Add pig species and published demographies (SusScr)

[gregorgorjanc]

• Name: Sus Scrofa
• Common name: pig

Just starting this - will continue in time

https://en.wikipedia.org/wiki/Sus_(genus)

[gregorgorjanc]

Adding some pig demography papers

2012: Analyses of pig genomes provide insight into porcine demography and evolution
https://www.nature.com/articles/nature11622

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ∼1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

2015: Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes
https://www.nature.com/articles/ng.3394

Traditionally, the process of domestication is assumed to be initiated by humans, involve few individuals and rely on reproductive isolation between wild and domestic forms. We analyzed pig domestication using over 100 genome sequences and tested whether pig domestication followed a traditional linear model or a more complex, reticulate model. We found that the assumptions of traditional models, such as reproductive isolation and strong domestication bottlenecks, are incompatible with the genetic data. In addition, our results show that, despite gene flow, the genomes of domestic pigs have strong signatures of selection at loci that affect behavior and morphology. We argue that recurrent selection for domestic traits likely counteracted the homogenizing effect of gene flow from wild boars and created 'islands of domestication' in the genome. Our results have major ramifications for the understanding of animal domestication and suggest that future studies should employ models that do not assume reproductive isolation.

2022: Revisiting the evolutionary history of pigs via De Novo mutation rate estimation in a three-generation pedigree
https://doi.org/10.1016/j.gpb.2022.02.001

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary history. Herein, we estimated the de novo mutation rate of pigs as 3.6 × 10−9 per site per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. Using this mutation rate, we re-investigated the evolutionary history of pigs. The estimated divergence time of ∼ 10 kiloyears ago (Kya) between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggested that Sus speciation occurred ∼ 1.36 million years ago (Mya); European pigs split from Asian pigs only ∼ 219 Kya; South and north Chinese wild pigs split ∼ 25 Kya. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, north China, approximately 20 Kya, supporting the possibly independent domestication in north China along the middle Yellow River. We also found the maximum effective population size of pigs was ∼ 6 times larger than the previous estimate. An archaic migration from other Sus species originating ∼ 2 Mya to European pigs was detected during western colonization of pigs; this interfered with the previous demographic inference. Our de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

[gregorgorjanc]

@AprilYUZhang are there any good published models we could implement for the pig in stdpopsim or do we wait for future publications?

[AprilYUZhang]

The studies so far are enough to build a pig model. Because the key time points in the divergence and domestication of sus scrofa are relatively clear. The third paper supplies new pieces of information. I think the model will be more complicated than what I built before. A robust model could be developed by integrating elements from both the second and third papers. By incorporating divergence and migration models across Asian domesticated pigs, wild boars, European domesticated pigs, and wild boars, we could add a population that diverged early with a strong migration with WB and Dom pigs but now has been extinct.

[gregorgorjanc]

@AprilYUZhang let's cover this in our next 1:1 and see if currently published models have enough information.