DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
Data files
Nov 13, 2023 version files 57.28 KB
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ES2_cyt_b.FASTA
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ES2_ND2.FASTA
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ES3_Cyt_b.FASTA
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ES3_ND2.FASTA
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F5_cyt_b.FASTA
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F5_ND2.FASTA
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G11_cyt_b.FASTA
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G11_ND2.FASTA
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M1_cyt_b.FASTA
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M1_ND2.FASTA
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M10_cyt_b.FASTA
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M10_ND2.FASTA
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M107_CYT_B.FASTA
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M107_ND2.FASTA
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M108_CYT_B.FASTA
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M108_ND2.FASTA
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M110_CYT_B.FASTA
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M110_ND2.FASTA
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M111_CYT_B.FASTA
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M111_ND2.FASTA
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M116_CYT_B.FASTA
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M116_ND2.FASTA
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M12_CYT_B.FASTA
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M12_ND2.FASTA
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M18_CYT_B.FASTA
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M18_ND2.FASTA
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M21_CYT_B.FASTA
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M21_ND2.FASTA
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M36_CYT_B.FASTA
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M36_ND2.FASTA
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M45_CYT_B.FASTA
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M45_ND2.FASTA
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M5_cyt_b.FASTA
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M5_ND2.FASTA
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M55_CYT_B.FASTA
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M55_ND2.FASTA
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M64_CYT_B.FASTA
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M64_ND2.FASTA
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P22_CYT_B.FASTA
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P22_ND2.FASTA
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P28_CYT_B.FASTA
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P28_ND2.FASTA
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P31_CYT_B.FASTA
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P31_ND2.FASTA
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P34_CYT_B.FASTA
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P34_ND2.FASTA
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P39_CYT_B.FASTA
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P39_ND2.FASTA
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P40_CYT_B.FASTA
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P40_ND2.FASTA
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P45_CYT_B.FASTA
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P45_ND2.FASTA
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P46_CYT_B.FASTA
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P46_ND2.FASTA
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P5_CYT_B.FASTA
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P5_ND2.FASTA
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P6_CYT_B.FASTA
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P6_ND2.FASTA
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README.md
Abstract
As an island endemic with a decreasing population, the Critically Endangered Grenada Dove Leptotila wellsi is threatened by accelerated loss of genetic diversity resulting from ongoing habitat fragmentation. Small, threatened populations are difficult to sample directly but advances in molecular methods mean that non-invasive samples can be used. We performed the first assessment of genetic diversity of populations of Grenada Dove by a) assessing mtDNA genetic diversity in the only two areas of occupancy on Grenada, b) defining the number of haplotypes present at each site and c) evaluating evidence of isolation between sites. We used non-invasively collected samples from two locations: Mt Hartman (n=18) and Perseverance (n=12). DNA extraction and PCR were used to amplify 1,751 bps of mtDNA from two mitochondrial markers: NADH dehydrogenase 2 (ND2) and Cytochrome b (Cyt b). Haplotype diversity (h) of 0.4, a nucleotide diversity (π) of 0.00023 and two unique haplotypes were identified within the ND2 sequences; a single haplotype was identified within the Cyt b sequences. Of the two haplotypes identified; the most common haplotype (haplotype A = 73.9%) was observed at both sites and the other (haplotype B = 26.1%) was unique to Perseverance. Our results show low mitochondrial genetic diversity and clear evidence for genetically isolated populations. The Grenada Dove needs urgent conservation action, including habitat protection and potential augmentation of gene flow by translocation in order to increase genetic resilience and diversity with the ultimate aim of securing the long-term survival of this Critically Endangered species.
README: DNA sequence data generated using non-invasive feather and eggshell samples from the Grenada Dove for two gene regions: Cyt b and ND2
https://doi.org/10.5061/dryad.dv41ns252
This data set contains DNA sequence data generated for the Grenada Dove in FASTA file format.
Description of the data and file structure
Data are provided for each sample and each gene region in separate FASTA files and are named as follows: SAMPLE_NAME_ GENE_REGION.FASTA
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Methods
DNA extraction was carried out with the QIAGEN DNeasy® Blood and Tissue kit (QIAGEN Inc., Crawley) using the optimised protocol outlined in Peters et al. (2019). PCR was used to amplify mitochondrial markers: ND2 and Cyt b using primers and cycling parameters outlined in Peters et al. (2022). Samples were prepared and submitted to Eurofins Genomics following the Mix2Seq kit (Eurofins Genomics, Luxembourg) instructions for sequencing using Sanger sequencing methods. Sequence assembly was performed using Sequencher 5.4.6 (Gene Codes Corporation 2017).