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.