Receding ice drove parallel expansions in Southern Ocean penguins

International audienceClimate shifts are key drivers of ecosystem change. Despite the critical importance of Antarctica and the Southern Ocean for global climate, the extent of climate-driven ecological change in this region remains controversial. In particular, the biological effects of changing sea ice conditions are poorly understood. We hypothesize that rapid postglacial reductions in sea ice drove biological shifts across multiple widespread Southern Ocean species. We test for demographic shifts driven by climate events over recent millennia by analyzing population genomic datasets spanning 3 penguin genera ( Eudyptes , Pygoscelis , and Aptenodytes ). Demographic analyses for multiple species (macaroni/royal, eastern rockhopper, Adélie, gentoo, king, and emperor) currently inhabiting southern coastlines affected by heavy sea ice conditions during the Last Glacial Maximum (LGM) yielded genetic signatures of near-simultaneous population expansions associated with postglacial warming. Populations of the ice-adapted emperor penguin are inferred to have expanded slightly earlier than those of species requiring ice-free terrain. These concerted high-latitude expansion events contrast with relatively stable or declining demographic histories inferred for 4 penguin species (northern rockhopper, western rockhopper, Fiordland crested, and Snares crested) that apparently persisted throughout the LGM in ice-free habitats. Limited genetic structure detected in all ice-affected species across the vast Southern Ocean may reflect both rapid postglacial colonization of subantarctic and Antarctic shores, in addition to recent genetic exchange among populations. Together, these analyses highlight dramatic, ecosystem-wide responses to past Southern Ocean climate change and suggest potential for further shifts as warming continues

Independent evolution of intermediate bill widths in a seabird clade

16 pages, 5 figures, 5 tables, supplementary information https://doi.org/10.1007/s00438-021-01845-3.-- Availability of data and material: DNA sequences: GenBank accession numbers are provided in Table 1. All data are available in the manuscript or in the Supplementary information fileInterspecific introgression can occur between species that evolve rapidly within an adaptive radiation. Pachyptila petrels differ in bill size and are characterised by incomplete reproductive isolation, leading to interspecific gene flow. Salvin’s prion (Pachyptila salvini), whose bill width is intermediate between broad-billed (P. vittata) and Antarctic (P. desolata) prions, evolved through homoploid hybrid speciation. MacGillivray’s prion (P. macgillivrayi), known from a single population on St Paul (Indian Ocean), has a bill width intermediate between salvini and vittata and could also be the product of interspecies introgression or hybrid speciation. Recently, another prion population phenotypically similar to macgillivrayi was discovered on Gough (Atlantic Ocean), where it breeds 3 months later than vittata. The similarity in bill width between the medium-billed birds on Gough and macgillivrayi suggest that they could be closely related. In this study, we used genetic and morphological data to infer the phylogenetic position and evolutionary history of P. macgillivrayi and the Gough medium-billed prion relative other Pachyptila taxa, to determine whether species with medium bill widths evolved through common ancestry or convergence. We found that Gough medium-billed prions belong to the same evolutionary lineage as macgillivrayi, representing a new population of MacGillivray’s prion that originated through a colonisation event from St Paul. We show that macgillivrayi’s medium bill width evolved through divergence (genetic drift) and independently from that of salvini, which evolved through hybridisation (gene flow). This represents the independent convergence towards a similarly medium-billed phenotype. The newly discovered MacGillivray’s prion population on Gough is of utmost conservation relevance, as the relict macgillivrayi population in the Indian Ocean is very smallOpen Access funding enabled and organized by Projekt DEAL. PQ, JFM, TLC and LC were supported by the Deutsche Forschungsgemeinschaft (Germany), Heisenberg program (grant number DFG, Qu 148-5 to P.Q.). Logistical and financial support was obtained from the South African Department of Environmental Affairs, through the South African National Antarctic Programme. LDS was supported by a Rutherford Discovery Fellowship from the Royal Society of New ZealandWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Earth history and the passerine superradiation.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

From farm to forest – 50 years of ecological transformation on Mana Island, New Zealand

