Gene flow on the ice: genetic differentiation among Adélie penguin colonies around Antarctica

Palaeoclimatic changes resulted in range expansion and subsequent divergence in brown fur seals, Arctocephalus pusillus

Past climatic change as a driving force of marine diversification is still largely unclear, particularly for Southern Hemisphere species. Here, we present a case using the brown fur seal, Arctocephalus pusillus, assessing the geographical structure and demographic history using mitochondrial and nuclear data. Results show the two previously defined subspecies (one from Australia and the other from southern Africa) are phylogeographically distinct. Migration analyses based on nuclear data suggest the absence of migrants among the two genetically close assemblages. The demographic history of A. pusillus is characterized by a glacial population expansion (approx. 18 kya) in the southern African lineage, which coincides with time estimates of population expansion of prey species of seals. Approximate Bayesian calculations support an eastward dispersal event during the Last Glacial Maximum when sea levels were lower, followed by a postglacial divergence event, approximately 13 kya. The demographic history of the brown fur seal in the Southern Oceans provides support that recent palaeoclimatic changes could have facilitated expansions in some marine species and that postglacial sea-level rise may have acted as a dispersal barrier for species mostly confined to continental shelves.

Genetic diversity and structure of captive gentoo penguin populations in Japan

Until the last decade, gentoo penguins were usually split into two subspecies, northern gentoo penguins (Pygoscelis papua papua) breeding in the Falkland Islands, South Georgia, and other subantarctic islands and southern gentoo penguins (P. papua ellsworthi) breeding in the South Sandwich, South Orkney and South Shetland islands, and Antarctic Peninsula. Recent genetics research, however, suggests that the population at South Georgia is much more closely related to those further south and should be included in P. papua ellsworthi. In Japanese zoos and aquariums, captive breeding of gentoo penguins is conducted separately in three populations: "Captive-South Georgia," originating from South Georgia, "Captive-South Shetlands," originating from South Shetlands, and "Captive-Unknown," originating from at least one founder of unknown subspecies. The aims of the present study were to investigate the genetic diversity and differentiation of these captive populations using microsatellite analysis. Genetic diversity in each captive population was similar to that found in the wild, although they had much lower contemporary effective population sizes. Pairwise genetic differentiation indexes (F_ST ) among the three captive populations were as follows: 0.0309 ("Captive-South Georgia" and "Captive-Unknown"), 0.1094 ("Captive-South Georgia" and "Captive-South Shetlands"), and 0.1214 ("Captive-South Shetlands" and "Captive-Unknown"). Using Bayesian clustering, there was relatively high genetic differentiation between the "Captive-South Shetlands" group, which formed a distinct cluster, and individuals of the "Captive-Unknown" group, which were assigned to clusters in common with "Captive-South Georgia." The results from the present study are useful for future management of captive gentoo penguin populations in Japan.

Demographic reconstruction from ancient DNA supports rapid extinction of the great auk

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.

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.

Contrasting phylogeographic pattern among Eudyptes penguins around the Southern Ocean

Since at least the middle-Miocene, the Antarctic Polar Front (APF) and the Subtropical Front (STF) appear to have been the main drivers of diversification of marine biota in the Southern Ocean. However, highly migratory marine birds and mammals challenge this paradigm and the importance of oceanographic barriers. Eudyptes penguins range from the Antarctic Peninsula to subantarctic islands and some of the southernmost subtropical islands. Because of recent diversification, the number of species remains uncertain. Here we analyze two mtDNA (HVRI, COI) and two nuclear (ODC, AK1) markers from 13 locations of five putative Eudyptes species: rockhopper (E. filholi, E. chrysocome, and E. moseleyi), macaroni (E. chrysolophus) and royal penguins (E. schlegeli). Our results show a strong phylogeographic structure among rockhopper penguins from South America, subantarctic and subtropical islands supporting the recognition of three separated species of rockhopper penguins. Although genetic divergence was neither observed among macaroni penguins from the Antarctic Peninsula and sub-Antarctic islands nor between macaroni and royal penguins, population genetic analyses revealed population genetic structure in both cases. We suggest that the APF and STF can act as barriers for these species. While the geographic distance between colonies might play a role, their impact/incidence on gene flow may vary between species and colonies.

Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here, we used a comparative framework and genomewide data obtained through RAD-Seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing dispersal patterns. Our findings show that at-sea range and oceanography underlie patterns of dispersal in these penguins. The pelagic niche of emperor (Aptenodytes forsteri), king (A. patagonicus), Adélie (Pygoscelis adeliae) and chinstrap (P. antarctica) penguins facilitates gene flow over thousands of kilometres. In contrast, the coastal niche of gentoo penguins (P. papua) limits dispersal, resulting in population divergences. Oceanographic fronts also act as dispersal barriers to some extent. We recommend that forecasts of extinction risk incorporate dispersal and that management units are defined by at-sea range and oceanography in species lacking genetic data.

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.

The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions, particularly whether the Ross Sea, a major stronghold for the species, is isolated or not. We assessed emperor penguin population structure using 4,596 genome-wide single nucleotide polymorphisms (SNPs), characterized in 110 individuals (10-16 per colony) from eight colonies around Antarctica. In contrast to a previous conclusion that emperor penguins are panmictic around the entire continent, we find that emperor penguins comprise at least four metapopulations, and that the Ross Sea is clearly a distinct metapopulation. Using larger sample sizes and a thorough assessment of the limitations of different analytical methods, we have shown that population structure within emperor penguins does exist and argue that its recognition is vital for the effective conservation of the species. We discuss the many difficulties that molecular ecologists and managers face in the detection and interpretation of subtle population structure using large SNP data sets, and argue that subtle structure should be taken into account when determining management strategies for threatened species, until accurate estimates of demographic connectivity among populations can be made.

Does genetic structure reflect differences in non-breeding movements? A case study in small, highly mobile seabirds

Background

In seabirds, the extent of population genetic and phylogeographic structure varies extensively among species. Genetic structure is lacking in some species, but present in others despite the absence of obvious physical barriers (landmarks), suggesting that other mechanisms restrict gene flow. It has been proposed that the extent of genetic structure in seabirds is best explained by relative overlap in non-breeding distributions of birds from different populations. We used results from the analysis of microsatellite DNA variation and geolocation (tracking) data to test this hypothesis. We studied three small (130–200 g), very abundant, zooplanktivorous petrels (Procellariiformes, Aves), each sampled at two breeding populations that were widely separated (Atlantic and Indian Ocean sectors of the Southern Ocean) but differed in the degree of overlap in non-breeding distributions; the wintering areas of the two Antarctic prion (Pachyptila desolata) populations are separated by over 5000 km, whereas those of the blue petrels (Halobaena caerulea) and thin-billed prions (P. belcheri) show considerable overlap. Therefore, we expected the breeding populations of blue petrels and thin-billed prions to show high connectivity despite their geographical distance, and those of Antarctic prions to be genetically differentiated.

Results

Microsatellite (at 18 loci) and cytochrome b sequence data suggested a lack of genetic structure in all three species. We thus found no relationship between genetic and spatial structure (relative overlap in non-breeding distributions) in these pelagic seabirds.

Conclusions

In line with other Southern Ocean taxa, geographic distance did not lead to genetic differences between widely spaced populations of Southern Ocean petrel species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-1008-x) contains supplementary material, which is available to authorized users.

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.

Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range

Background

Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population recovery, and expansion.

Results

We investigated the genetic population structure and patterns of colonisation of king penguins across their current range using a dataset of 5154 unlinked, high-coverage single nucleotide polymorphisms generated via restriction site associated DNA sequencing (RADSeq). Despite breeding at a small number of discrete, geographically separate sites, we find only very slight genetic differentiation among colonies separated by thousands of kilometers of open-ocean, suggesting migration among islands and archipelagos may be common. Our results show that the South Georgia population is slightly differentiated from all other colonies and suggest that the recently founded Falkland Island colony is likely to have been established by migrants from the distant Crozet Islands rather than nearby colonies on South Georgia, possibly as a result of density-dependent processes.

Conclusions

The observed subtle differentiation among king penguin colonies must be considered in future conservation planning and monitoring of the species, and demographic models that attempt to forecast extinction risk in response to large-scale climate change must take into account migration. It is possible that migration could buffer king penguins against some of the impacts of climate change where colonies appear panmictic, although it is unlikely to protect them completely given the widespread physical changes projected for their Southern Ocean foraging grounds. Overall, large-scale population genetic studies of marine predators across the Southern Ocean are revealing more interconnection and migration than previously supposed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0784-z) contains supplementary material, which is available to authorized users.

