期刊
BMC GENOMICS
卷 23, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s12864-022-08510-y
关键词
Single Nucleotide Polymorphism (SNP); Lion; Genomics; Genotyping; Evolutionary history; Genomic variation; Wildlife; Conservation; Africa; Biodiversity
资金
- Division for Earth and Life Sciences (ALW)
- Netherlands Organization for Scientific Research (NWO) [820.01.002]
This study used low-depth whole genome sequencing to analyze ten lions sampled across their geographic range, resulting in the discovery of over 150,000 single nucleotide polymorphisms (SNPs). Phylogenetic analysis revealed the split between northern and southern populations, as well as four population clusters on a local scale. A SNP panel was designed and tested on over 200 lions, allowing individuals to be assigned to one of the four major clades and providing detailed delineation of these clades.
Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.
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