The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.

The Intriguing Biogeographic Pattern of the Italian Wall Lizard Podarcis siculus (Squamata: Lacertidae) in the Tuscan Archipelago Reveals the Existence of a New Ancient Insular Clade

The Tuscan Archipelago is one of the most ancient and ecologically heterogeneous island systems in the Mediterranean. The biodiversity of these islands was strongly shaped by the Pliocene and Pleistocene sea regressions and transgression, resulting in different waves of colonization and isolation of species coming from the mainland. The Italian wall lizard, Podarcis siculus, is present on the following islands of the Tuscan Archipelago: Elba, Giglio, Giannutri, Capraia, Montecristo and Cerboli. The species in the area displays a relatively high morphological variability that in the past led to the description of several subspecies. In this study, both the genetic and morphological diversity of P. siculus of the Tuscan Archipelago were investigated. Specifically, the meristic characters and the dorsal pattern were analyzed, while the genetic relationships among these populations were explored with mtDNA and microsatellite nuclear markers to reconstruct the colonization history of the Archipelago. Our results converge in the identification of at least two different waves of colonization in the Archipelago: Elba, and the populations of Cerboli and Montecristo probably originate from historical introductions from mainland Tuscany, while those of Giglio and Capraia are surviving populations of an ancient lineage which colonized the Tuscan Archipelago during the Pliocene and which shares a common ancestry with the P. siculus populations of south-eastern Italy. Giannutri perhaps represents an interesting case of hybridization between the populations from mainland Tuscany and the Giglio-Capraia clade. Based on the high phenotypic and molecular distinctiveness of this ancient clade, these populations should be treated as distinct units deserving conservation and management efforts as well as further investigation to assess their taxonomic status.

Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The "Mascaruna" is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the Illumina Goat_IGGC_65K_v2 BeadChip with the aim to characterize the genetic diversity, population structure and relatedness with another 31 Italian goat populations. The results displayed a moderate level of genetic variability for Mascaruna, in concordance with the estimated values for Italian goats. Runs of homozygosity islands are linked to genes involved in milk production, immune response and local adaptation. Population structure analyses separated Mascaruna from the other goat populations, indicating a clear genetic differentiation. Although they are not conclusive, our current results represent a starting point for the creation of monitoring and conservation plans. Additional analyses and a wider sampling would contribute to refine and validate these results. Finally, our study describing the diversity and structure of Mascaruna confirms the usefulness of applied genomic analyses as valid tools for the study of the local uncharacterized genetic resources.

Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19^th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.