Projected asymmetric response of Adélie penguins to Antarctic climate change

The contribution of climate change to shifts in a species’ geographic distribution is a critical and often unresolved ecological question. Climate change in Antarctica is asymmetric, with cooling in parts of the continent and warming along the West Antarctic Peninsula (WAP). The Adélie penguin (Pygoscelis adeliae) is a circumpolar meso-predator exposed to the full range of Antarctic climate and is undergoing dramatic population shifts coincident with climate change. We used true presence-absence data on Adélie penguin breeding colonies to estimate past and future changes in habitat suitability during the chick-rearing period based on historic satellite observations and future climate model projections. During the contemporary period, declining Adélie penguin populations experienced more years with warm sea surface temperature compared to populations that are increasing. Based on this relationship, we project that one-third of current Adélie penguin colonies, representing ~20% of their current population, may be in decline by 2060. However, climate model projections suggest refugia may exist in continental Antarctica beyond 2099, buffering species-wide declines. Climate change impacts on penguins in the Antarctic will likely be highly site specific based on regional climate trends, and a southward contraction in the range of Adélie penguins is likely over the next century.

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.

Proliferation of East Antarctic Adélie penguins in response to historical deglaciation

Background

Major, long-term environmental changes are projected in the Southern Ocean and these are likely to have impacts for marine predators such as the Adélie penguin (Pygoscelis adeliae). Decadal monitoring studies have provided insight into the short-term environmental sensitivities of Adélie penguin populations, particularly to sea ice changes. However, given the long-term nature of projected climate change, it is also prudent to consider the responses of populations to environmental change over longer time scales. We investigated the population trajectory of Adélie penguins during the last glacial-interglacial transition to determine how the species was affected by climate warming over millennia. We focussed our study on East Antarctica, which is home to 30 % of the global population of Adélie penguins.

Methods

Using mitochondrial DNA from extant colonies, we reconstructed the population trend of Adélie penguins in East Antarctica over the past 22,000 years using an extended Bayesian skyline plot method. To determine the relationship of East Antarctic Adélie penguins with populations elsewhere in Antarctica we constructed a phylogeny using mitochondrial DNA sequences.

Results

We found that the Adélie penguin population expanded 135-fold from approximately 14,000 years ago. The population growth was coincident with deglaciation in East Antarctica and, therefore, an increase in ice-free ground suitable for Adélie penguin nesting. Our phylogenetic analysis indicated that East Antarctic Adélie penguins share a common ancestor with Adélie penguins from the Antarctic Peninsula and Scotia Arc, with an estimated age of 29,000 years ago, in the midst of the last glacial period. This finding suggests that extant colonies in East Antarctica, the Scotia Arc and the Antarctic Peninsula were founded from a single glacial refuge.

Conclusions

While changes in sea ice conditions are a critical driver of Adélie penguin population success over decadal and yearly timescales, deglaciation appears to have been the key driver of population change over millennia. This suggests that environmental drivers of population trends over thousands of years may differ to drivers over years or decades, highlighting the need to consider millennial-scale trends alongside contemporary data for the forecasting of species’ abundance and distribution changes under future climate change scenarios.

Paternity testing using microsatellite DNA markers in captive Adélie penguins (Pygoscelis adeliae)

We investigated the paternity of 39 Adélie penguins (Pygoscelis adeliae) hatched at the Port of Nagoya Public Aquarium between 1995 and 2005 breeding seasons using microsatellite DNA markers. Among the 13 microsatellite marker loci tested in this study, eight markers amplified and were found to be polymorphic in the colony's founders of the captive population (n = 26). Multiple marker analysis confirmed that all the hatchlings shared alleles with their social fathers and that none of them were sired by any male (all males ≥4 years old in the exhibit tank during each reproductive season; n = 9-15) other than the one carrying out parental duties, except in the case of two inbred hatchlings whose half-sibling parents shared the same father. These results demonstrated that extra-pair paternity (EPP) did not occur in this captive population and that even if EPP has been detected among them, the probability of excluding all other possible fathers in the exhibit tank is extremely high based on paternity exclusion probabilities across the investigated loci. The paternity exclusion probabilities were almost the same between 1994 and 2005. The probability of identity across the investigated loci declined between the two time points, but was still high. These results are reflected in a very short history of breeding in this captive population. In other words, the parentage analyses using a suite of microsatellite markers will be less effective as generations change in small closed populations, such as zoo and aquarium populations.

