Bowhead whales were heavily exploited during commercial whaling between the 16th and 20th centuries. Current and near-future climate warming poses a new threat. Assessing bowhead vulnerability to climatic change remains challenging due to insufficient knowledge regarding responses to past climates and pre-whaling population dynamics. We integrate paleogenomics and stable isotopes (δ13C and δ15N) from 206 bowhead fossils from the Atlantic Arctic with paleoclimate and ecological modeling based on 823 radiocarbon-dated fossils, including 140 from this study. We find long-term resilience of bowheads to Holocene environmental perturbations, with no detectable changes in genetic diversity or population structure. Simulated commercial-whaling-driven genetic and fitness changes indicate that population subdivision and loss of genetic diversity are unlikely to be fully realized, despite nearly a century since whaling ceased. Furthermore, even in simulated complete population recovery scenarios, overall fitness did not return to pre-whaling levels, potentially compromising the future resilience of bowhead whales.

ABSTRACT Motivation Timing, duration and severity of marine heatwaves are changing rapidly in response to anthropogenic climate change, thereby increasing the frequency of coral bleaching events. Mass coral bleaching events result from cumulative heat stress, which is commonly quantified through degree heating weeks (DHW). Here we introduce CoralBleachRisk , a daily‐resolution global dataset that characterises sea surface temperatures, heat stress anomalies and the timing, duration and magnitude of severe coral bleaching conditions from the recent past (1985) to the future (2100) under three contrasting Shared Socioeconomic Pathways. Our projections are downscaled to a 0.5° resolution ( ~ 50 km), bias‐corrected and validated using remotely sensed data of sea surface temperatures and a global dataset of historical coral bleaching events. An accompanying online software tool allows non‐specialist users to access aggregated metrics of coral bleaching risk and generate time series projections of coral vulnerability for Earth's coral reefs. Our dataset enables regional to global comparisons of future trends in severe coral bleaching risk. Main Types of Variables Contained Sea surface temperature (SST), SST anomaly, DHW, annual timing and duration of Bleaching Alerts. Spatial Location Global. Time Period 1985–2100. Major Taxa and Level of Measurement Coral communities. Software Format Netcdf (.nc).

Rangifer tarandus (caribou or reindeer) survived periods of abrupt climatic warming during the last deglaciation but are currently in global decline. Using process-explicit models of likely climate-human-Rangifer interactions and inferences of demographic change from radiocarbon-dated fossils and ancient DNA, we reconstruct and decipher 21,000 years of Rangifer population dynamics. These high-resolution population reconstructions pinpoint ecological characteristics and life-history traits that most likely enabled Rangifer to survive rapid warming events following the Last Glacial Maximum. Projecting these process-driven models into the future reveals that these attributes are unlikely to buffer Rangifer against wide-scale population declines from expected 21st Century climatic warming. Our findings highlight a need to boost investments in the management and conservation of Rangifer, particularly in North America, where projected losses are expected to exceed 80%. This will not only support the survival of the species and the vital services it renders in Arctic ecosystems, but also help sustain the socioeconomic, cultural, and emotional well-being of many Rangifer-dependent communities.

Aim European colonisation of Australia triggered a cascade of processes that continue to threaten biodiversity today. These include the introduction of invasive species, responsible for rapid and widescale extinctions. Here, we integrated process-based models with thousands of first sighting records to reconstruct the arrival and spread of European red foxes (Vulpes vulpes) in Australia at a high spatiotemporal resolution. Location: Continental Australia. Methods We constructed tens of thousands of spatially explicit population models of fox colonisation dynamics, using historical records, demographic estimates and spatiotemporal patterns of climate and environmental change. We then tested model outputs against inferences of timings of fox arrival from newspaper articles and empirical estimates of population sizes. Results We show that it took just 60 years for foxes to infill their entire potential distribution of Australia. Foxes colonised mesic regions of Australia earlier than the more arid regions of central and north-western Australia, reaching carrying capacity shortly after the middle of the 20th century. Conclusions These new insights into the temporal pattern of spread of foxes across Australia, its underpinning processes, and associated maps of abundances promise to help better explain past losses of biodiversity, providing critical information needed to avert future extinctions of Australia's unique fauna. Our process-based approach for projecting invasion histories should prove similarly useful for reconstructing the biogeography of other invasive species, including cryptic populations at the early stages of invasion.

