Species delimitation beyond phylogenomics: integrative approaches reveal gentoo penguin speciation ...

• Main Authors: Noll, Daly, Younger, Jane, Pertierra, Luis R., Greve, Michelle, Pizarro, Eduardo J., León, Fabiola, Brandt, Debora Y. C., Tyler, Josh, Clucas, Gemma, Levy, Hila, Simison, W. Brian, McInnes, Julie, Pistorius, Pierre, Le Bohec, Céline, Bonadonna, Francesco, Trathan, Phil, Barbosa, Andrés, Rey, Andrea Raya, Dantas, Gisele P. M., Bowie, Rauri, Poulin, Elie, Vianna, Juliana
• Format: Dataset
• Language: English
• Published: Dryad 2023
• Subjects: comparative population genomics; adaptation; Speciation; positive selection; future niche projections; polar regions; Climate change; FOS Biological sciences; Antarctic; Antarctic Peninsula; Kerguelen; Southern Ocean; The Antarctic; Antarc*; Antarctica; Gentoo penguin; Pygoscelis papua
• Online Access: https://dx.doi.org/10.5061/dryad.6djh9w15t; https://datadryad.org/stash/dataset/doi:10.5061/dryad.6djh9w15t

Isolation and adaptation to new environments are important steps for reproductive isolation and consequently speciation. Seabirds have low phenotypic variation along their ranges in the absence of clear geographic or environmental barriers to dispersal. Despite the lacking visible phenotypic differences, the number of taxa for the gentoo penguin (Pygoscelis papua, Forster 1781) in the Southern Ocean has been under debate for the last decade, ranging from one to six different taxa. Here, we provide several lines of evidence from genomics, ecology, morphological data, and a complete systematic review that supports four distinctive gentoo penguin species, including the description of a new species. We also provide future niche projections for each of these species. Gentoo penguin genomes (n = 64) recover four main lineages: the northern gentoo (from South America), the southern gentoo (Antarctic Peninsula and maritime Antarctica, south of the Antarctic Polar Front, APF), the southeastern gentoo (from Kerguelen ... : The whole genomes of gentoo penguins were resequenced from 60 individuals and four GenBank genomes (Vianna et al. 2020) were included to complement the number of samples per breeding colony. The genome data set contains individuals distributed within the four main evolutionary lineages previously identified. This study contains several lines of evidence, from genomics, ecology, morphology, and population trends and future niche projections that support the existence of four distinctive gentoo penguin species around the Southern Ocean. The bioinformatic processing of genomic data includes cleaning of low-quality reads and remotion of adapters. Fastq trimmed reads were mapped to the reference genome (GenBank access GCA_010090195.1) and BAM files were generated using BWA-mem2 and processed using GATK. Variant calling was performed using bcftools mpileup/call and after SNPs processing, a fasta consensus file was generated using bcftools consensus. From the fasta files, CDS were extracted with gffread using ...