Tracing the colonization and diversification of the worldwide seabird ectoparasite Ixodes uriae

Historical patterns of dispersal and population isolation are key components shaping contemporary genetic diversity across landscapes and require explicit consideration when examining the relative role of different factors in driving the evolution of host specificity in parasitic organisms. In this study, we investigate the worldwide colonization history of a common ectoparasite of seabirds, the tick Ixodes uriae. This tick has a circumpolar distribution across both hemispheres but has repeatedly formed host-specific races within different regions. By combining mitochondrial and nuclear data, we infer how this species spread to its present-day distribution and how the colonization process may have affected the geographic and host-associated structure of this tick within regions. We demonstrate that I. uriae is highly structured at a global scale and isolates into four genetic groups that correspond to well-defined geographical regions. Molecular dating suggests that the diversification of I. uriae began in the early Miocene (22 Myr) and that this tick colonized most of the southern hemisphere before moving into northern latitudes via two independent routes. However, no relationship between the degree of host race divergence and colonization history was evident, supporting previous hypotheses that host specialization evolves relatively rapidly in this parasite, but does not typically lead to speciation. We discuss the possible historical and contemporary mechanisms of large-scale dispersal for this ectoparasite and how its biological characteristics may condition current patterns of genetic diversity. More generally, our results illustrate how combining broad-scale sampling and modern molecular tools can help disentangle complex patterns of diversification in widespread parasites.

King penguin demography since the last glaciation inferred from genome-wide data

How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum (ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus. Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition.

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

The West Antarctic Peninsula (WAP) has been suffering an increase in its atmospheric temperature during the last 50 years, mainly associated with global warming. This increment of temperature trend associated with changes in sea-ice dynamics has an impact on organisms, affecting their phenology, physiology and distribution range. For instance, rapid demographic changes in Pygoscelis penguins have been reported over the last 50 years in WAP, resulting in population expansion of sub-Antarctic Gentoo penguin (P. papua) and retreat of Antarctic Adelie penguin (P. adeliae). Current global warming has been mainly associated with human activities; however these climate trends are framed in a historical context of climate changes, particularly during the Pleistocene, characterized by an alternation between glacial and interglacial periods. During the last maximal glacial (LGM∼21,000 BP) the ice sheet cover reached its maximum extension on the West Antarctic Peninsula (WAP), causing local extinction of Antarctic taxa, migration to lower latitudes and/or survival in glacial refugia. We studied the HRVI of mtDNA and the nuclear intron βfibint7 of 150 individuals of the WAP to understand the demographic history and population structure of P. papua. We found high genetic diversity, reduced population genetic structure and a signature of population expansion estimated around 13,000 BP, much before the first paleocolony fossil records (∼1,100 BP). Our results suggest that the species may have survived in peri-Antarctic refugia such as South Georgia and North Sandwich islands and recolonized the Antarctic Peninsula and South Shetland Islands after the ice sheet retreat.

Survival differences and the effect of environmental instability on breeding dispersal in an Adelie penguin meta-population

High survival and breeding philopatry was previously confirmed for the Adélie penguin (Pygoscelis adeliae) during a period of stable environmental conditions. However, movements of breeding adults as a result of an unplanned natural experiment within a four-colony meta-population provided interesting insights into this species' population dynamics. We used multistate mark-recapture models to investigate apparent survival and dispersal of breeding birds in the southwestern Ross Sea during 12 breeding seasons (1996-2007). The natural experiment was facilitated by the temporary grounding of two immense icebergs that (i) erected a veritable fence separating colonies and altering migration routes and (ii) added additional stress by trapping extensive sea ice in the region during 5 of 12 y. Colony size varied by orders of magnitude, allowing investigation of apparent survival and dispersal rates in relation to both environmental conditions and colony size within this meta-population. Apparent survival was lowest for the smallest colony (4,000 pairs) and similar for the medium (45,000 pairs) and large colonies (155,000 pairs), despite increased foraging effort expended by breeders at the largest colony. Dispersal of breeding birds was low (<1%), except during years of difficult environmental conditions when movements increased, especially away from the smallest colony (3.5%). Decreased apparent survival at the smallest colony could reflect differences in migration chronology and winter habitat use compared with the other colonies, or it may reflect increased permanent emigration to colonies outside this meta-population. Contrary to current thought, breeding penguins are not always philopatric. Rather, stressful conditions can significantly increase dispersal rates.

