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.