Genetic Architecture Underlying Nascent Speciation—The Evolution of Eurasian Pigs under Domestication

Abstract

Speciation is a process whereby the evolution of reproductive barriers leads to isolated species. Although many studies have addressed large-effect genetic footprints in the advanced stages of speciation, the genetics of reproductive isolation in nascent stage of speciation remains unclear. Here, we show that pig domestication offers an interesting model for studying the early stages of speciation in great details. Pig breeds have not evolved the large X-effect of hybrid incompatibility commonly observed between “good species.” Instead, deleterious epistatic interactions among multiple autosomal loci are common. These weak Dobzhansky–Muller incompatibilities confer partial hybrid inviability with sex biases in crosses between European and East Asian domestic pigs. The genomic incompatibility is enriched in pathways for angiogenesis, androgen receptor signaling and immunity, with an observation of many highly differentiated cis-regulatory variants. Our study suggests that partial hybrid inviability caused by pervasive but weak interactions among autosomal loci may be a hallmark of nascent speciation in mammals.

Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish

“…The possibility of survival is always related to the capacity to tolerate excessive developmental abnormalities arising from genome duplication. The destruction of regulatory systems is the main cause of the death of allopolyploid individuals, especially in the early stages of embryonic development [ 10 ]. Mismatches between regulatory factors and target genes, and increased gene copy numbers, are always fatal to normal development.…”

“…One type of polyploidization in animals resulting from unreduced gametes in hybrid progenies can reverse the reduction in fertility arising from hybrid incompatibility [ 7 , 9 ]. However, increased gene copy numbers after polyploidization disrupt regulatory systems and result in the death of individuals [ 10 ]. To date, the factors in evolutionarily divergent genomes that contribute to establishing stable regulatory systems in allopolyploid lineages have yet to be clearly elucidated in vertebrates.…”

Multi-omics analysis reveals signatures of selection and loci associated with complex traits in pigs

“…Finally, the top 1% of windows (with the highest CLR scores) were considered to be candidate selective regions. To evaluate the association between candidate variants and traits of economic importance in pigs, we leveraged genotype and phenotype data of 589 F2 individuals from our collaborator, which was derived from a cross between five Large White (European, WED) boars and sixteen Min (Chinese, EAD) sows 23 . We first sorted the pedigree information according to the birth order by a custom python script, and next established the relative kinship coefficients matrix.…”

Rearrangements and accelerated mutation rates on Dendrodorididae mitogenomes rumble their evolution

“…(Myers, 2021; Díaz et al , 2018). In addition, non-adaptive mutations also have a prevalent role in speciation (Schluter & Rieseberg, 2022; Wolf et al , 2010; Ravinet et al , 2017; Xie et al , 2021; Wu, 2001). Drastic changes at the DNA structural level can suddenly occur, changing chromosome conformation and the interaction between their regions, such as in cases of speciation by chromosome partitioning and fission (de Vos et al , 2020).…”