DOI: 10.5061/dryad.dr7sqvb5d
title: Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia

description: The genetic identification of significant evolutionary units and
 information on their connectivity can be used to design effective
 management and conservation plans. Despite having high dispersal capacity,
 several seabird species show population structure due to both abiotic and
 biotic barriers to gene flow. The Kelp Gull is the most abundant species
 of gull in the southern hemisphere. In Argentina it reproduces in both
 marine and freshwater environments, with more than 100,000 pairs following
 a metapopulation dynamic across 140 colonies in the Atlantic coast of
 Patagonia. However, little is known about the demography and connectivity
 of inland populations. We aim to provide information on the connectivity
 of the largest freshwater colonies (those from Nahuel Huapi Lake) with the
 closest Pacific and Atlantic populations to evaluate if these freshwater
 colonies are being subsidized by the larger coastal populations. We
 sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and
 Pacific coasts) and employed a reduced-representation genomic approach to
 genotype individuals for single-nucleotide polymorphisms (SNPs). We found,
 using clustering and phylogenetic analyses, that there are three genetic
 groups, each corresponding to one of our sampled regions. Individuals from
 marine environments are more closely related to each other than to those
 from Nahuel Huapi Lake, indicating that the latter population constitutes
 the first freshwater Kelp Gull colony to be identified as a significant
 evolutionary unit in Patagonia.
description: These are ddRAD data generated following this paper.
 Thrasher DJ, Butcher BG, Campagna L, Webster MS, Lovette IJ.
 Double‐digest RAD sequencing outperforms microsatellite loci at assigning
 paternity and estimating relatedness: A proof of concept in a highly
 promiscuous bird. Mol Ecol Res. 2018; 18(5): 953-965.
description: # Description of the files in Kelp\_assembly.tar.gz ## There are a total
 of 133 files in the folder. These belong to a ddRAD assembly generated
 with the software Stacks version 2.3e. The files can be devided in the
 categories shown below. ## Aligned Sequences There are 117 files derived
 from sequences from different individuals (one file per individual)
 aligned to the Herring Gull reference genome
 (`GCA_013400295.1_ASM1340029v1_genomic.fna`) as indicated in the paper.
 Each file is named with a number and a series of letters. The letters
 indicate both the species (starting wit GC for the common Spanish name of
 the study species, "Gaviota Cocinera") and the geographic origin
 of the sample. The geographic origin is indicated first with letters
 denoting the specific locality and subsequently with the general region as
 follows: Pacific coast (CP) * Maiquillahue (VA) * Isla Conejo (IC) *
 Puñihuil (PU) Nahuel Huapi Lake (LNH) * Islets Gaviotero 1 and Gaviotero 2
 (G1, G2) * Isla el Roble (RO) Atlantic coast (CA) * Isla de Los Pájaros
 (IP) * Punta León (PL) Finally, the numbers give each individual a unique
 identifier (as there are several individuals sampled in the same
 geographic region). This is an example of how each file is named: *
 Kelp_assembly/100GCG1LNH.bam * Kelp_assembly/101GCG1LNH.bam *
 Kelp_assembly/102GCG1LNH.bam * ... * Kelp_assembly/98GCG1LNH.bam *
 Kelp_assembly/99GCG1LNH.bam ## STACKS Catalog and Associated Statistics
 The following four files were generated by the gstacks module of the
 Stacks software. The catalog of RAD loci is generated from the collection
 of individuals aligned to the reference genome. The populations module of
 the software can be used to export different subsets of the dataset (e.g.,
 after filtering). * Kelp_assembly/catalog.calls *
 Kelp_assembly/catalog.fa.gz * Kelp_assembly/gstacks.log *
 Kelp_assembly/gstacks.log.distribs ## Population Module Output Files from
 STACKS The following 12 files are derived from the ddRAD assembly (see
 details next to each file). * Kelp_assembly/Kelp.structure #Genotypes for
 each individual in Stucture format. *
 Kelp_assembly/populations.fst_1-2.tsv #F-statistics between LNH (pop 1)
 and CA (pop 2). * Kelp_assembly/populations.fst_1-3.tsv #F-statistics
 between LNH (pop 1) and CP (pop 3). *
 Kelp_assembly/populations.fst_3-2.tsv #F-statistics between CA (pop 2) and
 CP (pop 3). * Kelp_assembly/populations.fst_summary.tsv #Summary of
 F-statistics for the three populations. *
 Kelp_assembly/populations.haps.radpainter #Haplotypes exported in
 radpainter format for the software fineRadStructure. *
 Kelp_assembly/populations.haps.vcf #Haplotypes exported in vcf format. *
 Kelp_assembly/populations.phistats_1-2.tsv #Phi-statistics derived from
 haplotype frequencies (populations numbered as for F-statistics). *
 Kelp_assembly/populations.phistats_1-3.tsv #Phi-statistics derived from
 haplotype frequencies (populations numbered as for F-statistics). *
 Kelp_assembly/populations.phistats_3-2.tsv #Phi-statistics derived from
 haplotype frequencies (populations numbered as for F-statistics). *
 Kelp_assembly/populations.phistats_summary.tsv #Summary of Phi-statistics
 for the three populations. *
 Kelp_assembly/populations.sumstats_summary.tsv #Other statistics like FIS,
 heterozygosity, etc, per population.