DOI: 10.5061/dryad.7pvmcvdqm
title: Data from: Late Quaternary environmental and human impacts on the mitochondrial DNA diversity of four commensal rodents in Myanmar

description: We addressed the spatiotemporal characteristics of four commensal rodent
 species occurring in Myanmar in comparison with other areas of the
 Indo-Malayan region. We examined sequence variations of the mitochondrial
 cytochrome bgene (Cytb) in the Pacific rat (Rattus exulans), roof
 rat(Rattus rattuscomplex, RrC), lesser bandicoot rat (Bandicota
 bengalensis), and house mouse(Mus musculus) using the recently
 developed time-dependent evolutionary rates of mtDNA.
 The Cytbsequences of RrC from Myanmar were shown to belong to RrC
 Lineage II, and their level of genetic diversity was relatively high
 compared to those of the other three species. RrC was found to have
 experienced bottleneck and rapid expansion events at least twice in the
 late Pleistocene period in Myanmar and a nearby region. Accordingly,
 paleoclimatic environmental fluctuations were shown to be an important
 factor affecting rodents in the subtropics of the Indo-Malayan region. Our
 results show that human activities during the last 10,000 years of the
 Holocene period affected the population dynamics of the rodent species
 examined, including introducing them to Myanmar from neighboring
 countries. Further study of these four commensal rodents in other
 geographic areas of the Indo-Malayan region would allow us to better
 understand the factors that drove their evolution and their ecological
 trends.
description: Sample collection in Myanmar was conducted mainly by staff members of the Department of Zoology, University of Yangon from 2013 to 2018. For this study, 35 individuals of <i>Rattus exulans</i>, 13 individuals of RrC, and 4 individuals of<i>M. musculus</i> were collected and subjected to molecular analysis.  DNA was extracted from the liver tissue from each individual using a Qiagen DNA Isolation kit (Hilden, Germany) following the manufacturer’s protocol. Sequence determination was performed for <i>Cytb</i> (1,034–1,140 bp) in accordance with a method described previously (Suzuki et al. 2015). The gene region was amplified through polymerase chain reaction (PCR) using the following protocol: 95°C for 10 min, followed by 30 cycles of 95°C for 30 s, 50°C for 30 s, and 60°C for 60 s, and finally, 72°C for 7 min. PCR products were sequenced using a PRISM Ready Reaction Dye DeoxyTerminator Cycle Sequencing kit Ver 3.1 and an ABI 3500 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA). The nucleotide sequences reported in the present study appear in the DDBJ, EMBL, and GenBank nucleotide sequence databases under accession numbers LC510767–LC510818.  Long (1,034 bp) and short (381 bp) <i>Cytb </i>sequences<i> </i>of <i>R. exulans </i>were obtained from databases and used for phylogenetic inference based on datasets of the MSEA and MSEA plus ISEA haplotypes. Database sequences of RrC (1,140 bp, 1,034 bp) were used in this study. We obtained 24 <i>Cytb</i> sequences of <i>B. bengalensis</i> (1,026 bp, 1,140 bp) from the databases, 23 of which were collected from Myanmar (MK654761–MK654784) and one from Pakistan (AM408336). <i>Cytb</i> sequences of <i>M. musculus</i> from Myanmar were obtained from databases (LC426295–LC426303).
description: <strong>The repository consists of 11 files used in this
 study, in addition to the readme file. </strong>
 <em><strong>Rattus
 exulans</strong></em> 
 #1_MEGA_Rexulans_MgMg.meg   52.16 kB. This file is the MEGA file
 including the Cytb sequences of <em>Rattus exulans</em> (1034
 bp). The data were used in construting the ML tree shown in Figure
 2a.  #1a_Arlequin_Rexulans_n42.nex   46.30 kB. This
 file is the nexus file including the Cytb sequences of <em>Rattus
 exulans</em> (1034 bp). The data were used in construting the MJ
 network (Figure 3a, "1,034 bp") and the analyses with Arlequin
 (Table 2).  #1b_Arlequin_Rexulans_381bp_n34.nex  
 14.10 kB. This file is the nexus file including the <em>Cytb
 </em>sequences of <em>Rattus exulans</em> (381 bp). The
 data were used in construting the betwork (Figure 3a, "381 bp")
 and the analyses with Arlequin (Table 2).  
 <strong><em>Rattus rattus </em>complex, Lineage
 II</strong> 
 #2_MEGA_RrC_Lineage_II_MgMG.meg   39.56 kB.  This file is the
 MEGA file including the<em> Cytb</em> sequences of
 <em>Rattus rattus </em>complex (Lineage II, 1140 bp). The data
 were used in construting the ML tree shown in Figure 2b. 
 #2a_Arlequin_RrC_II_n25.nex   30.12 kB. This file is the
 nexus file including the <em>Cytb</em> sequences of
 <em>Rattus rattus </em>complex<em> </em>(Lineage
 II, 1140 bp). The data were used in construting the MJ network (Figure 3b)
 and the analyses with Arlequin (Table 2). 
 #2b_Arlequin_RrC_n21nex   25.35 kB. This file is the nexus file
 including the <em>Cytb</em> sequences of <em>Rattus
 exulans</em> (1140 bp). The data were used in the analyses with
 Arlequin (Table 2).  
 <b><i>Bandicota
 bengalensis</i></b> 
 #3_Arlequin_Bbengalensis_n23.nex   24.94 kB. This file is the
 nexus file including the <em>Cytb</em> sequences of
 <i>Bandicota bengalensis </i>(1026 bp). The data were used in
 construting the MJ network (Figure 3c) and the analyses with Arlequin
 (Table 2).  #3_MEGA_Bbengalensiis_MgMg.meg   27.33
 kB. This file is the MEGA file including the <em>Cytb</em>
 sequences of <i>Bandicota bengalensis </i>(1026 bp). The data
 were used in construting the ML tree shown in Figure 2c. 
 <strong><em>Mus musculus
 castaneus</em>, CAS-1</strong> 
 #4_MEGA_CAS1.meg   34.72 kB. This file is the MEGA file
 including the <em>Cytb</em> sequences of <i>Mus
 musculus</i> <em>castaneus</em> (CAS-1, 1140 bp). The
 data were used in construting the ML tree shown in Figure 2d. 
 #4a_Arlequin_CAS1_1140bp_n23.nex   28.06 kB. This file is the
 nexus file including the <em>Cytb</em> sequences of
 <i>Mus musculus</i> <em>castaneus</em> (CAS-1,
 1140 bp). The data were used in construting the MJ network (Figure 3d) and
 the analyses with Arlequin (Table 2). 
 #4b_Arlequin_CAS1_MyanmarImphal_n19.nex   23.22 kB. This file is
 the nexus file including the <em>Cytb</em> sequences of
 <i>Mus musculus</i> <em>castaneus</em> (CAS-1,
 1140 bp). The data were used in analyses with Arlequin (Table 2).