Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout

Abstract

The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological ‘ecotypes’ observed in polyploid snowtrout (Cyprinidae: Schizothorax ). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq ( N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples ( N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational ‘ecotypes’ were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively ‘masks’ previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.

The Himalayan uplift and evolution of aquatic biodiversity across Asia: Snowtrout (Cyprininae: Schizothorax) as a test case

“…Despite morphological differences [ 29 ], the two species are genetically more similar within than among basins, which could be driven by ecological diversification along elevational gradients, allowing for emergence of similar phenotypes in each basin (i.e., homoplasy). This perspective stems from mtDNA data, but a recent study using ddRADseq indicated substantial admixture between the two in each drainage [ 84 ]. Our study does not (and cannot) revise taxonomy, but it does identify regions (e.g., Nepal, Bhutan) where more focused research is needed to assess genetic and phenotypic diversity, and thus clarify taxonomy of Schizothorax in the Central and Eastern Himalaya.…”

The Conservation Genetics of Iris lacustris (Dwarf Lake Iris), a Great Lakes Endemic

“…This statement should be treated with skepticism because it is based only on one, empirical, study. Others who have used polyRAD to subset their datasets and identify diploid loci to use for population genomics [28,29], which is a practice aligned with assumptions of common methods [28], have not explored the use of all loci and/or tetraploid loci in comparison to only ones that segregate as diploids. It would be useful for additional studies on the population genomics of polyploid species to examine data employing all, diploid, and tetraploid (and higher) loci to determine if similar or divergent results are recovered.…”

First record of the genus Schizothorax in rivers of the Central Himalayas in China

“…In addition, S. plagiostomus and S. curvifrons have shared Cyt b haplotypes with S. richardsonii (referred to GenBank sequence accession numbers AF53203–AF532086), even though they have remarkably different mouth and lip characters that were considered as the main criteria for classifying into genera or species (Chen & Cao, 2000; Talwar & Jhingran, 1991; Wu & Wu, 1992). On the contrary, the Schizothorax fishes are generally distributed based on the drainages, with species sampled from the same drainage system often grouped together with high statistical support (Chafin et al ., 2021; He & Chen, 2006). Although molecular phylogeny did not support the monophyly of S. richardsonii , the specimens of this study were grouped with species collected from the Gandak River in Nepal.…”