ABSTRACT Bowhead whales (Balaena mysticetus) are strongly associated with Arctic sea ice during their crucial summer feeding period. However, anthropogenic climate change is causing a decline in sea ice concentrations, threatening bowhead whale suitable habitat. To characterise the long‐term affinity of bowhead whales to sea ice across the Holocene and project the response of populations to 21st century climate change, we built ecological models of occurrence–environmental relationships using distribution‐wide fossil, historical, and contemporary records. We found that throughout the Holocene, bowhead whale habitat suitability was consistently highest in summer average sea ice concentrations of 15%–30%. Projecting these models forward in time to 2100 ce showed that 21st century climate change is set to erode these critical sea ice conditions, resulting in the circumpolar range of bowhead whales contracting by up to 75%. We project that during this century, habitat suitability will decline in all four management populations of bowhead whales by at least 52%, with suitable habitat predicted to vanish completely in the Sea of Okhotsk. It is likely that most viable habitat for bowhead whales will exist outside their current distribution by the end of the century, directly impacting conservation policies. Our results further highlight the vulnerability of Arctic marine endemics in a warming world, showcasing how knowledge of the past can strengthen predictions of species future vulnerability to rapid ocean warming.

Spatial and temporal patterns of future coral bleaching are uncertain, hampering global conservation efforts to protect coral reefs against climate change. Our analysis of daily projections of ocean warming establishes the severity, annual duration, and onset of severe bleaching risk for global coral reefs this century, pinpointing vital climatic refugia. We show that low-latitude coral regions are most vulnerable to thermal stress and will experience little reprieve from climate mitigation. By 2080, coral bleaching is likely to start on most reefs in spring, rather than late summer, with year-round bleaching risk anticipated to be high for some low-latitude reefs regardless of global efforts to mitigate harmful greenhouse gasses. By identifying Earth's reef regions that are at lowest risk of accelerated bleaching, our results will prioritize efforts to limit future loss of coral reef biodiversity.

Drivers and dynamics of initial human migrations across individual islands and archipelagos are poorly understood, hampering assessments of subsequent modification of island biodiversity. We developed and tested a new statistical-simulation approach for reconstructing the pattern and pace of human migration across islands at high spatiotemporal resolutions. Using Polynesian colonisation of New Zealand as an example, we show that process-explicit models, informed by archaeological records and spatiotemporal reconstructions of past climates and environments, can provide new and important insights into the patterns and mechanisms of arrival and establishment of people on islands. We find that colonisation of New Zealand required there to have been a single founding population of approximately 500 people, arriving between 1233 and 1257 AD, settling multiple areas, and expanding rapidly over both North and South Islands. These verified spatiotemporal reconstructions of colonisation dynamics provide new opportunities to explore more extensively the potential ecological impacts of human colonisation on New Zealand’s native biota and ecosystems.

The extinction of the woolly rhinoceros ( Coelodonta antiquitatis ) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.

Human settlement of islands across the Pacific Ocean was followed by waves of faunal extinctions that occurred so rapidly that their dynamics are difficult to reconstruct in space and time. These extinctions included large, wingless birds endemic to New Zealand called moa. We reconstructed the range and extinction dynamics of six genetically distinct species of moa across New Zealand at a fine spatiotemporal resolution, using hundreds of thousands of process-explicit simulations of climate-human-moa interactions, which were validated against inferences of occurrence and demographic change from an extensive fossil record. This statistical-simulation analysis revealed important interspecific differences in the ecological and demographic attributes of moa that influenced the timing and pace of their geographic and demographic declines following colonization of New Zealand by Polynesians. Despite these interspecific differences in extinction dynamics, the spatial patterns of geographic range collapse of moa species were similar. The final populations of all moa species persisted in suboptimal habitats in cold, mountainous areas that were generally last and least impacted by people. These isolated refugia for the last populations of moa continue to serve as sanctuaries for New Zealand’s remaining flightless birds, providing novel insights for conserving endemic species in the face of current and future threats.

