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Abstract Background Activation of Toll-like receptors (TLRs) is widely accepted as an essential event for defence against infection. Many TLRs utilize a common signalling pathway that relies on activation of the kinase IRAK4 and the transcription factor NFκB for the rapid expression of immunity genes. Methods 21 K DNA microarray technology was used to evaluate LPS-induced (TLR4) gene responses in blood monocytes from a child with an IRAK4-deficiency. In vitro responsiveness to LPS was confirmed by real-time PCR and ELISA and compared to the clinical predisposition of the child and IRAK4-deficient mice to Gram negative infection. Results We demonstrated that the vast majority of LPS-responsive genes in IRAK4-deficient monocytes were greatly suppressed, an observation that is consistent with the described role for IRAK4 as an essential component of TLR4 signalling. The severely impaired response to LPS, however, is inconsistent with a remarkably low incidence of Gram negative infections observed in this child and other children with IRAK4-deficiency. This unpredicted clinical phenotype was validated by demonstrating that IRAK4-deficient mice had a similar resistance to infection with Gram negative S. typhimurium as wildtype mice. A number of immunity genes, such as chemokines, were expressed at normal levels in human IRAK4-deficient monocytes, indicating that particular IRAK4-independent elements within the repertoire of TLR4-induced responses are expressed. Conclusions Sufficient defence to Gram negative immunity does not require IRAK4 or a robust, 'classic' inflammatory and immune response.

Understanding the dynamics of population recovery in threatened species requires robust longitudinal monitoring datasets. However, evidence-based decision-making is often impeded by variable data collection approaches, necessitating critical evaluation of restricted available baselines. The Hainan gibbon, the world's rarest primate, had possibly declined to only seven or eight individuals in 1978 at Bawangling National Nature Reserve but has experienced subsequent population growth. Past population estimates lack detailed reporting of survey effort, and multiple conflicting estimates are available, hindering assessment of gibbon recovery. We investigated all reported estimates of Bawangling gibbon population size from 1978 to 2022, to evaluate the biological signal of population trends and the extent to which noise associated with varying survey effort, reporting and estimation may mask or misrepresent any underlying signal. This longitudinal dataset demonstrates that the Bawangling population experienced a series of bottlenecks and recoveries, with three successive periods of growth interspersed by population crashes (1978-1989, 1989-2000 and 2000-2022). The rate of gibbon population recovery was progressively slower over time in each successive period of growth, and this potential decline in recovery rate following serial bottlenecks suggests that additional management strategies may be required alongside "nature-based solutions" for this species. However, population viability analysis suggests the 1978 founder population is unlikely to have been as low as seven individuals, raising concerns for interpreting reported historical population counts and understanding the dynamics of the species' recovery. We caution against overinterpreting potential signals within "messy" conservation datasets, and we emphasise the crucial importance of standardised replicable survey methods and transparent reporting of data and effort in all future surveys of Hainan gibbons and other highly threatened species., Competing Interests: The authors have no competing interests., (© 2024 The Author(s). Ecology and Evolution published by John Wiley & Sons Ltd.)

Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups-such as testudines, crocodylians, amphibians and chondrichthyans-as conservation priorities from a phylogenetic perspective., (© 2024. The Author(s).)

