DOI: 10.5061/dryad.wstqjq2z4
title: Data from: Genetic differentiation in a wide-ranging tropical seabird in the Indian Ocean is linked with oceanographic factors

description: Knowledge of the main drivers of population differentiation is crucial for
 understanding evolutionary processes and preserving biodiversity. While
 primarily studied in terrestrial habitats, the mechanisms operating in the
 marine realm are less well understood. This study reconstructed the
 phylogeographic history of a tropical seabird to identify relevant marine
 barriers promoting intraspecific diversity in the Western Indian Ocean.
 Three subspecies of tropical shearwater: Puffinus bailloni bailloni, P. b.
 *nicolae, P. b. colstoni. *We used restriction site-associated DNA
 sequencing and applied population genomics to birds from six breeding
 colonies to assess intraspecific diversity, population genetic structure,
 and connectivity in the tropical shearwater. Results were complemented
 with data from six oceanographic variables and effective migration
 surfaces to evaluate the role of oceanographic factors in driving
 population differentiation. All analyses consistently separated the birds
 from the northern colonies (subsp. nicolae and colstoni) from those of the
 southern islands (subsp. bailloni), but failed to assign the colstoni
 birds as a different taxon. Results revealed remarkable levels of genetic
 differentiation within an ocean basin in a highly vagile species, and
 suggested higher levels of gene flow at the northern limit of the species’
 distribution compared to the southern range. Our study suggests that ocean
 surfaces and sea surface temperature may constitute an important barrier
 to gene flow for the tropical shearwater, and potentially other marine
 species in the region. This study does not support the colstoni form as a
 different subspecies, highlighting the need for further taxonomic
 reassessment. Ultimately, the results allowed us to identify Europa and
 Aldabra as the most threatened management units and propose conservation
 strategies directly applicable to these most at-risk colonies.
description: Single Nucleotide Polymorphism (SNP) genotyping was carried out
 by Diversity Arrays Technology (DarT Pty Ltd, Canberra) using the DArTseq
 protocol. DArT library was prepared using DNA from 90 birds and the
 restriction enzymes <em>PstI</em> and
 <em>SphI</em>. Loci were mapped to the genome assembly of the
 <em>Puffinus mauretanicus</em> (family Procellariidae; ASM2333356v1). The raw DArTseq data (78,676 SNPs) were filtered by the authors using the “dartRverse” package (<strong>ingroup dataset</strong>). The tropical shearwater dataset was additionally co-analyzed with generated Mascarene Petrel sequences to include a suitable outgroup for complementary analyses (<strong>outgroup dataset</strong>). Specimen metadata was collected during fieldwork.
description: # Data from: Genetic differentiation in a wide-ranging tropical seabird in
 the Indian Ocean is linked with oceanographic factors Dataset DOI:
 [10.5061/dryad.wstqjq2z4](10.5061/dryad.wstqjq2z4) ## Description of the
 data and file structure This README file was generated by Helena Teixeira.
 **GENERAL INFORMATION** 1. Title of Dataset: Data from: Genetic
 differentiation in a wide-ranging tropical seabird in the Indian Ocean is
 linked with oceanographic factors 1. Corresponding author Information:
 Helena Teixeira UMR ENTROPIE (Université de La Réunion, IRD, CNRS,
 IFREMER, Université de Nouvelle-Calédonie) ISEM, Univ Montpellier, CNRS,
 IRD, Montpellier, France Email:
 [helena-marisa.osorio-teixeira@ird.fr](mailto:helena-marisa.osorio-teixeira@ird.fr) 1. Date of data collection: 2005 - 2023 1. Geographic location of data collection: Europa (Mozambique Channel), Réunion Island, Aldabra atoll, Aride and Cousin (Seychelles archipelago) and South Brother Island (Chagos archipelago) 1. Information about funding sources that supported the collection of the data, data analyses, and computing and storage resources: Bertarelli Foundation as part of the Bertarelli Programme in Marine Science (Project 822916) FEDER Smac (2020-2022, N° RE0022954) FEDER “Pathogenes associés à la Faune Sauvage Océan Indien” (Programme Opérationnel de Coopération Territoriale 2007-2013; #31189) CNRS - INEE/TAAF (AAP Iles Eparses “OMABIO” project) Toulouse Occitanie (Bioinfo Genotoul, doi: 10.15454/1.5572369328961167E12) 1. Recommended citation for this dataset: Teixeira, H. et al. Genetic differentiation in a wide-ranging tropical seabird in the Indian Ocean is linked with oceanographic factors. [10.5061/dryad.wstqjq2z4](10.5061/dryad.wstqjq2z4) **DATA & FILE OVERVIEW** ## ***Ingroup dataset*** Tropical shearwater (*Puffinus bailloni*, n = 90 birds) raw genotypes file generated by Diversity Arrays Technology (DarT Pty Ltd, Canberra) using the DArTseq protocol. Report_DPuf23-8385_ingroup-dataset.csv ## ***Outgroup dataset*** Tropical shearwater raw genotypes were also co-analysed with Mascarene Petrel sequences from Teixeira et al. (2024) (n = 20 birds) to include a suitable outgroup for complementary analyses. Report_DPuf23-8385_outgroup-dataset.csv ## ***Puffinus metadata*** Specimen metadata to accompany the raw genotypes data files when read into a genlight object using the function gl.read.dart in the “dartRverse” package. Puffinus_metadata.csv Abbreviations used: M = male; F = female; Lat = latitude; Long = longitude, RIR = Rivière des Remparts; RDC = Rond Des Chevrons, NA = Not Applicable ## README Description of files. DATA-SPECIFIC INFORMATION FOR: Report_DPuf23-8385_ingroup-dataset.csv and Report_DPuf23-8385_outgroup-dataset.csv 1. File description: SNP 1 Row Mapping Format: "0" = Reference allele homozygote, "1" = SNP allele homozygote, "2"= heterozygote, and "-" = double null/null allele homozygote (absence of fragment with SNP in genomic representation) 2. Variable List: * AlleleID: Unique identifier for the sequence in which the SNP marker occurs * CloneID: Unique identifier of the sequence tag * AlleleSequenceRef/ AlleleSequenceSnp: The sequence of the Reference allele is in the Ref row, the sequence of the SNP allele in the SNP row * TrimmedSequenceRef/ TrimmedSequenceSnp: Same as the full sequence, but with removed adapters in short marker tags * Chrom_Calonectris_borealis_v2: Contig with the best alignment of marker/tag to the Calonectris_borealis_v2 reference genome. Missing data = contigs that were not aligned to the Calonectris_borealis_v2 reference genome (% identity &lt; 80). * ChromPosTag_Calonectris_borealis_v2: Position on contig with the best alignment of marker/tag to the Calonectris_borealis_v2 reference genome * ChromPosSnp_Calonectris_borealis_v2: Calculated position of the SNP for best aligned marker on a contig to the Calonectris_borealis_v2 reference genome * AlnCnt_Calonectris_borealis_v2: Total count of aligning markers/tags with selection criteria described below * AlnEvalue_Calonectris_borealis_v2: E value of the best alignment to the Calonectris_borealis_v2 reference genome * Strand_Calonectris_borealis_v2: Strand of the marker alignment - Plus for forward and Minus for reverse. Missing data = Not available as contigs that were not aligned to the Calonectris_borealis_v2 reference genome. * Chrom_Puffinus_mauretanicus_v1: Contig with the best alignment of marker/tag to the Puffinus_mauretanicus_v1 reference genome. Missing data = contigs that were not aligned to the Puffinus_mauretanicus_v1 reference genome (% identity &lt; 80). * ChromPosTag_Puffinus_mauretanicus_v1: Position on contig with the best alignment of marker/tag to the Puffinus_mauretanicus_v1 reference genome * ChromPosSnp_Puffinus_mauretanicus_v1: Calculated position of the SNP for best aligned marker on a contig to the Puffinus_mauretanicus_v1 reference genome * AlnCnt_Puffinus_mauretanicus_v1: Total count of aligning markers/tags with selection criteria described below * AlnEvalue_Puffinus_mauretanicus_v1: E value of the best alignment to the Puffinus_mauretanicus_v1 reference genome * Strand_Puffinus_mauretanicus_v1: Strand of the marker alignment - Plus for forward and Minus for reverse. Missing data = Not available as contigs that were not aligned to the Puffinus_mauretanicus_v1 reference genome. * SNP: base position and base variant details * SnpPosition: The position in the sequence tag at which the defined SNP variant base occurs * CallRate: The proportion of samples for which the genotype call is either "1" or "0" * OneRatioRef: The proportion of samples for which the genotype score is "1", in the Reference allele row * OneRatioSnp: The proportion of samples for which the genotype score is "1", in the SNP allele row * FreqHomRef: The proportion of samples which score as homozygous for the Reference allele * FreqHomSnp: The proportion of samples which score as homozygous for the SNP allele * FreqHets: The proportion of samples which score as heterozygous * PICRef: The polymorphism information content (PIC) for the Reference allele row * PICSnp: The polymorphism information content (PIC) for the SNP allele row * AvgPIC: The average of the polymorphism information content (PIC) of the Reference and SNP allele rows * AvgCountRef: The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the Reference allele row * AvgCountSnp: The sum of the tag read counts for all samples, divided by the number of samples with non-zero tag read counts, for the SNP allele row * RepAvg: The proportion of technical replicate assay pairs for which the marker score is consistent Note: Although we have tested the reads mapping against two alternative reference genomes (*Calonectris borealis* and *Puffinus mauretanicus*), we considered the reads mapped to the congener *Puffinus mauretanicus* in all the analyses.