European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.

BackgroundDeveloping genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions.ResultsUsing PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.ConclusionsThese resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.

Globular proteins are well-folded model proteins, where ions can substantially influence their structure and aggregation. Ionic liquids (ILs) are salts in the liquid state with versatile ion combinations. Understanding the IL effect on protein behavior remains a major challenge. Here, we employed small angle X-ray scattering to investigate the effect of aqueous ILs on the structure and aggregation of globular proteins, namely, hen egg white lysozyme (Lys), human lysozyme (HLys), myoglobin (Mb), β-lactoglobulin (βLg), trypsin (Tryp) and superfolder green fluorescent protein (sfGFP). The ILs contain ammonium-based cations paired with the mesylate, acetate or nitrate anion. Results showed that only Lys was monomeric, whereas the other proteins formed small or large aggregates in buffer. Solutions with over 17 mol% IL resulted in significant changes in the protein structure and aggregation. The Lys structure was expanded at 1 mol% but compact at 17 mol% with structural changes in loop regions. HLys formed small aggregates, with the IL effect similar to Lys. Mb and βLg mostly had distinct monomer and dimer distributions depending on IL type and IL concentration. Complex aggregation was noted for Tryp and sfGFP. While the anion had the largest ion effect, changing the cation also induced the structural expansion and protein aggregation.

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

Fossil leaf anatomy has previously been used as a proxy for paleoclimate. However, the exposure of leaves to sun or shade during their growth can lead to morphotype differences that confound the interpretation of fossil leaf anatomy in relation to climate and prevent reliable paleoclimate reconstruction. This work aims to model the differences in leaf anatomy that are due to various climatic drivers and differences attributable to sun or shade positions, using Nothofagus cunninghamii as the model species. Leaves from the sun and shade parts of three trees have been sampled from each of 11 sites in Victoria and Tasmania, Australia. The gross morphological and cuticular features have been scored and modelled with climate data from the sites. Random forest models can accurately predict Nothofagus cunninghamii contemporary climatic conditions of the spring temperature and summer rainfall based on leaf anatomical measurements. Leaf area, stomatal density and epidermal cell density are the most accurate predictors of whether a leaf grew in the sun or shade. Leaf area is also the strongest predictor of the maximum and minimum spring temperatures and rainfall. The models have implications for the use of fossilised leaves in paleoclimate reconstruction. The models we have built can be used to effectively predict whether a fossil leaf was from a sun or shade position on the tree and thus enable more reliable inference of paleoclimate by removing the confounding issues of variable leaf anatomy due to sun exposure during growth. Finally, these models could conceivably be used to make predictions of past paleoclimatic conditions provided suitable training and validation data on climatic conditions are available.

An emerging research program on population and geographic range dynamics of Australia's mammals illustrates an approach to better understand and respond to geographic range collapses of threatened wildlife in general. In 1788, Europeans colonized an Australia with a diverse and largely endemic mammal fauna, where many species that are now extinct or threatened were common and widespread. Subsequent population declines, range collapses and extinctions were caused by introduced predators and herbivores, altered land use, modified fire regimes and the synergies between these threats. Declines in population and range size continue for many Australian mammals despite legislative protection and conservation interventions. Here, we propose an approach that integrates museum data and other historical records into process-explicit macroecological models to better resolve mammal distributions and abundances as they were at European arrival. We then illustrate how this integrative approach can identify the likely synergistic mechanisms causing mammal population declines across these and other landscapes. This emerging research approach, undertaken with fine temporal and spatial resolution, but at large geographic scales, will provide valuable insights into the different pathways to, and drivers of, extinction. Such insights may, in turn, underpin conservation strategies based on a process-explicit understanding of population decline and range collapse under alternative scenarios of impending climate and environmental change. Given that similar information is available for other regional biotas, the approach we describe here can be adapted to conserve threatened wildlife in other regions across the globe.

