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Data from: Late Quaternary environmental and human impacts on the mitochondrial DNA diversity of four commensal rodents in Myanmar

Citation

Suzuki, Hitoshi (2020), Data from: Late Quaternary environmental and human impacts on the mitochondrial DNA diversity of four commensal rodents in Myanmar, Dryad, Dataset, https://doi.org/10.5061/dryad.7pvmcvdqm

Abstract

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.

Methods

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 Rattus exulans, 13 individuals of RrC, and 4 individuals ofM. musculus 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 Cytb (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 LC510767LC510818

Long (1,034 bp) and short (381 bp) Cytb sequences of R. exulans 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 Cytb sequences of B. bengalensis (1,026 bp, 1,140 bp) from the databases, 23 of which were collected from Myanmar (MK654761–MK654784) and one from Pakistan (AM408336). Cytb sequences of M. musculus from Myanmar were obtained from databases (LC426295–LC426303).

Usage Notes

The repository consists of 11 files used in this study, in addition to the readme file. 

Rattus exulans

  • #1_MEGA_Rexulans_MgMg.meg   52.16 kB. This file is the MEGA file including the Cytb sequences of Rattus exulans (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 Rattus exulans (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 Cytb sequences of Rattus exulans (381 bp). The data were used in construting the betwork (Figure 3a, "381 bp") and the analyses with Arlequin (Table 2). 

Rattus rattus complex, Lineage II

  • #2_MEGA_RrC_Lineage_II_MgMG.meg   39.56 kB.  This file is the MEGA file including the Cytb sequences of Rattus rattus 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 Cytb sequences of Rattus rattus complex (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 Cytb sequences of Rattus exulans (1140 bp). The data were used in the analyses with Arlequin (Table 2). 

Bandicota bengalensis

  • #3_Arlequin_Bbengalensis_n23.nex   24.94 kB. This file is the nexus file including the Cytb sequences of Bandicota bengalensis (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 Cytb sequences of Bandicota bengalensis (1026 bp). The data were used in construting the ML tree shown in Figure 2c. 

Mus musculus castaneus, CAS-1

  • #4_MEGA_CAS1.meg   34.72 kB. This file is the MEGA file including the Cytb sequences of Mus musculus castaneus (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 Cytb sequences of Mus musculus castaneus (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 Cytb sequences of Mus musculus castaneus (CAS-1, 1140 bp). The data were used in analyses with Arlequin (Table 2).