Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation

Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.

Molecular genetic studies of Chilean avifauna: an overview about current progress

The biodiversity of Chilean avifauna has been shaped by geological events, geographical factors and extreme climatic regimens. Molecular genetic studies developed to date have begun to provide valuable information to elucidate the effect of these factors on the evolutionary history of Chilean birds. We conducted a search in two bibliographic databases (PubMed and Scopus) over the period between 1998 and 2018 to identify the number and class of articles published in this research field. The quantification of specific research categories was also performed to assess progress in different molecular genetic issues of Chilean birds. Representative studies of the more active research areas: population structure, phylogeography, systematics and taxonomy and genetic diversity, were briefly commented on. Studies on genetic divergence analysis of cryptic species and the underlying genetics at molecular level of adaptive phenotypes in populations, were very scarce. Several types of mitochondrial and nuclear markers have been used, with COI plus D-loop and microsatellite loci, respectively, being the most widely-used markers. However, high-throughput analyses based on complete mitochondrial genomes have also been published. More than one hundred species have been analyzed; the most studied groups being penguins, followed by New World swallows. Although, to date, molecular genetic studies of Chilean birds still require further analysis, the studies available on some species or groups have provided important data to improve our understanding of the origin and evolution of this avifauna.

Uncovering population structure in the Humboldt penguin (Spheniscus humboldti) along the Pacific coast at South America

The upwelling hypothesis has been proposed to explain reduced or lack of population structure in seabird species specialized in food resources available at cold-water upwellings. However, population genetic structure may be challenging to detect in species with large population sizes, since variation in allele frequencies are more robust under genetic drift. High gene flow among populations, that can be constant or pulses of migration in a short period, may also decrease power of algorithms to detect genetic structure. Penguin species usually have large population sizes, high migratory ability but philopatric behavior, and recent investigations debate the existence of subtle population structure for some species not detected before. Previous study on Humboldt penguins found lack of population genetic structure for colonies of Punta San Juan and from South Chile. Here, we used mtDNA and nuclear markers (10 microsatellites and RAG1 intron) to evaluate population structure for 11 main breeding colonies of Humboldt penguins, covering the whole spatial distribution of this species. Although mtDNA failed to detect population structure, microsatellite loci and nuclear intron detected population structure along its latitudinal distribution. Microsatellite showed significant R_st values between most of pairwise locations (44 of 56 locations, R_st = 0.003 to 0.081) and 86% of individuals were assigned to their sampled colony, suggesting philopatry. STRUCTURE detected three main genetic clusters according to geographical locations: i) Peru; ii) North of Chile; and iii) Central-South of Chile. The Humboldt penguin shows signal population expansion after the Last Glacial Maximum (LGM), suggesting that the genetic structure of the species is a result of population dynamics and foraging colder water upwelling that favor gene flow and phylopatric rate. Our findings thus highlight that variable markers and wide sampling along the species distribution are crucial to better understand genetic population structure in animals with high dispersal ability.

Correction to: Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean?

Correction to: BMC Evolutionary Biology (2018) 18:90 https://doi.org/10.1186/s12862-018-1207-0 .