DOI: 10.5061/dryad.fbg79cntk
title: Data for: The Sela macaque (Macaca selai) is a distinct phylogenetic species that evolved from the Arunachal macaque following allopatric speciation

description: Arunachal macaque (Macaca munzala) is an endangered and recently
 discovered cercopithecine primate from Western Arunachal Pradesh, India.
 On genetic analyses of Arunachal macaques, we observed spatially
 distributed substantial inter-species genetic divergence. The results
 suggested that the Arunachal macaque evolved into two phylogenetic species
 about 1.96 mya following allopatric speciation using the Sela mountain
 pass in Arunachal Pradesh, India. We describe - the Sela macaque (M.
 selai) as a new macaque species that interestingly exhibited high
 intra-specific genetic variation and also harbors at least two
 conservation units. Further, we report the past demographic trajectories
 and quantify the genetic variation required for taxonomic clarification.
 The present study also identifies gap areas for undertaking surveys to
 document the relic and unknown transboundary populations of macaques
 through multinational, multi-lateral cross-border collaboration.
description: Study area and sample collection We carried
 out opportunistic field surveys in the Tawang and West Kameng districts of
 Arunachal Pradesh from 2018 to 2020 and collected 65 faecal samples of
 Arunachal macaque with due permission obtained from the forest
 department. DNA extraction and PCR
 amplification We extracted genomic DNA using the
 QIAamp Fast DNA Stool Mini Kit (QIAGEN, Germany) following the
 manufacturer’s instructions. For species identification, we sequenced
 partial fragments of mitochondrial d-loop and cytochrome b gene following
 Li and Zhang (2005 and 2004). We put independent PCRs in a 10 μl reaction
 that comprised 20-30 ng of template DNA, 0.5U Taq polymerase, 1X PCR
 buffer, 2.5mM MgCl<sub>2</sub>, 1mM dNTPs mix, 0.1 µM of each
 primer, 0.1 µg/µL BSA on Veriti thermal cycler (Applied Biosystems, USA).
 Thermal cycling conditions were: initial denaturation at 94°C for 5 min,
 followed by 35 cycles at 94°C for 30 s, 50°C for 45 s and 72°C for 1 min.
 The final extension was at 72°C for 10 min. Sanger sequencing was
 performed on an ABI 3730 Genetic analyzer (Applied Biosystems, USA) using
 Big-Dye Terminator Cycle Sequencing Kit version 3.1 (Thermo Scientific,
 USA). Microsatellite genotyping We
 amplified ten nuclear polymorphic microsatellite loci
 <em>i.e.</em> D01S548, D05S1457, D06S1768, D06S501, D08S1106,
 D19S255, D22S685, D04S2365, D11S2002, D13S765 (Kanthaswamy et al., 2006)in
 four multiplex PCRs (Table A.1). The fluorescent based genotyping was
 performed in triplicate reactions using Multiplex PCR Kit (QIAGEN,
 Germany) following manufacturer’s instructions. The PCR conditions were:
 initial denaturation at 95° C for 15 min, followed by 40 cycles of PCR
 (denaturation at 95° C for 30 s, annealing at a specific temperature for 1
 minute, and extension at 72° C for 45 s) with a final step of 72° C for 30
 min. The resultant products were electrophoresed on ABI 3730 Genetic
 analyzer (Applied Biosystems, USA) and allele scoring was done using Gene
 Mapper V. 4.1 (Applied Biosystems, USA). Sequencing of
 the mitochondrial gene For species identification, we
 sequenced partial fragments of mitochondrial d-loop and cytochrome b gene
 following Li and Zhang (2005 and 2004). We put independent PCRs in a 10 μl
 reaction that comprised 20-30 ng of template DNA, 0.5U Taq polymerase, 1X
 PCR buffer, 2.5mM MgCl<sub>2</sub>, 1mM dNTPs mix, 0.1 µM of
 each primer, 0.1 µg/µL BSA on Veriti thermal cycler (Applied Biosystems,
 USA). Thermal cycling conditions were: initial denaturation at 94°C for 5
 min, followed by 35 cycles at 94°C for 30 s, 50°C for 45 s and 72°C for 1
 min. The final extension was at 72°C for 10 min. Sanger sequencing was
 performed on an ABI 3730 Genetic analyzer (Applied Biosystems, USA) using
 Big-Dye Terminator Cycle Sequencing Kit version 3.1 (Thermo Scientific,
 USA).  We validated sequences using Sequencher v5.4.6
 (Gene Codes Corporation, USA) and also mined the complementary d-loop and
 cytochrome b sequences of ‘sinica’ group of macaques from NCBI/GenBank
 (Table A.2). We aligned all sequences using ClustalW algorithm (Thompson
 et al., 2003) as implemented in MEGA X (Kumar et al., 2018). Since only a
 few sequences of cytochrome b were available on NCBI, we used these
 sequences in drawing phylogenetic inferences, and, all other population
 genetics analyses were carried out with d-loop data.
description: # Data for: The Sela macaque (*Macaca selai*) is a distinct phylogenetic
 species that evolved from the Arunachal macaque following allopatric
 speciation
 [https://doi.org/10.5061/dryad.fbg79cntk](https://doi.org/10.5061/dryad.fbg79cntk) Allelic data of microsatellites and aligned sequences of d-loop as well as concatenated sequences of d-loop and cytochrome b. ## Description of the data and file structure The Excel file contains information for 6 microsatellites. The combined tree and Macaca d-loop phylogeny fasta files are included. ## Sharing/Access information NA ## Code/Software NA