tree constructed with the 60K SNP data. The 69 pigs selected for whole-genome sequencing are highly rep­resentative of populations at the geographical extremes of China.

{credit}Lusheng Huang{/credit}

Most of the sampled pigs were originally raised in government-sponsored conservation farms. We selected animals to cover a majority of consanguinity of each breed according to their pedigree information. However, samples of several breeds were collected from isolated villages or farms at rural areas. For example, it was a big challenge for us to collect samples of Tibetan pigs from different geographic populations in the vast region of the Tibet Plateau. To find purebred Tibetan pigs that were not influenced by human-mediated hybrid with exotic breeds, we had to travel to remote pastoral areas at high altitudes and make an in-depth field investigation with the kind help of local residents. To cover the consanguinity of each Tibetan population as broad as possible, we preferably collected samples from Tibetan boars that are usually aggressive like wild boars and were really difficult to get (see above picture).

What do the positively selected regions tell us about the history of pig domestication?

These regions clearly illustrate that pigs have experienced natural selection for local fitness before (ancient event) or after (recent event) domestication. The selection footprints in the pig genomes can be visualized by whole-genome sequencing, characterized by reduced heterozygosity, excess of low-frequency variants, extended and differentiated haplotypes. The selected sweep regions harbor functional genes that play a role in adaptation to local environments. DCF17 and VPS13A are two such examples highlighted in this study.

What do you think was the most unexpected result in this study? Did you believe it at first?

The extremely divergent haplotype in the X-linked sweep region between Southern and Northern Chinese pigs, an indication of a possible ancient interspecies introgression event, was the most unexpected result in this study. It is a big surprise. Frankly speaking, we did not believe it at first.

The pattern of haplotype sharing in diverse populations. The haplotypes were reconstructed for each individual using all of the variants on the X chromosome. Alleles that are identical to or different from the ones in the Wuzhishan reference genome are indicated by red and blue, respectively. Adapted from Fig. 4a in Huashui Ai et al. 2014{credit}Nature Genetics{/credit}

Why is the finding of a large introgression region on the X chromosome important?

Although evidence of adaptive evolution driven by introgression from archaic species has been recently identified in some species including humans, the X-linked introgression region shows that adaptive introgression is not limited to closely related species, but in some cases, introgression with very divergent species can provide the basis for the evolution of radically new traits in a species. This radical example of so-called ‘reticulate evolution’ in mammals shakes the foundation of most modern evolutionary biology and provides a new view of adaptive evolution that emphasizes saltationist (sudden) processes driven by introgression. Moreover, as discussed in the paper, our ability to detect this, potentially quite old, introgression event is facilitated by the fact that the introgression fragment falls in a recombination-decreasing region. This has allowed the introgressed haplotype to be maintained for a prolonged period. Our results may suggest that introgression generally plays a much more dominant role in adaptive evolution than previously thought, but has been difficult to detect because introgression fragments in other systems degenerate quickly due to recombination.

Do you think similar ancient introgressions have occurred in other domesticated species? If so, how would you test this?

We cannot rule out the possibility. If one wants to test this hypothesis, we would suggest to use a research strategy similar to that used in this study. First, we would need to get the genome sequences of multiple species divergent from a domesticated species. Then, we can perform a genome-wide scan for possible introgression regions from another divergent species in the domestic species. Several statistics of ABBA, F4, haplotype sharing and phylogenetic analysis can be explored to identify such ancient introgressions.

{credit}Lusheng Huang{/credit}

Bonus question: What is your favorite breed of domestic pig?

Erhualian, the most prolific pig breed in the world.