PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene

Abstract

<jats:title>Abstract</jats:title> <jats:p>Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single nucleotide polymorphism (SNP) information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5 to 0.2 Mya and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.</jats:p>

Building an atlas of transposable elements reveals the extensive roles of young SINE in gene regulation, genetic diversity, and complex traits in pigs

“…SINE was shorter and more complete than LINE. Similar to our previous findings 53 , SINE, especially the PRE1-SS, PRE0-SS, and PRE1a families in SINE/tRNA, displayed the most recent ages and most polymorphic insertions. These polymorphic SINEs contributed nearly 90% of medium-length SVs among different assemblies, especially the L13 subfamilies, with 36.15% that were classified as the youngest SINEs in the pig genome.…”

“…Further exploring the ages of highly homologous subfamilies in SINE classes ( Fig. 1f with an average divergence of 4%, labelled in purple), we found that 3 out of 26 SINE families (PRE1-SS, PRE0-SS, and PRE1a) were recently active and had been proved to be polymorphic within pig breeds in a previous study 53 , and thus can be viewed as the young SINE families.…”

“…Obviously, the amplification of most TE families occurred Mya (divergence at 30 ± 5%), consistent with that the Paleocene Epoch (65-54 Mya) opened up vast ecological niches for surviving mammals, birds, reptiles, and marine animals 56 . The latest obvious burst of TEs was mainly concerned with SINE/tRNA, LINE/L1, and LTR/ERV1 families, of which SINE/tRNA was still most active in the modern pig genome [57][58][59] . Further exploring the ages of highly homologous subfamilies in SINE classes (Fig.…”

“…TEs produce abundant raw materials for evolution in natural populations, and the burst of TEs was tightly related to significant evolutionary events such as the population admixture and local adaptation 23,[94][95] . Young SINE polymorphisms represented the vast majority of TE polymorphisms in the pig genome 48,57,59,96 . Therefore, we developed a comprehensive map of polySINE from WGS of over 300 pigs, representing the majority of Eurasian pig breeds, to explore the roles of young SINEs and their derived genes in pig population admixture and local adaptation.…”

Ancient Faunal History Revealed by Interdisciplinary Biomolecular Approaches

“…The task of disentangling the multistage domestication process of suids has involved a number of disciplines (e.g., archaeology, biology, anthropology, genetics). Besides the traditional archaeological approach [256,257], additional insights into population dispersal and introgression events have been gained using modern genetic data [258][259][260][261]. However, the genetic legacy derived from modern organisms provides only a peek into this protracted and reticulated process; additional lines of evidence need to be drawn from palaeogenomic research.…”