Isolation and characterization of macaroni penguin (Eudyptes chrysolophus) microsatellite loci and their utility in other penguin species (Spheniscidae, AVES)

We report the characterization of 25 microsatellite loci isolated from the macaroni penguin (Eudyptes chrysolophus). Thirteen loci were arranged into four multiplex sets for future genetic studies of macaroni penguin populations. All 25 loci were tested separately in each of four other penguin species [Adélie penguin (Pygoscelis adeliae), chinstrap penguin (Pygoscelis antarctica), gentoo penguin (Pygoscelis papua) and king penguin (Aptenodytes patagonicus)]. Between eight and 12 loci were polymorphic per species. These loci are expected to be useful for studies of population genetic structure in a range of penguin species.

Multilocus assignment analyses reveal multiple units and rare migration events in the recently expanded yellow-eyed penguin (Megadyptes antipodes)

The identification of demographically independent populations and the recognition of management units have been greatly facilitated by the continuing advances in genetic tools. Managements units now play a key role in short-term conservation management programmes of declining species, but their importance in expanding populations receives comparatively little attention. The endangered yellow-eyed penguin (Megadyptes antipodes) expanded its range from the subantarctic to New Zealand's South Island a few hundred years ago and this new population now represents almost half of the species' total census size. This dramatic expansion attests to M. antipodes' high dispersal abilities and suggests the species is likely to constitute a single demographic population. Here we test this hypothesis of panmixia by investigating genetic differentiation and levels of gene flow among penguin breeding areas using 12 autosomal microsatellite loci along with mitochondrial control region sequence analyses for 350 individuals. Contrary to our hypothesis, however, the analyses reveal two genetically and geographically distinct assemblages: South Island vs. subantarctic populations. Using assignment tests, we recognize just two first-generation migrants between these populations (corresponding to a migration rate of < 2%), indicating that ongoing levels of long-distance migration are low. Furthermore, the South Island population has low genetic variability compared to the subantarctic population. These results suggest that the South Island population was founded by only a small number of individuals, and that subsequent levels of gene flow have remained low. The demographic independence of the two populations warrants their designation as distinct management units and conservation efforts should be adjusted accordingly to protect both populations.

Genetic homogeneity among colonies of the white-nest swiftlet (Aerodramus fuciphagus) in Thailand

The white-nest swiftlet, Aerodramus fuciphagus, originally lived in large colonies in natural caves, but now it also occurs in man-made buildings. We investigated the patterns of genetic differentiation in two mitochondrial DNA genes (cyt-b and ND2) and eight microsatellite loci among and within colonies of A. fuciphagus from across recently established man-made colonies in Thailand. Ten white-nest swiftlet colonies were sampled along the coast of the Gulf of Thailand and the Andaman Sea in Thailand during 2003-2006. The genetic diversity of mtDNA was very low, and few significant PhiST values were found between pairs of colonies. Analyses of haplotype relationships did not show genetic structure across the sampled distribution. The level of genetic diversity for microsatellite loci was high, but FST values were not significant. However, due to small sample sizes for some colonies that could limit conclusions on genetic differentiation from PhiST and FST, we also analyzed the microsatellite data using STRUCTURE and found that number of subpopulations of white-nest swiftlets in sampled colonies was one. The lack of genetic differentiation among swiftlet house colonies could be a result of high gene flow between colonies and large population sizes. Our results suggest that A. fuciphagus living in recently established man-made colonies in Thailand should be considered members of a single panmictic population. Future work will be necessary to determine whether this panmixia is stable or a temporary result of the recent explosive expansion of the number of colonies, and comparisons to natural colonies may provide an understanding of mechanisms producing the lack of genetic structure in swiftlet house colonies.

