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.