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The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset of >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs and evolutionary simulations to investigate the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate the effect of population history. We investigated the role of recombination using both a physical map and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating that population history and local recombination rate have an effect on ROH. Finally, we ran forward genetic simulations with varying population histories, recombination rates and levels of selection, allowing us to further interpret our empirical data. These simulations showed that population history has a greater effect on ROH distribution than either recombination or selection. We further show that selection can cause genomic regions where ROH is common, only when the effective population size (N e ) is large or selection is particularly strong. In populations having undergone a population bottleneck , genetic drift can outweigh the effect of selection. Overall, we conclude that in this population, genetic drift resulting from a historical population bottleneck is most likely to have resulted in the observed ROH distribution, with selection possibly playing a minor role., (© 2023. The Author(s).)

Comparative maps between ruminant species and humans are increasingly important tools for the discovery of genes underlying economically important traits. In this article we present a primary linkage map of the deer genome derived from an interspecies hybrid between red deer (Cervus elaphus) and Père David's deer (Elaphurus davidianus). The map is approximately 2500 cM long and contains >600 markers including both evolutionary conserved type I markers and highly polymorphic type II markers (microsatellites). Comparative mapping by annotation and sequence similarity (COMPASS) was demonstrated to be a useful tool for mapping bovine and ovine ESTs in deer. Using marker order as a phylogenetic character and comparative map information from human, mouse, deer, cattle, and sheep, we reconstructed the karyotype of the ancestral Pecoran mammal and identified the chromosome rearrangements that have occurred in the sheep, cattle, and deer lineages. The deer map and interspecies hybrid pedigrees described here are a valuable resource for (1) predicting the location of orthologs to human genes in ruminants, (2) mapping QTL in farmed and wild deer populations, and (3) ruminant phylogenetic studies.

Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer. [ABSTRACT FROM AUTHOR]

This review considers the application of new technologies to beef cattle and deer improvement. Many potential opportunities are linked to the concept of monitoring and then tracing the unique identity (ID) of livestock through the use of DNA methods and electronic IDs, including: identifying or confirming pedigrees; collection of field, yard or abattoir data linked to an electronic ID; marker-assisted selection using DNA and measured phenotypes; and trace-back facilities for meat products at the point of sale by matching a DNA sample taken there with one taken earlier in the abattoir. Opportunities with assisted reproduction are described, with the greatest potential payoffs being from much wider use of artificial insemination, provided that more practical and economical insemination methods can be found (especially in beef herds). Some new goal traits are considered which could become more important than at present, when applied to new production environments (e.g., selection to improve feed conversion efficiency, resistance to feed-borne toxins, resistance to nematode parasites, and deer calving earlier in the season). We conclude with a discussion of technology adoption for beef cattle and deer improvement. [ABSTRACT FROM AUTHOR]

Overhunting of red deer (Cervus elaphus) in eastern Switzerland led to its extinction in the second half of the 17th century. Natural recolonization must have taken place later, because red deer were seen again in the canton of the Grisons (eastern Switzerland) in the 1870s. According to historical data, three different populations could have served as the source population. To determine the genetic origin of the eastern Swiss red deer population, we collected samples from five different subpopulations in the canton of the Grisons as well as from four adjacent populations in Germany, Liechtenstein, Austria, and Italy. We analyzed the samples by genotyping 18 microsatellite loci. FST values, assignment tests, correspondence analysis, and fuzzy clustering clearly pointed to Liechtenstein as the most probable source population for the red deer in eastern Switzerland. In addition, our analyses revealed high gene diversity in all examined populations. Gene flow and the high genetic admixture are discussed. [ABSTRACT FROM AUTHOR]