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Mantel and partial Mantel test data and scripts of mimetic evolution of Papilio polytes in the Ryukyu Islands, Japan

Citation

Sato, Yukuto; Tatsuta, Haruki; Tsurui-Sato, Kaori; Tsuji, Kazuki (2020), Mantel and partial Mantel test data and scripts of mimetic evolution of Papilio polytes in the Ryukyu Islands, Japan, Dryad, Dataset, https://doi.org/10.5061/dryad.p8cz8w9ns

Abstract

Batesian mimicry is a striking example of Darwinian evolution, and the swallowtail butterfly Papilio polytes exhibits Batesian mimicry polymorphism. These P. polytes populations show various mimic ratios among the Ryukyu Islands in Japan. We conducted Mantel and partial Mantel tests regarding the possible relationship among the mimic ratio differences, geographic distances, and average genetic distances among five islands of the Ryukyus based on 259 single nucleotide polymorphisms (SNPs) from 93 individuals.

Methods

Average genetic distances were estimated on the basis of 259 SNPs analysis for 93 individuals determined by inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and the software package Stacks with the parameters of minimum coverage depth of respective loci, maximum number of mismatched bases among alleles, and maximum number of mismatch bases among alleles from other individuals set to 4, 3, and 3, respectively. The Nei's net number of nucleotide differences DA was estimated using MEGA 7 version 7.0.14 (Kumar et al. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874) as average genetic distances. The definition of mimic ratio (MR) is relative abundance of the mimetic individual among all individuals sampled by the field survey described in the Tsurui-Sato et al., 2019, Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan, Ecology and Evolution, 9(10), 5991-6002. Geographic distances were in kilometers between the centers of sampling regions (i.e., city hall or downtown area) of each island except for the Okinawa Island, for which the location of the Nakijin village office was used because the butterflies were collected in the Nakijin region in the northern Okinawa Island. All of the measurement methods of additional indices in the data file including advantage index (AI), AI[Uesugi], average genetic distances based on the mitochondrial gene sequneces, and environmental distances were described in the Tsurui-Sato et al. (2019) mentioned above. 

Usage Notes

The Mantel test input files (with the file extension 'arp') can be executed by the program Arlequin (Excoffier and Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564-567). The outputfiles including results presented in the manuscript are also attached as text files. The partial Mantel test program (with the file extension 'R.txt') can be executed by R Console (R Core Team. 2017. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Retrieved from https://www.R-project.org). This file includes data of Mantel and partial Mantel tests of the present manuscript and the related publication Tsurui-Sato et al. 2019 (Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic Papilio polytes in multiple islands in the Ryukyus, Japan, Ecology and Evolution, 9(10), 5991-6002).

Funding

University of the Ryukyus, Award: 16SP01302