Many species are restricted to a marginal or suboptimal fraction of their historical range due to anthropogenic impacts, making it hard to interpret their ecological preferences from modern-day data alone. However, inferring past ecological states is limited by the availability of robust data and biases in historical archives, posing a challenge for policy makers . To highlight how historical records can be used to understand the ecological requirements of threatened species and inform conservation, we investigated sperm whale (Physeter macrocephalus) distribution in the Western Indian Ocean. We assessed differences in information content and habitat suitability predictions based on whale occurrence data from Yankee whaling logs (1792-1912) and from modern cetacean surveys (1995-2020). We built maximum entropy habitat suitability models containing static (bathymetry-derived) variables to compare models comprising historical-only and modern-only data. Using both historical and modern habitat suitability predictions  we assessed marine protected area (MPA) placement by contrasting suitability in- and outside MPAs. The historical model predicted high habitat suitability in shelf and coastal regions near continents and islands, whereas the modern model predicted a less coastal distribution with high habitat suitability more restricted to areas of steep topography. The proportion of high habitat suitability inside versus outside MPAs was higher when applying the historical predictions than the modern predictions, suggesting that different marine spatial planning optimums can be reached from either data sources. Moreover, differences in relative habitat suitability predictions between eras were consistent with the historical depletion of sperm whales from coastal regions, which were easily accessed and targeted by whalers, resulting in a modern distribution limited more to steep continental margins and remote oceanic ridges. The use of historical data can provide important new insights and, through cautious interpretation, inform conservation planning and policy, for example, by identifying refugee species and regions of anticipated population recovery., (© 2023 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Understanding how species respond to different anthropogenic pressures is essential for conservation planning. The archaeological record has great potential to inform extinction risk assessment by providing evidence on past human-caused biodiversity loss, but identifying specific drivers of past declines from environmental archives has proved challenging. We used 17 684 Holocene zooarchaeological records for 15 European large mammal species together with data on past environmental conditions and anthropogenic activities across Europe, to assess the ability of environmental archives to determine the relative importance of different human pressures in shaping faunal distributions through time. Site occupancy probability showed differing significant relationships with environmental covariates for all species, and nine species also showed significant relationships with anthropogenic covariates (human population density, % cropland, % grazing land). Across-species differences in negative relationships with covariates provide ecological insights for understanding extinction dynamics: some mammals (red deer, aurochs, wolf, wildcat, lynx, pine marten and beech marten) were more vulnerable to past human-environmental interactions, and differing single and synergistic anthropogenic factors influenced likelihood of past occurrence across species. Our results provide new evidence for pre-industrial population fragmentation and depletion in European mammals, and demonstrate the usefulness of historical baselines for understanding species' varying long-term sensitivity to multiple threats.

Islands have long been recognized as distinctive evolutionary arenas leading to morphologically divergent species, such as dwarfs and giants. We assessed how body size evolution in island mammals may have exacerbated their vulnerability, as well as how human arrival has contributed to their past and ongoing extinctions, by integrating data on 1231 extant and 350 extinct species from islands and paleo islands worldwide spanning the past 23 million years. We found that the likelihood of extinction and of endangerment are highest in the most extreme island dwarfs and giants. Extinction risk of insular mammals was compounded by the arrival of modern humans, which accelerated extinction rates more than 10-fold, resulting in an almost complete demise of these iconic marvels of island evolution.

Traditional Chinese medicine (TCM) is highlighted by conservation practitioners as an ongoing threat to many overharvested plant and animal species, including several charismatic threatened vertebrates. However, studies that provide evidence-based and practical recommendations on how to better regulate the TCM trade for sustainability and biodiversity conservation remain limited. China is the biggest promotor of and market for TCM and understanding the TCM trade in China is important for global biodiversity conservation. In particular, conservation researchers need to better understand how the TCM trade and its regulations interact with China's development needs and should collaborate with TCM communities to propose locally adapted suggestions to decision makers. However, progress in these areas has been restricted by language, cultural, and knowledge barriers. In this paper, we provide an overview of the current status of TCM-related regulations in China, identify weaknesses in regulation frameworks, and highlight issues that currently limit our understanding of the magnitude, dynamics, and impact of the trade. We propose changes in trade regulations, actions to enhance law enforcement, and future research directions to encourage a more sustainable TCM trade that benefits both global biodiversity conservation and TCM development., (© 2022 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Dugongs ( Dugong dugon ) experienced a serious population decline in China during the twentieth century, and their regional status is poorly understood. To determine their current distribution and status, we conducted a large-scale interview survey of marine resource users across four Chinese provinces and reviewed all available historical data covering the past distribution of dugongs in Chinese waters. Only 5% of 788 respondents reported past dugong sightings, with a mean last-sighting date of 23 years earlier, and only three respondents reported sightings from within the past 5 years. Historical records of dugongs peak around 1960 and then decrease rapidly from 1975 onwards; no records are documented after 2008, with no verified field observations after 2000. Based on these findings, we are forced to conclude that dugongs have experienced rapid population collapse during recent decades and are now functionally extinct in China. Our study provides evidence of a new regional loss of a charismatic marine megafaunal species, and the first reported functional extinction of a large vertebrate in Chinese marine waters. This rapid documented population collapse also serves as a sobering reminder that extinctions can occur before effective conservation actions are developed., (© 2022 The Authors.)