Objectives: Smoking is the commonest cause of oral cavity squamous cell carcinoma (OC-SCC), but the etiology of OC-SCC in nonsmokers is unknown. Our primary goal was to use metagenomic shotgun sequencing (MSS) to define the taxonomic composition and functional potential of oral metagenome in nonsmokers with OC-SCC. Methods: We conducted a case-control study with 42 OC-SCC case and 45 control nonsmokers. MSS was performed on DNA extracted from mouthwash samples. Taxonomic analysis and pathway analysis were done using MetaPhlAn2 and HUMAnN2, respectively. Statistical difference was determined using the Mann-Whitney test controlling false discovery rate. Results: There was no significant difference in age, sex, race, or alcohol consumption between OC-SCC and control patients. There was a significant difference in beta diversity between OC-SCC and controls. At the phylum level, Bacteroidetes and Synergistetes were overly represented in OC-SCC while Actinobacteria and Firmicutes were overly represented in controls. At the genus level, Fusobacterium was overly represented in OC-SCC compared with controls, while Corynebacterium, Streptococcus, Actinomyces, Cryptobacterium, and Selenomonas were overly represented in controls. Bacterial pathway analysis identified overrepresentation in OC-SCC of pathways related to metabolism of flavin, biotin, thiamin, heme, sugars, fatty acids, peptidoglycans, and tRNA and overrepresentation of nucleotides and essential amino acids in controls. Conclusions: The oral microbiome in nonsmoker patients with OC-SCC is significantly different from that of nonsmoker control patients in taxonomic compositions and functional potentials. Our study's MSS findings matched with previous 16S-based methods in taxonomic differentiation but varied greatly in functional differentiation of microbiomes in OC-SCC and controls.

Reconstructions of the spatiotemporal dynamics of human dispersal away from evolutionary origins in Africa are important for determining the ecological consequences of the arrival of anatomically modern humans in naive landscapes and interpreting inferences from ancient genomes on indigenous population history. While efforts have been made to independently validate these projections against the archaeological record and contemporary measures of genetic diversity, there has been no comprehensive assessment of how parameter values and choice of palaeoclimate model affect projections of early human migration. We simulated human migration into North America with a process-explicit migration model using simulated palaeoclimate data from two different atmosphere-ocean general circulation models and did a sensitivity analysis on the outputs using a machine learning algorithm. We found that simulated human migration into North America was more sensitive to un-certainty in demographic parameters than choice of atmosphere-ocean general circulation model used for simulating climate-human interactions. Our findings indicate that the accuracy of process-explicit human migration models will be improved with further research on the population dynamics of ancient humans, and that uncertainties in model parameters must be considered in estimates of the timing and rate of human colo-nisation and their consequence on biodiversity.

The vulnerability of marine biodiversity to accelerated rates of climatic change is poorly understood. By developing a new method for identifying extreme oceanic warming events during Earth's most recent deglaciation, and comparing these to 21st century projections, we show that future rates of ocean warming will disproportionately affect the most speciose marine communities, potentially threatening biodiversity in more than 70% of current-day global hotspots of marine species richness. The persistence of these richest areas of marine biodiversity will require many species to move well beyond the biogeographic realm where they are endemic, at rates of redistribution not previously seen. Our approach for quantifying exposure of biodiversity to past and future rates of oceanic warming provides new context and scalable information for deriving and strengthening conservation actions to safeguard marine biodiversity under climate change.

Pathways to extinction start long before the death of the last individual. However, causes of early-stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.