Genomic diversity and structure
We investigated whether gene flow would be limited between populations on either side of the GRV by examining genetic variation in eastern and western populations of six bird species. The six species showed clearly different magnitudes of genetic diversity (Table 1), with estimates of observed heterozygosity ranging from 0.0008 to 0.0047 across individuals. Generally, genomic diversity was consistent within each species (Table 1; Fig. 3) with the exception of the Brown-rumped Seedeater which exhibited relatively lower diversity in individuals from the east side of the GRV.
Similar to diversity, genomic differentiation also strongly varied between species (Table 1; Fig. 5). Three species had generally low estimates of genome wide FST, with estimates below 0.06: the Abyssinian Slaty Flycatcher, the Abyssinian Thrush, and the Ethiopian White-eye. Two species with either very low (Abyssinian Catbirds) or inconsistent patterns (Brown-rumped Seedeater) of genomic diversity exhibited the highest values of FST. Estimates of between population diversity (also known as absolute genetic differentiation) as measured by DXY also showed large variability between species (Table 1) and is largely correlated with mean observed heterozygosity with both eastern (r = 0.71) and western (r = 0.85) populations. DXY is a measure of diversity proportional to the time to the most recent common ancestor (TMRCA), and is akin to nucleotide diversity estimates within a populations. Generally, estimates of FST and DXY were consistent across the entire genome (Fig. S2, Fig. S3), suggesting that our mean estimates from the entire genome should be reasonably accurate. However, there were a few outlier regions for both statistics; first, FST estimates were slightly higher on the Z chromosome, and second, part of the 4A chromosome shows elevated values of DXY in both the Abyssinian Catbird and the Ethiopian White-eye. These increased relative values of DXY in these two taxa are expected, as part of the Zebra Finch chromosome 4A has been shown to be part of a neo-sex chromosome region in the Sylvioidea clade (Leroy et al., 2019) sensu Oliveros and colleagues (2019). We may expect higher genetic differentiation on sex chromosomes due to their lower relative effective population size compared to autosomes and the propensity for sex chromosomes to accumulate structural variants (e.g., Hooper, Griffith, & Price, 2018).
Regardless of substantial variation in FST, genetic structure as estimated in STRUCTURE solidly differentiated individuals from either side of the GRV (Fig. 2). Only a single individual of Rüppell’s Robin-chat showed any probability of ancestry not to its respective genetic cluster. Additionally, the phylogenomic results corroborated population differentiation between populations separated by the GRV, but with varying branch lengths to the MRCA of both populations (Fig. 2). These results suggest that the genome-wide information used here exhibits strong diagnostic power even when differentiation between populations is low.