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

Gandaki River/western Himalayan clades subsequently diverged at 1.9 Ma (CI = 3.9–0.9), while Bhutan-2/ Koshi River did so at 0.4 Ma (CI = 0.8–0.2). TCS Haplotype network Geographic groups are also apparent in the haplotype network (Fig 5), and are distinct from one other by at least 19 mutations (numbers in black circle). The network shows fine-scale pat- terns, with the location of certain haplotypes reflecting inconsistencies between ML and BA trees (e.g., Bhutan-1A,B,C and YLTR East). Some haplotypes display multiple linkages or star- burst patterns within the network, a characteristic of recently evolved, within-population genetic diversity (e.g., Rara Lake). In contrast, several other clusters divide into distinct sub- groups separated by numerous mutations, and thus reflect deeper phylogenetic divergences (e.g., E-QTP/ SEA-A,B,C). Haplotypes in Central Asia (top, left) and E-QTP/ SEA (bottom, left) are quite distinct, with each regional group separated by >58 mutations. Clusters representing Bhutan-1 (A,B,C) and YLTR (East, West-A, West-B) are nested in-between. The Gandaki River (top, right) reflects subgroups generally representing S. progastus and S. richardsonii (respectively), while the Karnali River (middle, right) contains a starburst incor- porating the three Rara Lake species. Haplotypes from the Indus and the Ganges rivers (middle right) are the most similar and, in turn, reflect geographic groupings with no clear separation. Similarly, Koshi River and Bhutan-2 (lower right) are likewise quite similar, yet clearly distinct

from other Western Himalaya haplotypes (>50 mutations). Our network exhibits two distinct patterns: (a) Clusters of similar haplotypes, such as the Karnali and Gandaki river groups, reflecting scant internal divergence normally characteristic of within/among population genetic diversity; and (b) Groups comprised of considerably divergent haplotypes, such as the E-QTP/ SEA assemblage (sensu lato, lower left). The latter is to be expected given the geographic spread of its constituent samples ([21], S2 Table). Discussion Synergy between tectonism and climate Orogeny and tectonism drive the diversification of aquatic ecosystems, and act synergistically with climate to impact both hydrology [62] and resident freshwater fishes [63]. For example, iqtree.org). Numbers only at specific nodes represent UFBOOT values. Letters within composite species-triangles at tips of the tree represent species, with R = S. richardsonii, P = S. progastus, and x = Both species, with numbers representing individuals contained. https://doi.org/10.1371/journal.pone.0289736.g004 Table 1. Results of an analysis of molecular variance (AMOVA) based on 132 haplotypes of snowtrout (Cyprini- dae: Schizothorax). Source represents: (1) Geographic regions (= Among regions); (2) Lineages within regions (= Within regions/among lineages); (3) Haplotypes within lineages (= Within lineages). Source = Grouping; D.F. = Degrees of freedom; S.S. = Sums of squares; Var. = Variance; % = Percent variance. Probability values for each Fst-

value (derived via 1,000 permutations) are significant at a Bonferroni-adjusted value of p<0.005. Source D.F. S.S. Var. % Among regions 10 3958.7 31.4 77.9 Within regions/among lineages 18 466.1 5.6 13.5 Within lineages 104 350.6 3.4 8.5 Total 132 4775.3 40.3 99.9 https://doi.org/10.1371/journal.pone.0289736.t001 PLOS ONE Himalayan uplift and aquatic evolution PLOS ONE | https://doi.org/10.1371/journal.pone.0289736 October 24, 2023 14 / 27