Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

Abstract

Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts three species of Rattus endemic to elevations above 2,000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the three high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (< 390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages, and attributed the greater non-synonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

The phylogeny of the Anderson's White‐bellied Rat (Niviventer andersoni) based on complete mitochondrial genomes

“…The most appropriate substitution and variant sites model of each PCG through ModelFinder program was estimated according to the Bayesian Information Criterion (BIC) method (Kalyaanamoorthy et al, 2017 ), the result is shown in Table S1 . Referring to previous reports of divergence dates in Rattus genus, two priors of the most recent common ancestor (tMRCA) were used to calibrate the molecular clock (Camacho‐Sanchez & Leonard, 2020 ; Robins et al, 2008 ). The tMRCA of Rattus genus was set to normal distribution with mean value of 3.5 Mya and sdtev value of 0.25; the tMRCA of Rattus baluensis and Rattus tiomanicus was set to normal distribution with mean value of 0.31 Mya and sdtev value of 0.1.…”

“…The most appropriate substitution and variant sites model of each PCG through ModelFinder program was estimated according to the Bayesian Information Criterion (BIC) method (Kalyaanamoorthy et al, 2017), the result is shown in Table S1. Referring to previous reports of divergence dates in Rattus genus, two priors of the most recent common ancestor (tMRCA) were used to calibrate the molecular clock (Camacho-Sanchez & Leonard, 2020;Robins et al, 2008). The…”

A new Rattus species and its associated micromammals from the Pliocene Yangyi Formation in Baoshan, western Yunnan, China

“…The Rattus division plus Berylmys , Bunomys , Dacnomys , Echiothrix , Maxomys , Micromys divisions, Srilankamys and Anoymomys comprise the monophyletic Tribe Rattini Burnett, 1830 (Rowe et al, 2019). The divergence time at which Rattus (sensu stricto) is considered to have separated from its relatives varies according to different researchers, including 3.5 Ma (Furano & Usdin, 1995), 1.84–3.17 Ma (Rowe et al, 2011), 2.5–3.3 Ma (Fabre et al, 2013), 2.9–3.6 Ma (Steppan & Schenk, 2017), 2.11–2.75 Ma (Rowe et al, 2019), and 2.82–3.85 Ma (Camacho - Sanchez & Leonard, 2020). These divergence times are all based on molecular estimations.…”

Mice on the borders: genetic determinations of rat and house mouse species in Lampedusa and Pantelleria islands (Southern Italy)

“…Similar species e.g. the Polynesian rat R. exulans (Peale, 1848) and the Tanezumi rat R. tanezumi Temminck, 1844 are at the beginning of their invasion processes in several islands, and their identification mostly relies on genetic analyses (West et al, 2017;Guo et al, 2019;Camacho-Sanchez & Leonard, 2020). The invasion of the Mediterranean basin by synanthropic rodents is mostly due to the intensification of the trade with Asian countries, which are the native distribution areas of these species (Puckett et al, 2016).…”