DOI: 10.5061/dryad.p8cz8w9ns
title: Mantel and partial Mantel test data and scripts of mimetic evolution of Papilio polytes in the Ryukyu Islands, Japan

description: 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.
description: 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
 <em>D</em><sub>A</sub> was estimated using MEGA 7
 version 7.0.14 (Kumar <em>et al</em>. 2016. MEGA7: molecular
 evolutionary genetics analysis version 7.0 for bigger datasets.
 <i>Molecular Biology and Evolution, </i>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 <em>et al</em>.,
 2019, Evidence for frequency-dependent selection maintaining polymorphism
 in the Batesian mimic <em>Papilio polytes</em> in multiple
 islands in the Ryukyus, Japan, <em>Ecology and Evolution</em>,
 9(10), 5991-6002. Geographic distances were in kilometers between the
 centers of sampling regions (<em>i.e.</em>, 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<sub>[Uesugi]</sub>, average
 genetic distances based on the mitochondrial gene sequneces, and
 environmental distances were described in the Tsurui-Sato <em>et
 al</em>. (2019) mentioned above. 
description: 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. <i>Molecular
 Ecology Resources,</i> 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. <em>R Foundation for
 Statistical Computing</em>, 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 <em>et al</em>. 2019 (Evidence for
 frequency-dependent selection maintaining polymorphism in the Batesian
 mimic <em>Papilio polytes</em> in multiple islands in the
 Ryukyus, Japan, <em>Ecology and Evolution</em>, 9(10),
 5991-6002).