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SNP genotyping of Lord Howe woodhen (Hypotaenidia sylvestris) from museum skins and contemporary blood samples

Citation

Major, Richard et al. (2020), SNP genotyping of Lord Howe woodhen (Hypotaenidia sylvestris) from museum skins and contemporary blood samples, Dryad, Dataset, https://doi.org/10.5061/dryad.63xsj3v07

Abstract

These data are from a conservation genetics project investigating population structure, dispersal and genetic bottlenecks in the Lord Howe woodhen Hypotaenidia sylvestris. This species recovered from near extinction in the 1970s to approximately 250 individuals in 2017. We used single nucleotide polymorphisms (SNPs) to genotype samples of both the contemporary population and 100-year-old museum specimens. We discovered strong population structuring between mountain and lowland "subpopulations" in both the contemporary and historic populations. This is indicative of restricted dispersal at fine spatial scales associated with rugged topography. There was also a decline in genetic diversity over the past century. We recommend ongoing genetic monitoring and translocations to increase genetic diversity within the re-established lowland subpopulation which although numerically stronger is genetically depleted relative to the mountain subpopulation.

Methods

DNA was extracted from blood samples taken from 67 wild-caught and released woodhens in 2017, and from 54 toepad biopsies from museum skins.  DNA was supplied  to Diversity Arrays Technology (DArT) for analysis using their proprietary restriction-enzyme-based genome complexity reduction technology, termed DArTseq™. Complete methods are provided in the paper published in Animal Conservation.

Usage Notes

The datset comprises three self-explanatory files consisting of  (1) species identifiers, (2) metadata for SNP genotyping file, (3) main SNP genotyping file.

1) individual_woodhen_identifiers_for_Report_DGall18-3372_1_moreOrders_SNP_singlerow_1.csv

This file lists the individual identifiers referenced in the other two files and includes sampling locations and dates.

 

2) metadata_for_Report_DGall18-3372_1_moreOrders_SNP_singlerow_1.csv

This file provides the metadata for the main SNP genotyping file with crossreference to the identifiers in File 1.

 

3) Report_DGall18-3372_1_moreOrders_SNP_singlerow_1.csv

This file is the main datafile comprised of the SNP genotyping.

 

Please note that while the paper only considered SNPs with a >95% call rate, the submitted datset includes all SNPs with a call rate of 70% or greater (6382 SNPs). Thus the 1458 SNPs analysed in the paper are listed at the top of  File 3 (ordered on the column "CallRate").

Funding

Australian Museum Foundation