Evolution and biodiversity of Antarctic organisms: a molecular perspective

The Antarctic biota is highly endemic, and the diversity and abundance of taxonomic groups differ from elsewhere in the world. Such characteristics have resulted from evolution in isolation in an increasingly extreme environment over the last 100 Myr. Studies on Antarctic species represent some of the best examples of natural selection at the molecular, structural and physiological levels. Analyses of molecular genetics data are consistent with the diversity and distribution of marine and terrestrial taxa having been strongly influenced by geological and climatic cooling events over the last 70 Myr. Such events have resulted in vicariance driven by continental drift and thermal isolation of the Antarctic, and in pulses of species range contraction into refugia and subsequent expansion and secondary contact of genetically distinct populations or sister species during cycles of glaciation. Limited habitat availability has played a major role in structuring populations of species both in the past and in the present day. For these reasons, despite the apparent simplicity or homogeneity of Antarctic terrestrial and marine environments, populations of species are often geographically structured into genetically distinct lineages. In some cases, genetic studies have revealed that species defined by morphological characters are complexes of cryptic or sibling species. Climate change will cause changes in the distribution of many Antarctic and sub-Antarctic species through affecting population-level processes such as life history and dispersal.

Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes?--Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity

Background

Circum-Antarctic waters harbour a rare example of a marine species flock – the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survived Pleistocene climatic fluctuations characterised by repeated advances of continental glaciers as far as the shelf break that probably resulted in a loss of habitat for benthic organisms. Pelagic ecosystems, on the other hand, might have flourished during glacial maxima due to the northward expansion of Antarctic polar waters. In order to better understand the role of ecological traits in Quaternary climatic fluctuations, we performed demographic analyses of populations of four fish species from the tribe Trematominae, including both fully benthic and pelagic species using the mitochondrial cytochrome b gene and an intron from the nuclear S7 gene.

Results

Nuclear and cytoplasmic markers showed differences in the rate and time of population expansions as well as the likely population structure. Neutrality tests suggest that such discordance comes from different coalescence dynamics of each marker, rather than from selective pressure. Demographic analyses based on intraspecific DNA diversity suggest a recent population expansion in both benthic species, dated by the cyt b locus to the last glacial cycle, whereas the population structure of pelagic feeders either did not deviate from a constant-size model or indicated that the onset of the major population expansion of these species by far predated those of the benthic species. Similar patterns were apparent even when comparing previously published data on other Southern Ocean organisms, but we observed considerable heterogeneity within both groups with regard to the onset of major demographic events and rates.

Conclusion

Our data suggest benthic and pelagic species reacted differently to the Pleistocene ice-sheet expansions that probably significantly reduced the suitable habitat for benthic species. However, the asynchronous timing of major demographic events observed in different species within both "ecological guilds", imply that the species examined here may have different population and evolutionary histories, and that more species should be analysed in order to more precisely assess the role of life history in the response of organisms to climatic changes.

Microevolution and mega-icebergs in the Antarctic

Microevolution is regarded as changes in the frequencies of genes in populations over time. Ancient DNA technology now provides an opportunity to demonstrate evolution over a geological time frame and to possibly identify the causal factors in any such evolutionary event. Using nine nuclear microsatellite DNA loci, we genotyped an ancient population of Adélie penguins (Pygoscelis adeliae) aged approximately 6,000 years B.P. Subfossil bones from this population were excavated by using an accurate stratigraphic method that allowed the identification of individuals even within the same layer. We compared the allele frequencies in the ancient population with those recorded from the modern population at the same site in Antarctica. We report significant changes in the frequencies of alleles between these two time points, hence demonstrating microevolutionary change. This study demonstrates a nuclear gene-frequency change over such a geological time frame. We discuss the possible causes of such a change, including the role of mutation, genetic drift, and the effects of gene mixing among different penguin populations. The latter is likely to be precipitated by mega-icebergs that act to promote migration among penguin colonies that typically show strong natal return.

