A wide hybrid zone mediated by precipitation contributed to confused geographical structure of <i>Scutiger</i> <i>boulengeri</i>

Abstract

Confused geographical structure of a population and mitonuclear discordance are shaped by a combination of rapid changes in population demographics and shifts in ecology. In this study, we generated a time-calibrated phylogeny of Scutiger boulengeri , an endemic Xizang alpine toad occurring in mountain streams on the Qinghai-Xizang (Tibet) Plateau (QTP). Based on three mitochondrial DNA (mtDNA) genes, eight clades were assigned to three deeply divergent lineages. Analysis of nuclear DNA (nuDNA) genes revealed three distinct clusters without geographic structure, indicating significantly high rates of gene flow. Coalescent theory framework analysis (approximate Bayesian computation model DIYABC and Migrate-N) suggested that divergence of the main intraspecific clusters was the result of hybridization after secondary contact in the Holocene around 0.59 million years ago (Ma). The ratio of mtDNA F ST (fixation index) to nuDNA F ST was 2.3, thus failing to show male-biased dispersal. Geographic cline analysis showed that a wide hybrid zone was initially established in southwestern China, without significant reproductive isolation but with strong introgression in S . boulengeri , suggesting high hybrid fitness. Furthermore, mtDNA genes exhibited isolation by distance (IBD) while nuDNA genes exhibited significant isolation by environment (IBE). Results suggested that mitonuclear discordance may have initially been caused by geographic isolation, followed by precipitation-mediated hybridization, producing a wide hybrid zone and geographic structure confusion of nuDNA genes in S . boulengeri . This study indicated that complicated historical processes may have led to specific genetic patterns, with a specific climate factor facilitating gene flow in the system.

No evidence of a hybrid origin of the ashy‐throated parrotbill Sinosuthora alphonsiana

“…Furthermore, to test for putative hybrid speciation coalescent simulations could have been used to test for a best‐fit demographic scenario (Arekar et al 2021) like in ABC analysis (Shaner et al 2015) or DIYABC analysis (Pöschel et al 2018, Lin et al 2023) or to quantify introgression using ABBA‐BABA tests (Zarza et al 2016).…”

Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae)

“…The biodiversity of this region has been heavily studied with regard to taxonomy, evolution, biogeography, and population genetics (Che et al, 2010;Guo et al, 2011Guo et al, , 2016Guo et al, , 2019Guo et al, , 2020Hofmann et al, 2015;Wu et al, 2020;Yan et al, 2013;Zhu et al, 2016Zhu et al, , 2022. A large number of these studies have focused on the evolutionary history of species within this region and speciation patterns have been assessed among various taxa during the last two decades, including fish (Zhao et al, 2005), amphibians (Lin et al, 2023;Murphy et al, 2000;Wu et al, 2020;Zhang et al, 2008), birds (Chen et al, 2015), and mammals (Li et al, 2005;Pang et al, 2003;Patou et al, 2010). However, research on snakes, which are highly sensitive to climatic fluctuations and exhibit constrained dispersal capabilities, remains limited and heavily focused on venomous taxa (Ding et al, 2011;Guo et al, 2011Guo et al, , 2012Guo et al, , 2016Guo et al, , 2019Huang et al, 2007;Lin et al, 2014;Zhu et al, 2022).…”