Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra

Abstract

Aim Understanding the biotic and abiotic mechanisms underlying the generation and maintenance of biogeographic transitions represent long‐standing topics in evolutionary biology. The Isthmus of Kra (IOK) divides Sundaland and Indochina and constitutes a poorly characterized terrestrial biogeographic transition. Here we looked at population genetic structure of three species that are distributed across the IOK to gain insights into the drivers that have shaped this transition and regional diversification patterns. Location Tropical east Asia: Sundaland and Indochina. Taxa Callosciurus caniceps, Tamiops mcclellandii, and Dremomys rufigenis‐ornatus species complex (Mammalia: Rodentia: Sciuridae). Methods We generated complete mitogenomes and sequences of 11 nuclear intron fragments from 61 and 67 museum specimen samples, respectively. We assessed population structure by constructing Maximum Likelihood mitogenome phylogenies (IQTREE2), and nuclear marker haplowebs and conspecificity matrices (HaplowebMaker and CoMa). We estimated divergence dates through Bayesian phylogenetic inference (BEAST2) and put these results in the context of climatic and geological history. Results High levels of mitochondrial and nuclear divergence were identified across the IOK in all three squirrels. Lineage turnover was consistent with the two major mammal species distribution transitions near the Kangar‐Pattani Line and at the juncture between the Thai‐Malay peninsula and the mainland. Divergence of mitochondrial lineages across Kra was estimated in the late Pliocene/ early Pleistocene for all three taxa. Older Miocene/Pliocene divergences were estimated within Indochina in D. rufigenis‐ornatus and T. mcclellandii, which were paraphyletic. Main Conclusions Sundaic and Indochinese populations have possibly diverged in allopatric habitat refugia in or around mountains during periods of increased aridity and evergreen forest contraction. Ecological differences and/or topography might have influenced genetic differentiation during periods of rainforest expansion. Alternative hypotheses remain to be tested with more informative nuclear markers and additional geographic sampling.

Speciation on the Roof of the World: Parallel Fast Evolution of Cryptic Mole Vole Species in the Pamir-Alay—Tien Shan Region

“…A growing body of research on attempts to distinguish closely related species and forms suggests that different datasets require different rather than standardized approaches [ 28 , 29 ]. Haplotype network analysis, which allows us to work with both single-locus and multilocus models at different sample sizes, is gaining popularity in mammalian phylogenetic studies [ 30 ].…”

Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time

“…According to J. Doyle [ 74 ] “allele pools at each locus are a representation of the overall gene pool, which in turn can be inferred from multilocus genotypes; individuals sharing a common gene pool belong to the same multilocus field for recombination (ml-FFR)”. To date, this approach has been successfully applied to different vertebrate groups [ 75 , 76 , 77 , 78 ] to analyze the phylogenetic relationships and heterozygosity of populations.…”

“…According to J. Doyle [74] "allele pools at each locus are a representation of the overall gene pool, which in turn can be inferred from multilocus genotypes; individuals sharing a common gene pool belong to the same multilocus field for recombination (ml-FFR)". To date, this approach has been successfully applied to different vertebrate groups [75][76][77][78] to analyze the phylogenetic relationships and heterozygosity of populations. All newly sequenced nucleotide sequences of the haplotypes were deposited in Gen-Bank with access numbers CR: OR088768-OR088803, cytb: OR088804 -OR088840, SmcY: OR088841 -OR088846, BGN: OR088847 -OR088859, c-myc: OQ929560 -OQ929573, PRKCI: OQ954111 -OQ954121.…”