Persistent Gene Flow Suggests an Absence of Reproductive Isolation in an African Antelope Speciation Model

Area of Science:

• Evolutionary Biology
• Population Genetics
• Genomics

Background:

• African antelope diversity is a unique remnant of Pleistocene megafauna, yet evolutionary drivers of their radiation remain unclear.
• The waterbuck (Kobus ellipsiprymnus) serves as a model, potentially undergoing speciation, with distinct subspecies exhibiting unique traits.

Purpose of the Study:

• To investigate the genetic structure and population divergence of waterbuck subspecies.
• To understand the evolutionary processes, including vicariance and gene flow, shaping African antelope radiation.
• To identify genomic regions associated with divergence and assess their role in speciation.

Main Methods:

• Whole-genome sequencing of 145 waterbuck individuals from both subspecies.
• Analysis of genetic structure, population divergence, and genome-wide variation.
• Inference of historical gene flow patterns and identification of candidate speciation regions.

Main Results:

• Evidence of mid-Pleistocene separation across the eastern Great Rift Valley, linked to vicariance (Kingdon's Line).
• Pervasive historical and recent gene flow detected across the Rift Valley barrier.
• 14 genomic regions of elevated differentiation identified, including a locus potentially related to coat pigmentation, but showed no reduced gene flow or hybrid disadvantage.

Conclusions:

• Climatically driven vicariance appears to be a primary driver of African antelope radiation.
• Reproductive isolation likely occurs late in the divergence process, leading to ambiguous taxonomic status for many antelope taxa.
• Population genetics using low-depth whole-genome sequencing offers valuable insights into the speciation continuum.