Comparative host-parasite population structures: disentangling prospecting and dispersal in the black-legged kittiwake Rissa tridactyla

Although much insight is to be gained through the comparison of the population genetic structures of parasites and hosts, there are, at present, few studies that take advantage of the information on vertebrate life histories available through the consideration of their parasites. Here, we examined the genetic structure of a colonial seabird, the black-legged kittiwake (Rissa tridactyla) using seven polymorphic microsatellite markers to make inferences about population functioning and intercolony dispersal. We sampled kittiwakes from 22 colonies across the species' range and, at the same time, collected individuals of one of its common ectoparasites, the tick Ixodes uriae. Parasites were genotyped at eight microsatellite markers and the population genetic structure of host and parasite were compared. Kittiwake populations are only genetically structured at large spatial scales and show weak patterns of isolation by distance. This may be due to long-distance dispersal events that erase local patterns of population subdivision. However, important additional information is gained by comparing results with those of the parasite. In particular, tick populations are strongly structured at regional scales and show a stepping-stone pattern of gene flow. Due to the parasite's life history, its population structure is directly linked to the frequency and spatial extent of within-breeding season movements of kittiwakes. The comparison of host and parasite gene flow therefore helps us to disentangle the intercolony movements of birds from that of true dispersal events (movement followed by reproduction). In addition, such data can provide essential elements for predicting the outcome of local co-evolutionary interactions.

Mutational bias in penguin microsatellite DNA

Analysis of nucleotide sequence variation at a microsatellite DNA locus revealed extensive size homoplasy of alleles in Adélie penguins (Pygoscelis adeliae). Variation in the flanking regions at this locus allowed discrimination between mechanisms proposed for length changes in microsatellite DNA alleles. We further examined the structure of alleles for the same microsatellite DNA locus across 11 additional species of penguin (Spheniscidae) by mapping allele sequences onto an independent penguin phylogeny. Our analysis indicated that the repeat motifs appear to have evolved independently on several occasions. We observed sequence instability in the region bordering the repeat tract with a transversional bias predominating. We propose that this bias results from inaccurate DNA replication owing to the sequence context of this repeat tract. Because we show that regions flanking repeat sequences exhibit this mutational bias, this cautions against the use of such regions for phylogeny reconstruction.

Endangered Antarctic Environments

The Antarctic continent harbors a range of specialized and sometimes highly localized microbial biotopes. These include biotopes associated with desiccated mineral soils, rich ornithogenic soils, glacial and sea ice, ice-covered lakes, translucent rocks, and geothermally heated soils. All are characterized by the imposition of one or more environmental extremes (including low temperature, wide temperature fluctuations, desiccation, hypersalinity, high periodic radiation fluxes, and low nutrient status). As our understanding of the true microbial diversity in these biotopes expands from the application of molecular phylogenetic methods, we come closer to the point where we can make an accurate assessment of the impacts of environmental change, human intervention, and other natural and unnatural impositions. At present, it is possible to make reasonable predictions about the physical effects of local climate change, but only general predictions on possible changes in microbial community structure. The consequences of some direct human impacts, such as physical disruption of microbial soil communities, are obvious if not yet quantitated. Others, such as the dissemination of nonindigenous microorganisms into indigenous microbial communities, are not yet understood.

Inter-island movements and population differentiation in a pelagic seabird

We used mark-resight data and amplified fragment length polymorphism (AFLP) markers to assess movements and gene flow between Central Pacific breeding colonies of the great frigatebird, Fregata minor. Of 715 adult frigatebirds marked on Tern Island and Johnston Atoll, 21.3% were resighted at other frigatebird colonies at least 582 km away. Mark-resight data indicated regular movement of males and females between Tern Island and Johnston Atoll (873 km apart), and less frequent movements to other islands; no birds marked on Tern or Johnston were seen on Christmas Island, but one was seen in the Philippines, 7627 km from where it was marked. Despite the regular occurrence of interisland movements, Bayesian analyses of AFLP data showed significant genetic differentiation between Tern Island and Johnston Atoll, and more pronounced differentiation between these two islands and the more distant Christmas Island. The AFLP profiles of three birds breeding on Tern Island fell within the profile-cluster typical for Christmas Island birds, both in a nonmetric multidimensional scaling analysis and in a population assignment test, suggesting dispersal events from Christmas Island to Tern Island. Several factors could explain the persistence of genetic structure despite frequent movements between colonies: many movements occurred during the nonbreeding season, many breeding-season movements did not involve mate-acquisition behaviours and individuals that do disperse may be selected against, as suggested by morphometric differences between colonies. The persistence of genetic structure among breeding colonies despite significant interisland movements suggests limits to the effectiveness of migration as a homogenizing force in this broadly distributed, extremely mobile species.