Microevolutionary analyses
Estimates of nucleotide diversity, pairwise population sequence divergence andFST -values were similar for ORF and UCE datasets, suggesting general robustness. Synonymous nucleotide diversity was overall low for the ‘Malawi’ clade (average πS=0.00271) compared to species-level estimates from transcriptomic data across mollusks (πS=0.02878), or Metazoa altogether (πS=0.01912; see Romiguier et al., 2014). Our estimates of πNS were high compared to those of other Metazoa but similar to those of certain Darwin finches and Echinodermata (see Fig. S6; Leroy et al., 2021; Romiguier et al., 2014). This low diversity may relate to the brooding ability and parasitic life-cycle of Coelatura species, but also to Late Pleistocene ecological crises in the Malawi Basin, which may have caused population bottlenecks in the aquatic fauna, and which may explain high πNS ratios (Cohen et al., 2007; Ivory et al., 2016). Beyond low nucleotide diversity, also the pairwise nucleotide divergence among sampling localities is low, which is very similar to what has been observed in Malawi cichlids (Malinsky et al., 2018), as in recent speciation in Ficedula flycatchers (Ellegren et al., 2012). In Malawi cichlids the distributions of individual heterozygosity at nucleotide sites and of pairwise nucleotide divergence between species are partially overlapping, and multiple radiative events are interconnected by gene flow (Malinsky et al., 2018). Malawi Coelaturini display a similar pattern when comparing nucleotide diversity and pairwise nucleotide divergence (Fig. 6a), which may be driven by similar population histories due to ecological interactions, as Coelaturini have a fish-parasitizing larval stage, or by common environmental change. FST -values indicate moderate genetic differentiation comparable to that in theLanistes gastropod radiation of the Malawi Basin (Van Bocxlaer, 2017). Interestingly, several ORFs and UCEs for each pairwise population comparisons displayed both elevated FST andDXY values, indicating that suchFST values do not result from local reductions of genetic diversity in the genome (Charlesworth, 1998), but rather from diversifying selection. Despite the low degree of differentiation in Coelaturini, analyses of geographic structure differentiate several gene pools with a similar geographic pattern to that in Lanistes . Geographic differentiation between the northern and southern regions of the Malawi Basin is observed, however, the geographic structure inLanistes is more clearly delineated than that in Coelaturini. Further population samples are required to examine the demographic history and population divergence of Coelaturini from the Malawi Basin. Nevertheless, our results seem compatible with an early stage of speciation (see Seehausen et al., 2014). If generalizable to a macroevolutionary scale, this feature may have contributed to the lack of resolution within geographic clades in previous phylogenetic studies (Ortiz-Sepulveda et al., 2020). We are hopeful that the here described enrichment and analytical strategy will enable in-depth studies of genetic diversity and divergence, and therewith, an integration of diversification dynamics at micro- and macroevolutionary scales.