Patterns of Genomic Divergence
Differentiation between S. v. virens and S. v. waynei was
most pronounced in two regions of the genome, one along chromosome 6 and
the other on the Z chromosome (Figure 3). Baiz et al., (2021) compared
patterns of differentiation between nine sister species across theSetophaga genus. Notably, these regions on chromosome 6 and the Z
are also commonly differentiated between several other warbler pairs.
However, in those instances, regions of divergence are much larger, on
the scale of 1-2 Mb, whereas in the present case the divergent regions
are an order of magnitude smaller. We suggest this is likely because all
pairs in Baiz et al., (2021) are between fully reproductively isolated
species, each sharing a common ancestor much older than that betweenS. v. virens and S. v. waynei . Thus, divergence between
those pairs have had more time to accrue greater differences in their
genomes. Additionally, this study adds to the number of examples in
birds where the Z chromosome is highlighted as highly divergent between
related taxa, beyond expectations of a reduced effective population size
(Ellegren, 2011; Oyler-McCance et al., 2015; Ruegg et al., 2014).
Because the regions of divergence between S. v. virens andS. v. waynei are small, we can identify individual genes within
them that were potentially the target of divergent selection between the
subspecies. Although the two regions—on chromosome 6 and the Z
chromosome—include multiple genes, we focused on two that directly
intersected the two most divergent 10Kb windows. In the chromosome 6
region, the gene that intersects the most divergent window is broad
substrate specificity ATP-binding cassette transporter ABCG2 isoform X1
(ABCG2; NCBI reference XP_030131844.2). ABCG2 is involved
in protein transport, extra- and intra-cellularly (Ma et al., 2020), and
recently implicated in egg coloration differences in mallard ducks
(Anas platyrhynchos; Liu et al., 2021). The most divergent window
within the entire genome, on the Z chromosome, falls within the gene
Metallo-Beta-Lactamase Domain Containing 2 (MBLAC2 ). The MBL
superfamily of enzymes has a diverse phenotypic role but has been
associated with hydrolase activity (Malgapo et al., 2021). While we do
not know the function of these genes in warblers, they are both involved
in metabolic processes and cellular transport and present a possible
connection to the distinct habitat (and therefore diet) these warblers
inhabit. Both are good candidates for further study of the implications
of gene functionality in birds.
More broadly, the overall limited genomic differentiation suggests these
warblers are in the early stages of divergence. Previous studies of
closely related avian taxa have commonly identified shared divergence
peaks between independent groups (Delmore et al., 2015; Toews, Campagna,
et al., 2016). These have generally been understood as genomic regions
of reduced recombination, which amplify the influence of divergence via
linked selection. However, given the large size and many genes that fall
within these regions in previous studies, pinpointing putative targets
of selection has been challenging. In the S. v. virens complex,
however, the small size of these divergent regions has allowed us to
identify ABCG2 and MBLAC2 as two possible targets, and it
will be important to understand whether these specific genes have
contributed to common divergence patterns in other species pairs.