DOI: 10.5061/dryad.s1rn8pkfb
title: Data from: Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts

description: Humans are regularly cited as the main driver of current biodiversity
 extinction, but the impact of historic volcanic activity is often
 overlooked. Pre-human evidence of wildlife abundance and diversity are
 essential for disentangling anthropogenic impacts from natural events.
 Réunion Island, with its intense and well-documented volcanic activity,
 endemic biodiversity, long history of isolation and recent human
 colonization, provides an opportunity to disentangle these processes. We
 track past demographic changes of a critically endangered seabird, the
 Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs.
 Coalescent modeling suggested that a large ancestral population underwent
 a substantial population decline in two distinct phases, ca. 125,000 and
 37,000 years ago, coinciding with periods of major eruptions of Piton des
 Neiges. Subsequently, the ancestral population was fragmented into the two
 known colonies, ca. 1,500 years ago, following eruptions of Piton de la
 Fournaise. In the last century, both colonies declined significantly due
 to anthropogenic activities, and although the species was initially
 considered extinct, it was rediscovered in the 1970s. Our findings suggest
 that the current conservation status of wildlife on volcanic islands
 should be firstly assessed as a legacy of historic volcanic activity, and
 thereafter by the increasing anthropogenic impacts, which may ultimately
 drive species towards extinction.
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 93 birds and the
 restriction enzymes <em>PstI</em> and
 <em>SphI</em>.  Loci were aligned to the genome assembly of
 <em>Calonectris borealis</em> (family Procellariidae;
 GCA_013401115.1). The raw DArTseq data (67,095 SNPs)
 was filtered by the authors using the dartR v 2.1.4 R package (see
 manuscript for details). Four genomic datasets (dataset 1 – dataset 4)
 were generated and used for the downstream analyses (See Text S1 and Fig.
 S8 for details). Specimen metadata was collated during
 fieldwork.
description: This README file was generated by Helena Teixeira. **GENERAL INFORMATION**
 1. Title of Dataset: Past volcanic activity predisposes an endemic
 threatened seabird to negative anthropogenic impacts 2. Corresponding
 author Information: Helena Teixeira UMR ENTROPIE - Écologie marine
 Tropicale des Océans Pacifique et Indien Faculté des Sciences et
 Technologies Université de la Réunion 15 Av. René Cassin CS 92003 97744
 Saint Denis Cédex 9 La Réunion, France Email:
 1. Date of data
 collection: 2008 - 2018 2. Geographic location of data collection: Réunion
 Island, France 3. Information about funding sources that supported the
 collection of the data, data analyses, and computing and storage
 resources: Toulouse Occitanie (Bioinfo Genotoul, doi:
 10.15454/1.5572369328961167E12), FEDER Smac (2020-2022, N° RE0022954),
 LIFE + Petrels (grant number: LIFE13 BIO/FR/000075), Bertarelli Foundation
 as part of the Bertarelli Programme in Marine Science (Project 822916) 4.
 Recommended citation for this dataset: Teixeira, H. et al. Past volcanic
 activity predisposes an endemic threatened seabird to negative
 anthropogenic impacts. Dryad Digital Repository.
 ## **DATA & FILE
 OVERVIEW** ### Pseudobulweria genotypes *Pseudobulweria aterrima* raw
 genotypes file generated by Diversity Arrays Technology (DarT Pty Ltd,
 Canberra) using the DArTseq protocol. DNA sequences were aligned to the
 Calonectris_borealis_v1 reference genome.
 Report_DPsbu20-5021_SNP_mapping_1.csv ### *Pseudobulweria* metadata
 Specimen metadata to accompany the raw genotypes data file when read into
 a genlight object using the function gl.read.dart in R package dartR.
 Pseudobulweria_metadata.csv Abbreviations used: pop = population; RIR =
 Rivière des Remparts; RDC = Rond Des Chevrons; GB = light-grounded birds;
 CA = artificial colony; repro_season = ear of reproductive season; M =
 male; F = female; lat = latitude; lon = longitude. ### Genomic datasets
 Genomic datasets used for all the downstream analyses (dataset 1 – 4) in
 the genlight format. For details about each dataset see supplementary Text
 S1 and Fig. S8 (Teixeira et al. 2024; Scientific Reports).
 Pseudobulweria_dataset1.Rdata Pseudobulweria_dataset2.Rdata
 Pseudobulweria_dataset3.Rdata Pseudobulweria_dataset4.Rdata ###
 fastsimcoal2 files Template file for fastsimcoal2 describing the best
 demographic model for the *Pseudobulweria aterrima* (M7; “ancient &
 recent bottlenecks”) and respective parameter distributions.
 Pseudobulweria_M7.tpl Pseudobulweria_M7.est ## README Description of
 files.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Report_DPsbu20-5021_SNP_mapping_1.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_v1: Contig with the best alignment of
 marker/tag to the Calonectris_borealis_v1 reference genome. Missing data =
 contigs that were not aligned to the Calonectris_borealis_v1 reference
 genome (% identity &lt; 70). * ChromPosTag_Calonectris_borealis_v1:
 Position on contig with the best alignment of marker/tag to the
 Calonectris_borealis_v1 reference genome *
 ChromPosSnp_Calonectris_borealis_v1: Calculated position of the SNP for
 best aligned marker on a contig to the Calonectris_borealis_v1 reference
 genome * AlnCnt_Calonectris_borealis_v1: Total count of aligning
 markers/tags with selection criteria described below *
 AlnEvalue_Calonectris_borealis_v1: E value of the best alignment to the
 Calonectris_borealis_v1 reference genome * Strand_Calonectris_borealis_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
 Calonectris_borealis_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