VCF from: Genetic evidence of female philopatry in a socially polyandrous shorebird
Data files
Apr 04, 2025 version files 67.25 MB
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jacana_jacana_female.recode.vcf
4.52 MB
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jacana_jacana_male.recode.vcf
17.88 MB
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jacana_jacana.recode.vcf
16.98 MB
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jacana_spinosa_female.recode.vcf
8.05 MB
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jacana_spinosa_male.recode.vcf
12 MB
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jacana_spinosa.recode.vcf
7.81 MB
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README.md
3.88 KB
Abstract
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.
Dataset DOI: 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
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