DOI: 10.5061/dryad.d2547d87h
title: Data from: Hybridization and its impact on the ontogenetic allometry of skulls in macaques

description: The importance of hybridization in morphological diversification is a
 fundamental topic in evolutionary biology. However, despite accumulated
 knowledge concerning adult hybrid variations, how hybridization affects
 ontogenetic allometry is less well understood. Herein, we assessed the
 effects of hybridization on the postnatal ontogenetic allometry in skulls
 of a putative hybrid population of introduced Taiwanese macaques (Macaca
 cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses
 indicated that the population consisted of individuals with various
 degrees of admixture, formed by male migration of Japanese to Taiwanese
 macaques. No marked ontogenetic trajectory angle dissociation was observed
 in the overall skull shape of hybrids. Transgressive variations in the
 overall skull shape were observed mainly in non-allometric components.
 Hybridization collapsed an unknown mechanism found in Japanese macaques
 that restricts the growth rate of the maxillary sinus (the hollow space in
 the face), producing hybrids with a mosaic pattern, i.e., the maxillary
 sinus is as large as that in Taiwanese macaques, although the overall
 skull shape is intermediate. Our findings suggest that the transgressive
 variations can be caused by prenatal shape modifications and the lifting
 of the genetic restriction on the regional growth rate, highlighting the
 complex genetic and ontogenetic bases underlying hybridization-induced
 morphological diversification.
description: This study investigated the genetic and morphological variation
 of <em>Macaca cyclopis</em>, <em>M. fuscata</em>
 and their hybrids. Genetic variation was assessed using single nucleotide
 polymorphisms obtained by double-digested restriction site-associated DNA
 sequencing. Morphological variation was assessed using landmark-based
 geometric morphometrics. See the README and related paper for
 details.
description: The files are in text format and are accessible from R or any
 text editor.
description: # Data from: Hybridization and its impact on the ontogenetic allometry of
 skulls in macaques --- This dataset contains genomic variant data and
 landmark-based shape data from <i>Macaca cyclopis</i>,
 <i>M. fuscata</i> and their hybrids, and the statistical
 output from them. ## Description of the data and file structure This
 dataset consists of an R script, a data sheet, and five zip-archived
 directories containing some data files as follows. See the related paper
 for details. ### calc\_mismatch\_bias.R R script to compute
 "mismatch" and "bias", which evaluate transgressive
 segregation, based on the Procrustes distance. This script uses the R
 package "shapes" (Dryden 2023). ### data.csv Main data sheet
 with the following columns. NA indicates not applicable, not collected, or
 filtered for low quality prior to analysis. Note that some individuals
 lack morphological data, while others lack genetic data. Species are
 unknown prior to the analyses for the individuals in the Oike area and are
 indicated here as NA; see hybrid_class or hybrid_class_ed for the hybrid
 class identification of them. The five discordant samples have been
 filtered out. This data sheet includes all other screened samples,
 including captive samples and samples of unknown origin (referenced in the
 "environment" column), but only wild samples were used in the
 main analyses because small but significant shape differences were found
 between them. 1. morph_id: Identifier for morphological data. The acronym
 indicates the institution where the specimens are housed. PRI: Primate
 Research Institute, Kyoto University (now Center for the Evolutionary
 Origins of Human Behavior, Kyoto University) (Inuyama, JAPAN). JMC: Japan
 Monkey Centre (Inuyama, JAPAN). 2. genetic_id: identifier for genetic data
 3. sex 4. dental_satge: dental eruption-cranial suture stage 5.
 developmental_stage 6. species: Species name identified prior to this
 study. Note that individuals from the Oike region (some of which were
 identified as <i>M. cyclopis</i> in this study) are considered
 missing values here. 7. locality 8. environment 9. mtdna: Mitochondrial
 DNA ancestry 10. y: Y-chromosome ancestry 11. hybrid_class: Hybrid classes
 estimated by NewHybrids analysis, with some ambiguous data treated as
 missing. 12. hybrid_class2: The pure <i>M. cyclopis</i> and
 <i>M. fuscata</i> from other localities are added to the
 hybrid_class. 13. hybrid_index 14. interspecific_heterozygosity 15.
 admixture_a: Admixture Q score (K = 2) for autosomes 16. admixture_x:
 Admixture Q score (K = 2) for X-chromosomes 17. PC1_genetic: PC1 for
 autosomal single nucleotide polymorphisms (SNPs). 18. PC2_genetic: PC2 for
 autosomal SNPs. ### landmark\_raw Raw landmark coordinates of the cranium,
 mandible, and maxillary sinus (before estimating missing landmarks and
 Procrustes fitting). They were recorded twice by a single observer. Some
 of them with some degree of missing landmarks were filtered out before the
 main analyses. Each of the three regions was measured twice, resulting in
 six files. ### newhybrids Input data for NewHybrids. ### pca\_morph
 Results of PCA on shape data. Both sexes are analyzed together. ###
 stats\_morph Data from statistical analyses of shape data, where each sex
 was analyzed separately. 1. morph_id. 2. pred_line: PC1 for fitted values
 in multivariate regression. 3. reg_score: Regression score in multivariate
 regression 4. PC1_pta: PC1 for fitted values in phenotypic trajectory
 analysis 5. PC2_pta: PC2 for fitted values in phenotypic trajectory
 analysis 6. bgPC1: PC1 of the between-groups PCA, where the interspecific
 difference was detected and then admixed individuals were projected on the
 axis, for adult samples. ### symshape\_cs Centroid size (CS), natural
 logarithm transformed CS (lnCS), and symmetric shape component used for
 the statistical analyses. Prior to this, missing landmarks were imputed,
 generalized Procrustes analysis was performed, and means were calculated.
 ### vcf SNP data in vcf format of autosomes, X chromosomes and Y
 chromosomes genotyped with STACKS and filtered with PLINK. Since STACKS
 provides diploid genotypes, those on the sex chromosomes of males were
 converted to haploid.