Influence of gene flow on divergence dating – implications for the speciation history of Takydromus grass lizards

Abstract

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species-tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation-with-migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene- and species-based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.

Taxonomic reassessment of two subspecies of Chinese skink in Taiwan based on morphological and molecular investigations (Squamata, Scincidae)

“…Furthermore, since the light lines was reported by Van Denburgh (1912b) from the holotype, it helps to confirm that P. c. formosensis should be applied only to the western lizard, while P. leucostictus stands for a valid specific name. Their disjunct distribution suggests that the Central Mountain Range in Taiwan may have played a major role as a natural barrier for these lowland lizards, congruent to the other phylogeographic cases which have shown huge diversification between eastern and western clades such as cobras (Lin et al 2008), rhacophorid treefrogs (Lin et al 2012), and lacertid lizards (Tseng et al 2014, 2015). …”

Diversity of the snail‐eating snakes Pareas (Serpentes, Pareatidae) from Taiwan

“…; Tseng et al . ). In our samples, P. komaii (the yellow‐eyed form 1) has shown significant genetic differentiation between eastern and western populations, congruent to the patterns discovered in vipers (Creer et al .…”

Geographical and temporal origins of terrestrial vertebrates endemic to Taiwan

“…fossils; Kawamura et al., ) have provided strong and widely accepted evidence regarding the timing of the emergence of Taiwan. In addition, although in situ speciation events of terrestrial Taiwanese vertebrates have been reported (Lai & Lue, ; Li et al., ; Tseng, Li, Hsieh, Wang, & Lin, ; Tseng, Wang, Li, & Lin, ), few of these events pre‐date the early Pliocene ( c . 5 Ma; but see Li et al., for Hynobius spp.).…”

“…In addition, although in situ speciation events of terrestrial Taiwanese vertebrates have been reported (Lai & Lue, 2008;Li et al, 2011;Tseng, Li, Hsieh, Wang, & Lin, 2014;Tseng, Wang, Li, & Lin, 2015), few of these events pre-date the early Pliocene (c. 5 Ma; but see Li et al, 2011 for Hynobius spp.). Therefore, we advocate for the first explanation of Hawlitschek et al (2017) that the divergence events of extant species occurred before their colonization into Taiwan, and extinctions within the ancestral taxa resulted in relict populations in Taiwan (Mays et al, 2015;Wang et al, 2013).…”