Comparative genome scans in a broader context
In many cases, similarity in patterns revealed by genome scans among
species decreases with phylogenetic distance. Divergent populations of
the same species, and sister species that have recently diverged, often
have more strongly shared genetic patterns (Fischer et al. , 2013;
Renaut et al. , 2013; Westram et al. , 2014; Burri et
al. , 2015; Ravinet et al. , 2016; Vijay et al. , 2016). At
greater phylogenetic distances, species that diverged long ago often
show less similarity in their genetic patterns, with most of the
residual patterns being attributed to convergent evolution (Alan Le
Moan, Gaggiotti, Henriques, & Martinez, n.d.; Raeymaekers et al., 2017;
Vijay et al., 2017) . Henderson and Brelsford (2020) studied this
contrast explicitly in three hummingbird species-pairs, showing that
more distantly related species pairs had reduced correlations in genetic
diversity and increased FST across the genome.
Similarly, a meta-analysis (Conte et al. , 2012) demonstrated a
negative relationship between the proportion of shared signatures of
trait variation and the time since divergence of both species and
population pairs. Shared patterns of genome scan variation is not a
universal outcome, as Ræymaekers et al. (2017) showed no shared genetic
patterns among species despite significant phenotypic sharing. Our study
fits in with this latter category, without any signatures of convergent
evolution and widespread differences in genetic patterns along the
genome.
An interesting contrast to the results of this study is Vijay’s (et al.
2017) study of the long-term conservation of genomic patterns among
three species of birds. They compared species that had similar
generation and divergence times to the fishes used in this study (Bird
clades in Vijay et al. = 23-55mya; threespine to ninespine = 26mya
[Varadharajan et al., n.d.]; threespine to tubesnout = 50mya
[Betancur et al., 2013]); suggesting that patterns of genetic
diversity are conserved long past speciation. Vijay found stronger
correlations in genetic diversity among their species pairs (range of
Pearson’s r = 0.08-0.27) than were found in this study (range Spearman’s
ρ = -0.07 – 0.09). However, Manhattan plots of FST and
genetic diversity also did not show any clear overlapping peaks or
troughs (Fig. 2). Other studies looking at fewer genetic markers have
also identified more conserved levels of genetic diversity in birds than
fishes (Johns and Avise, 1998; Adams and Hadly, 2013), possibly as the
result of a faster genome-averaged mutation rate, which has been
observed between teleosts and mammals (Ravi and Venkatesh, 2008).
Alternatively, fish genomes may evolve faster than birds due to
differences in their recombination map or gene densities. Investigating
the differences in the rates of evolution among broad taxonomic groups
is an interesting question, which is now possible with the increase in
publicly available whole genome data.