Abstract
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African buffalo (Syncerus caffer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape buffalo (S. c. caffer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while differences in individual inbreeding coefficients reflected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape buffalo colonisation of southern Africa. The results of this study have implications for buffalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.
Highlights
Genomes retain records of demographic changes and evolutionary forces that shape species and populations
The transition/ transversion (Ti/Tv) ratio is an indication of the quality and specificity of single nucleotide polymorphism (SNP) calls, and is expected to be between ~ 2.0 and 2.1 for mammals[62]
Genomic resources are becoming increasingly accessible for non-model species as a result of the decreased costs of next-generation sequencing technologies[1]
Summary
Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Population genomics studies of non-model organisms have increased considerably in recent years, owing to the development of reduced-representation sequencing methods and the ever-decreasing cost of short-read sequencing[1]. The African buffalo, a large, gregarious ruminant, is classified as Near Threatened on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species, owing mainly to a decreasing population trend[5]. This trend is predicted to continue and likely accelerate, predominantly due to human population expansion and related activities, such as development, agriculture and biological resource u se[5]. The few buffalo studies employing more modern genetics techniques have focused on disease-related variants and variant discovery, while relying on the cattle genome as r eference[2,3,18,19]
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