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 πN/πS 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
πN/πS 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.