Have historical climate changes affected Gentoo penguin (Pygoscelis papua) populations in Antarctica?

Whole genome sequencing reveals stepping-stone dispersal buffered against founder effects in a range expanding seabird

Many species are shifting their ranges in response to climate-driven environmental changes, particularly in high-latitude regions. However, the patterns of dispersal and colonization during range shifting events are not always clear. Understanding how populations are connected through space and time can reveal how species navigate a changing environment. Here, we present a fine-scale population genomics study of gentoo penguins (Pygoscelis papua), a presumed site-faithful colonial nesting species that has increased in population size and expanded its range south along the Western Antarctic Peninsula. Using whole genome sequencing, we analysed 129 gentoo penguin individuals across 12 colonies located at or near the southern range edge. Through a detailed examination of fine-scale population structure, admixture, and population divergence, we inferred that gentoo penguins historically dispersed rapidly in a stepping-stone pattern from the South Shetland Islands leading to the colonization of Anvers Island, and then the adjacent mainland Western Antarctica Peninsula. Recent southward expansion along the Western Antarctic Peninsula also followed a stepping-stone dispersal pattern coupled with limited post-divergence gene flow from colonies on Anvers Island. Genetic diversity appeared to be maintained across colonies during the historical dispersal process, and range-edge populations are still growing. This suggests large numbers of migrants may provide a buffer against founder effects at the beginning of colonization events to maintain genetic diversity similar to that of the source populations before migration ceases post-divergence. These results coupled with a continued increase in effective population size since approximately 500-800 years ago distinguish gentoo penguins as a robust species that is highly adaptable and resilient to changing climate.

Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.

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.

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

Background

Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species’ easternmost breeding colony (Bouvetøya).

Results

Connectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite F_ST = 0.002, p = 0.273; mtDNA F_ST = − 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP.

Conclusions

The subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1207-0) contains supplementary material, which is available to authorized users.

Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing

Microsatellites are valuable molecular markers for evolutionary and ecological studies. Next generation sequencing is responsible for the increasing number of microsatellites for non-model species. Penguins of the Pygoscelis genus are comprised of three species: Adélie (P. adeliae), Chinstrap (P. antarcticus) and Gentoo penguin (P. papua), all distributed around Antarctica and the sub-Antarctic. The species have been affected differently by climate change, and the use of microsatellite markers will be crucial to monitor population dynamics. We characterized a large set of genome-wide microsatellites and evaluated polymorphisms in all three species. SOLiD reads were generated from the libraries of each species, identifying a large amount of microsatellite loci: 33,677, 35,265 and 42,057 for P. adeliae, P. antarcticus and P. papua, respectively. A large number of dinucleotide (66,139), trinucleotide (29,490) and tetranucleotide (11,849) microsatellites are described. Microsatellite abundance, diversity and orthology were characterized in penguin genomes. We evaluated polymorphisms in 170 tetranucleotide loci, obtaining 34 polymorphic loci in at least one species and 15 polymorphic loci in all three species, which allow to perform comparative studies. Polymorphic markers presented here enable a number of ecological, population, individual identification, parentage and evolutionary studies of Pygoscelis, with potential use in other penguin species.

Two new species of digeneans (Lecithasteridae and Haploporidae) of the intertidal blenny Scartichthys viridis (Valenciennes) from the central coast of Chile

Two new digenean species are described from the intertidal blenny Scartichthys viridis (Valenciennes) (Blenniidae) collected off the coasts of Chile. The digenean Monorchimacradena viridis n. sp. (Lecithasteridae: Macradenininae) differs from the only known species described in the genus, M. acanthuri Nahhas and Cable 1964, in the presence of Drüsenmagen in the caeca, the location of the seminal vesicle between the testis and ovary (anterior to the testis in M. viridis n. sp.), and the pre-ovarian vitellarium. Megasolena littoralis n. sp. (Haploporidae), which is also reported from Scartichthys gigas (Steindachner), differs from the five valid species of Megasolena in that the post-caecal region (from the posterior edge of the caeca to the end of the body) is larger in M. viridis n. sp., meaning that the caeca are shortest in this species. Also, M. littoralis n. sp. is distinguished, from the other congeneric species, in a combination of characteristics, e.g., body length, suckers, pharynx, testes, hermaphroditic sac and sucker-length ratio. Sequences of ITS2 rDNA were generated for specimens of both species from various localities, indicating that it was invariant within the species. This study describes species of Monorchimacradena and Megasolena in Chilean waters, here reported for the first time off the Pacific Coast of South America.

Marked phylogeographic structure of Gentoo penguin reveals an ongoing diversification process along the Southern Ocean

Two main hypotheses have been debated about the biogeography of the Southern Ocean: (1) the Antarctic Polar Front (APF), acting as a barrier between Antarctic and sub-Antarctic provinces, and (2) the Antarctic Circumpolar Current (ACC), promoting gene flow among sub-Antarctic areas. The Gentoo penguin is distributed throughout these two provinces, separated by the APF. We analyzed mtDNA (HVR1) and 12 microsatellite loci of 264 Gentoo penguins, Pygoscelis papua, from 12 colonies spanning from the Western Antarctic Peninsula and the South Shetland Islands (WAP) to the sub-Antarctic Islands (SAI). While low genetic structure was detected among WAP colonies (mtDNA Ф_ST=0.037-0.133; microsatellite F_ST=0.009-0.063), high differentiation was found between all SAI and WAP populations (mtDNA Ф_ST=0.678-0.930; microsatellite F_ST=0.110-0.290). These results suggest that contemporary dispersal around the Southern Ocean is very limited or absent. As predicted, the APF appears to be a significant biogeographical boundary for Gentoo penguin populations; however, the ACC does not promote connectivity in this species. Our data suggest demographic expansion in the WAP during the last glacial maximum (LGM, about 20kya), but stability in SAI. Phylogenetic analyses showed a deep divergence between populations from the WAP and those from the SAI. Therefore, taxonomy should be further revised. The Crozet Islands resulted as a basal clade (3.57Mya), followed by the Kerguelen Islands (2.32Mya) as well as a more recent divergence between the Falkland/Malvinas Islands and the WAP (1.27Mya). Historical isolation, local adaptation, and past climate scenarios of those Evolutionarily Significant Units may have led to different potentials to respond to climate changes.

