Genomic mechanisms underpinning phenotypic diversity in the spiral-horned antelopes (Genus: Tragelaphus)

Abstract

The world is old, full of diversity, and the history of all organisms that once lived on Earth is recorded in the DNA of its descendants. The genomes of living organisms contain ancestral information that, if analyzed, reveals the underlying mechanisms to explain an organism’s evolutionary history. Therefore, it is crucial to study the whole genomes of highly diverse and specialized groups of organisms that could help our understanding of the speciation process. The continent of Africa is home to phenotypically diverse spiral-horned antelopes (genus Tragelaphus) which have gone through a recent adaptive radiation. Previous studies on Tragelaphus have argued that they comprise either nine or ten species based on mtDNA and nuclear DNA respectively/chromosomal number difference. With the same mentioned molecular data, there is discordance in their previously reconstructed species tree, placing species in different clades with different markers. At the mtDNA level, the nyala (T. angasi) is sister to the bushbuck (T. scriptus) making the mtDNA diversity polyphyletic within the bushbuck complex. The two bushbuck species and other phenotypically similar non-sister Tragelaphus lineages lead to the suggestion by scientists that some phenotypes evolved through convergent evolution. In this study, one whole genome of each Tragelaphus lineage was sampled with the aim to analyze the genome-wide relationship of these species by reconstructing their phylogenetic species tree. The study also aims to assess the genome-wide levels of diversity and to assess whether there has been gene flow between species which could have led to phylogenetic discordance among traditional markers. The relationship was analyzed with non-model based PCA and biological model-based IBS and maximum likelihood. All the methods used for structure analysis revealed the same genomic structure and confirmed other studies showing that morphologically similar Tragelaphus species were not most closely related at the genome level. The reconstructed genome-wide species tree was used for the assessment of introgression between species. Most of the observed gene flow was ancestral, the alleles of which are randomly kept in some lineages and passed from generation to generation but lost in others. Therefore, I propose that some phenotypic similarities between unrelated species could be due to high ancestral gene flow between these non-sister lineages. To confirm this would require further investigation using more samples for each species.