Fig 1.
(A) Simplified drainage map of Asia, showing major basins from which Schizothorax were obtained. Area in yellow indicates the Tibetan Plateau, referred to as Qinghai-Tibetan Plateau (QTP) in China. The Tarim River, an endorheic basin north of the QTP in Central Asia, is not depicted. Three major rivers, the Irrawaddy, Salween, and Mekong, drain the QTP into Southeastern Asia (SEA), whereas the Yangtze River flows east into the China Sea (Republished from Fig 1 [100] under a CC BY license, with permission of the Council on Foreign Relations, original copyright 2016). (B) Schizothorax sp. cf richardsonii (i.e., potentially S. richardsonii) captured 02 December 2016 at confluence of Bibigang Chhu and Mangde Chuu, Bhutan (Total length = 540 mm).
Fig 2.
Map depicting sampling locations for Schizothorax, with metadata for ’Site,’ ’River,’ ’Location,’ ’Lat-Long,’ ’Haplotype,’ and ’Group’ compiled in S1–S3 Tables, respectively.
Red circles in map indicate sampling sites with samples identified by Group number in (A) Nepali as N = 1–9, and (B) Bhutan as B = 1–9. Maps were generated in ArcGIS 10.4.1 using publicly available data from HydroRIVERS and HydroBASIN (https://www.hydrosheds.org/products/hydrorivers).
Fig 3.
A collapsed maximum likelihood (ML) tree reflecting phylogenetic relationships among biogeographic groups.
The constituent samples comprising each biogeographic clade are provided in S3 Table under ’Species Name,’ ’Haplotype,’ ’Accession #,’ ’Location,’ and ’Group’ headings. Data were derived from sequence analysis of the cytochrome-b mitochondrial gene (1,140 bp, 140 haplotypes, clades collapsed). Red asterisk = SH-LRT (Shimodaira-Hasegawa approximate likelihood ratio test) ≥80% and UFboot (ultrafast bootstrap approximations) ≥95% (IQ-Tree v.2 Manual: http://www.iqtree.org). Numbers at colored triangles indicate the number of haplotypes grouped within each. Numbers at nodes represent RelTime Timetree mean divergence estimates (in Ma; confidence intervals in text; See also S1 Appendix).
Fig 4.
Maximum likelihood (ML) tree reflecting phylogenetic relationships among biogeographic samples.
The constituent samples representing each biogeographic clade are provided in S3 Table under ’Species Name,’ ’Haplotype,’ ’Accession #,’ ’Location,’ and ’Group’ headings.’ Data were derived from sequence analysis of the cytochrome-b mitochondrial gene (1,140 bp, 140 distinct haplotypes). Red asterisk = SH-aLRT (Shimodaira-Hasegawa approximate likelihood ratio test) ≥ 80% and UFboot (ultrafast bootstrap approximations) ≥ 95% (IQ-Tree v.2 Manual: http://www.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.
Table 1.
Results of an analysis of molecular variance (AMOVA) based on 132 haplotypes of snowtrout (Cyprinidae: 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.
Table 2.
Statistical topology tests comparing maximum likelihood (ML) and Bayesian (BA) phylogenetic results (= Tree).
logL = Log Likelihood value; deltaL = logL difference from maximal logL in the set; Bp-RELL = Bootstrap proportions using RELL method (weights sum to 1 across trees); p-KH = p-value of one-sided Kishino-Hasegawa test; p-SH = p-value of Shimodaira-Hasegawa test; c-ELW = Expected Likelihood Weight (weights sum to 1 across trees); p-AU = p-value of Approximately Unbiased test. A plus sign (+) next to a p-value denotes 95% confidence sets, whereas a minus sign (-) denotes a significant exclusion (i.e., the tree is rejected). All tests stemmed from 1,000 resamples using the RELL method.
Fig 5.
TCS haplotype network reflecting stepwise mutational differences between samples and among geographic groups.
The contents of each biogeographic clade are provided in S3 Table under ’Species Name,’ ’Haplotype,’ ’Accession #,’ ’Location,’ and ’Group’ headings. Data were derived from sequence analysis of the cytochrome-b mitochondrial gene (1,140 bp, 132 haplotypes). Geographic groupings (Fig 3, S3 Table) are labeled within rectangles, with group colors identical to those in Figs 3 and 4. Black circles represent hypothetical haplotypes to reflect stepwise mutations >14. See S1 Appendix for the associations between divergence intervals for clades and geomorphic/ climatic drivers in the Himalaya.