Ecological surveys of Mana Island, Wellington, in 1972 and 1975 confirmed that house mice (Mus musculus) were the only pest mammals present, and resulted in nationally significant populations of Cook Strait giant weta (Deinacrida rugosa) and of two threatened lizard species being confirmed or discovered. Photographs taken in June 1972 were re-taken in June 2022, and are used to document social and ecological change on the island over this 50-year interval. Mana Island was farmed until 1986, and has been a conservation reserve administered by the Department of Conservation (DOC) since 1987. Mice reached plague numbers after farm stock were removed, and caused a population crash of McGregor’s skink (Oligosoma macgregori). Following mouse eradication in 1989–90, the island has been free of introduced mammals. A major revegetation effort since 1987 included planting of more than 443,000 trees and shrubs over about 36% of the 217 ha island. For the last two decades, conservation management of the island has largely followed a comprehensive ecological restoration plan that was published in 1999. The Friends of Mana Island was formed in 1998, and has taken the lead role in most conservation initiatives on the island since then, in partnership with Ngāti Toa Rangatira (mana whenua) and DOC. In addition to the revegetation programme, weed control, and recreation of a wetland, 22 animal species have been translocated to the island, and several bird species have colonised naturally. Conservation successes and failures are described, and research relevant to restoration ecology undertaken on the island is summarised

Social and environmental constraints on breeding by New Zealand snipe Coenocorypha aucklandica.

New Zealand Snipe Coenocorypha aucklandica on the Snares Islands occurred at high densities and many males were unable to obtain territories. Territory ownership was a prerequisite for obtaining a mate, and most matings were monogamous. Territorial males guarded their mates, but did not exclude subordinate birds from territories. Females were courtship-fed by their mates for three weeks before laying; laying occurred earlier in years when food was more abundant, as females reached threshold laying weights sooner. Incubation was shared and took 22 days. Females that mated with males that were already paired incubated unaided; an egg in one such nest hatched after about 38 days. The earliest hatch dates coincided with the annual peak in food availability. Broods were split at hatching, each parent caring for one chick independently. Chicks were fed by their parents for at least 41 days. Food availability during the period that chicks were reared was significantly higher than during the pre-chick period. During chick-rearing, territories were usurped by subordinate males, which courted available females and sometimes bred. Failed pairs frequently renested, but no pairs were double-brooded. Some breeders of both sexes that lost their dependent chick bred a second time with a new mate while their first mate continued rearing the surviving chick. Territory and mate fidelity of breeding adults were very high, and were not affected by breeding success in the previous year. Nonbreeding adults obtained a permanent territory and mate only if a territorial bird died. Prior residency was an important factor in acquiring a territory both within and between seasons. Mortality of adults during the nonbreeding season was density-dependent. However, exceptionally high mortality occurred in the winter following the 1982-83 El Nino event. Widespread reproductive failure and late breeding by snipe in 1982-83, and high mortality during the 1983 winter were probably caused by climate-induced reduction in their invertebrate food supply. Compared with other snipe, New Zealand Snipe had much higher parental investment by both sexes, and much lower per pair potential reproductive output. The highly K-selected breeding system of New Zealand Snipe is considered an evolutionary response to high intraspecific competition for food during the breeding season. The low reproductive rate, and density-dependent mortality during the nonbreeding season indicate that New Zealand Snipe were limited by food throughout the year. These findings support Ricklefs' (1980) contention that bird populations in stable environments are limited by intraspecific regulatory processes

Mitochondrial DNA structuring of Antarctic prions (Pachyptila desolata, Procellariidae)

Prions (Pachyptila) are small seabirds with a Southern Hemisphere breeding distribution. Antarctic prion (Pachyptila desolata) and Salvin’s prion (P. salvini) are two species that are regularly recorded in New Zealand as beach-wrecks but they are difficult to distinguish morphologically. Salvin’s prion is restricted to breeding on the Prince Edward Islands and Crozet Islands in the Indian Ocean but Antarctic prions have a circumpolar breeding distribution on numerous sub-Antarctic and Antarctic islands in the Southern, South Atlantic and Indian Oceans. Our aim was to examine the level of mitochondrial DNA (mtDNA) structuring within Antarctic prion and Salvin’s prion colonies, to test whether this technique can determine the provenance of beach-cast birds. The Auckland Islands Antarctic prion population exhibited distinct mtDNA haplotypes from all other populations, supporting the suggestion that these islands may have been an ice-free refugium during the Last Glacial Maximum. All other sampled breeding populations shared haplotypes, limiting the use of these sequences for determining the provenance of beach-cast birds. None of our museum specimens of Salvin’s prion collected from breeding colonies produced DNA sequences. This result indicates that the method by which these specimens, which were collected in the 1960s and 70s, were preserved, or subsequent treatments, has resulted in the loss of their DNA

Clarification of collection data for the type specimens of Hutton\u27s Shearwater Puffinus huttoni Mathews, 1912, and implications for the accuracy of historic subantarctic specimen data

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