DOI: 10.5061/dryad.tdz08kq8x
title: VCF from: Genetic evidence of female philopatry in a socially polyandrous shorebird

description: Sex-biased dispersal plays a key role in shaping population dynamics and
 genetic structure. Two main hypotheses have been proposed for how
 territoriality and mating competition impact sex-biased dispersal.
 Female-biased dispersal is expected in monogamous systems with male
 resource defense, whereas male-biased dispersal is expected in polygynous
 systems with male competition over mates. However, patterns of sex-biased
 dispersal in socially polyandrous species, where females compete for both
 territories and mates, remain poorly understood. We investigated
 sex-biased dispersal in two polyandrous Jacana species across Central
 America, the Northern Jacana (Jacana spinosa) and Wattled Jacana (J.
 jacana), which exhibit intense female-female competition for territories
 and mates and differ in the strength of sexual selection. We analyzed
 sex-biased dispersal by assessing genetic differentiation and individual
 assignment indices to determine the probability of an individual being a
 recent immigrant or philopatric in relation to its sampling location. Our
 findings reveal strong male-biased dispersal in Northern Jacanas,
 indicated by higher genetic structuring and philopatry in females. In
 contrast, Wattled Jacanas showed no significant dispersal bias between
 sexes. Furthermore, sexually selected traits in Northern Jacana females,
 such as larger body mass and wing spur length, were associated with
 philopatry, suggesting that larger females retain territories, whereas
 smaller females disperse. To our knowledge, this is the first genetic
 evidence of male-biased dispersal in a polyandrous species. Our findings
 reveal that sexually selected traits, in addition to territorial and mate
 competition, are important for understanding species and sex differences
 in dispersal evolution.
description: # VCF from: Genetic evidence of female philopatry in a socially
 polyandrous shorebird Dataset DOI:
 [10.5061/dryad.tdz08kq8x](10.5061/dryad.tdz08kq8x) ## Description of the
 data and file structure We used genotype-by-sequencing for 271 Northern
 and Wattled Jacana samples from 15 localities in Costa Rica and Panama.
 Raw sequences were filtered and aligned to a Northern Jacana Hi-C
 reference genome using Stacks, BWA, and Samtools. A SNP catalog was
 generated, and putative hybrids were excluded to avoid confounding
 effects. Attempts to identify uniparental markers were limited by the
 sequencing approach, yielding few W-linked SNPs and no mitochondrial DNA.
 After excluding sex-linked scaffolds, we created four VCF files (males and
 females per species) and applied filtering for allele frequency, linkage
 disequilibrium, indels, and missing data. ### Files and variables ####
 File: jacana\_jacana\_female.recode.vcf **Description:** Filtered VCF
 containing biallelic SNPs with a minor allele frequency of 0.05, a maximum
 of 10% missing data, and indels removed. A minimum depth coverage of 3 was
 applied to 33 female *Jacana jacana* samples. The final dataset includes
 4,418 SNPs with a genotyping rate of 0.93. Scaffolds linked to sex
 chromosomes were excluded. #### File: jacana\_jacana\_male.recode.vcf
 **Description:** Filtered VCF containing biallelic SNPs with a minor
 allele frequency of 0.05, a maximum of 10% missing data, and indels
 removed. A minimum depth coverage of 3 was applied to 63 female *Jacana
 jacana* samples. The final dataset includes 9,413 SNPs with a genotyping
 rate of 0.94. Scaffolds linked to sex chromosomes were excluded. ####
 File: jacana\_spinosa.recode.vcf **Description:** Filtered VCF containing
 biallelic SNPs with a minor allele frequency of 0.05, a maximum of 10%
 missing data, and indels removed. A minimum depth coverage of 3 was
 applied to 115 *Jacana spinosa* (males and females)* *samples. The final
 dataset includes 2,291 SNPs with a genotyping rate of 0.93. Scaffolds
 linked to sex chromosomes were excluded. #### File:
 jacana\_jacana.recode.vcf **Description:** Filtered VCF containing
 biallelic SNPs with a minor allele frequency of 0.05, a maximum of 10%
 missing data, and indels removed. A minimum depth coverage of 3 was
 applied to 103 *Jacana jacana *(males and females)* *samples. The final
 dataset includes 5,548 SNPs with a genotyping rate of 0.93. Scaffolds
 linked to sex chromosomes were excluded. #### File:
 jacana\_spinosa\_female.recode.vcf **Description:** Filtered VCF
 containing biallelic SNPs with a minor allele frequency of 0.05, a maximum
 of 10% missing data, and indels removed. A minimum depth coverage of 3 was
 applied to 31 female *Jacana spinosa* samples. The final dataset includes
 8,333 SNPs with a genotyping rate of 0.93. Scaffolds linked to sex
 chromosomes were excluded. #### File: jacana\_spinosa\_male.recode.vcf
 **Description:** Filtered VCF containing biallelic SNPs with a minor
 allele frequency of 0.05, a maximum of 10% missing data, and indels
 removed. A minimum depth coverage of 3 was applied to 78 male *Jacana
 spinosa* samples. The final dataset includes 5,151 SNPs with a genotyping
 rate of 0.93. Scaffolds linked to sex chromosomes were excluded. ##
 Code/software * Stacks v2.68 (modules: process_radtags, gstacks,
 populations) * BWA v0.7.18 * Samtools v1.21 * VCFtools v4.2 ## Access
 information Other publicly accessible locations of the data: * These
 sequencing data are currently deposited on NCBI. * BioProject PRJNA494934:
 [https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA494934](https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA494934) Data was derived from the following sources: * The data was derived from the following sequencing project deposited on NCBI - BioProject PRJNA494934 and BioSamples SAMN10185940-SAMN10186205