Diversity of MHC class I alleles in Spheniscus humboldti

The major histocompatibility complex locus (MHC) is a gene region related to immune response and exhibits a remarkably great diversity. We deduced that polymorphisms in MHC genes would help to solve several issues on penguins, including classification, phylogenetic relationship, and conservation. This study aimed to elucidate the structure and diversity of the so far unknown MHC class I gene in a penguin species. The structure of an MHC class I gene from the Humboldt penguin (Spheniscus humboldti) was determined by using an inverse PCR method. We designed PCR primers to directly determine nucleotide sequences of PCR products from the MHC class I gene and to obtain recombinant clones for investigating the diversity of the MHC class I gene in Humboldt penguins. A total of 24 MHC class I allele sequences were obtained from 40 individuals. Polymorphisms were mainly found in exons 2 and 3, as expected from the nature of MHC class I genes in vertebrate species including birds and mammals. Phylogenetic analyses of MHC class I alleles have revealed that the Humboldt penguin is closely related to the Red Knot (Calidris canutus) belonging to Charadriiformes.

A new species of Hemipera Nicoll, 1913 (Digenea: Derogenidae) from fishes of the intertidal rocky zone of Chile

A new species, Hemipera cribbi sp. nov., is described. This trematode was found in three intertidal fish species: Scartichthys viridis (Valenciennes) (Blenniidae), Gobiesox marmoratus Jenyns (Gobiesocidae) and Myxodes viridis Valenciennes (Clinidae) from the central and southern coast of Chile. Of 233 individuals of S. viridis from the central coast examined, 19 were infected. From the southern coast, nine individuals of S. viridis (one infected), five individuals of G. marmoratus (four infected), and 16 individuals of M. viridis (one fish infected) were examined. Hemipera cribbi sp. nov. is distinguished from the five other congeneric species mainly in the body size, being the smallest and narrowest species in the genus, reaching five times longer than wide. This is the first species of the genus described for the South Pacific Ocean off South America. ITS2 rDNA sequences of Hemipera cribbi sp. nov. from each host and locality were identified.

Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

Climate change, fisheries' pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark-recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, particularly focused on newly established colonies, provide a snapshot of colonization and can reveal the extent to which shifts in abundance and occupancy result from changes in demographic rates (e.g., reproduction and survival) or migration among suitable patches of habitat. Here, we describe the population structure of a colonial seabird breeding across a large latitudinal range in the Southern Ocean. Using multilocus microsatellite genotype data from 510 Gentoo penguin (Pygoscelis papua) individuals from 14 colonies along the Scotia Arc and Antarctic Peninsula, together with mitochondrial DNA data, we find strong genetic differentiation between colonies north and south of the Polar Front, that coincides geographically with the taxonomic boundary separating the subspecies P. p. papua and P. p. ellsworthii. Using a discrete Bayesian phylogeographic approach, we show that southern Gentoos expanded from a possible glacial refuge in the center of their current range, colonizing regions to the north and south through rare, long-distance dispersal. Our findings show that this dispersal is important for new colony foundation and range expansion in a seabird species that ordinarily exhibits high levels of natal philopatry, though persistent oceanographic features serve as barriers to movement.

The influence of historical climate changes on Southern Ocean marine predator populations: a comparative analysis

The Southern Ocean ecosystem is undergoing rapid physical and biological changes that are likely to have profound implications for higher-order predators. Here, we compare the long-term, historical responses of Southern Ocean predators to climate change. We examine palaeoecological evidence for changes in the abundance and distribution of seabirds and marine mammals, and place these into context with palaeoclimate records in order to identify key environmental drivers associated with population changes. Our synthesis revealed two key factors underlying Southern Ocean predator population changes; (i) the availability of ice-free ground for breeding and (ii) access to productive foraging grounds. The processes of glaciation and sea ice fluctuation were key; the distributions and abundances of elephant seals, snow petrels, gentoo, chinstrap and Adélie penguins all responded strongly to the emergence of new breeding habitat coincident with deglaciation and reductions in sea ice. Access to productive foraging grounds was another limiting factor, with snow petrels, king and emperor penguins all affected by reduced prey availability in the past. Several species were isolated in glacial refugia and there is evidence that refuge populations were supported by polynyas. While the underlying drivers of population change were similar across most Southern Ocean predators, the individual responses of species to environmental change varied because of species specific factors such as dispersal ability and environmental sensitivity. Such interspecific differences are likely to affect the future climate change responses of Southern Ocean marine predators and should be considered in conservation plans. Comparative palaeoecological studies are a valuable source of long-term data on species' responses to environmental change that can provide important insights into future climate change responses. This synthesis highlights the importance of protecting productive foraging grounds proximate to breeding locations, as well as the potential role of polynyas as future Southern Ocean refugia.