Conservation outreach is regularly conducted to increase support for conservation by altering local awareness and attitudes about species or environmental issues. However, there is often little assessment of the effectiveness of these activities. We investigated knowledge of past conservation outreach in 26 villages adjacent to Bawangling National Nature Reserve, Hainan, China, which contains the last population of the Hainan gibbon (Nomascus hainanus). The medium of past outreach activities was reported most frequently by interviewees, followed by who delivered them and the outreach topic, with the fewest interviewees reporting the specific messages being communicated (the consequences of following conservation management policies). Negatively-framed messages, emphasizing prohibited activities and associated punishments, were reported more than positively-framed messages that aimed to foster conservation support. Male interviewees and those with higher education levels reported more aspects of past activities. The Hainan gibbon had higher salience than other threatened native species, and reporting the occurrence (but not necessarily the content) of past outreach was associated with increased likelihood of knowing that gibbons were threatened. These findings highlight the need for conservation outreach to increase both exposure and retention of key messages among target audiences. Meaningful and concrete conservation benefits should be communicated to local communities, and the effectiveness of outreach using a flagship species could be expanded to also improve awareness of other conservation-priority species within the same landscape., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW)., Location: Global., Taxon: All extant mammal species., Methods: Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species)., Results: Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use., Main Conclusion: Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control., Competing Interests: CONFLICT OF INTEREST The authors declare no competing interests.

Megafauna play a disproportionate role in developing and maintaining their biomes, by regulating plant dispersal, community structure and nutrient cycling. Understanding the ecological roles of extinct megafaunal communities, for example through dietary reconstruction using isotope analysis, is necessary to determine pre-human states and set evidence-based restoration goals. We use δ 13 C and δ 15 N isotopic analyses to reconstruct Holocene feeding guilds in Madagascar's extinct megaherbivores, which included elephant birds, hippopotami and giant tortoises that occurred across multiple habitats and elevations. We compare isotopic data from seven taxa and two elephant bird eggshell morphotypes against contemporary regional floral baselines to infer dietary subsistence strategies. Most taxa show high consumption of C 3 and/or CAM plants, providing evidence of widespread browsing ecology. However, Aepyornis hildebrandti , an elephant bird restricted to the central highlands region, has isotope values with much higher δ 13 C values than other taxa. This species is interpreted as having obtained up to 48% of its diet from C 4 grasses. These findings provide new evidence for distinct browsing and grazing guilds in Madagascar's Holocene megaherbivore fauna, with implications for past regional distribution of ecosystems dominated by endemic C 4 grasses.

Shifting baseline syndrome (SBS) describes changing perceptions of biological conditions due to a loss of historical knowledge. Perceptions of 'normal' environmental conditions are continually updated, leading to underestimation of the true magnitude of long-term ecological change and potential setting of unambitious management targets. There has been speculation as to the presence and impacts of SBS within conservation management since Daniel Pauly's seminal paper in 1995, which outlined the potential effects of SBS on target-setting in fisheries management. Previous case studies have suggested that SBS may not occur in management, despite empirical evidence of SBS in other systems. In this study, 44 professionals and volunteers involved in bird species management, monitoring and target-setting across England were interviewed. Interviews asked for personal perceptions of current, maximum and target abundance, long-term trends, and perceived conservation priority for six bird species. Using paired tests, this study found no significant effect of experience on perceptions of current, maximum or target abundance of all species, despite differences in national abundance and trends, and differences in participant experience. Further power analysis indicated that even if SBS was statistically detectible with a larger sample, the practical implications of the syndrome would be minimal due to small effect sizes. Finally, the effect of experience on individual perceptions of species conservation priority varied between species, with generational amnesia in the form of 'lifting baselines' suggested for only one of the six species. This study suggests that shifting baseline syndrome may not be as significant a threat in conservation management as first thought., (Copyright © 2021. Published by Elsevier Ltd.)

The International Union for Conservation of Nature's Red List of Threatened Species (RLS) is the key global tool for objective, repeatable assessment of species' extinction risk status, and plays an essential role in tracking biodiversity loss and guiding conservation action. Satellite remote sensing (SRS) data sets on global ecosystem distributions and functioning show exciting potential for informing range-based RLS assessment, but their incorporation has been restricted by low temporal resolution and coverage of data sets, lack of incorporation of degradation-driven habitat loss, and noninclusion of assumptions related to identification of changing habitat distributions for taxa with varying habitat dependency and ecologies. For poorly known mangrove-associated Cuban hutias (Mesocapromys spp.), we tested the impact of possible assumptions regarding these issues on range-based RLS assessment outcomes. Specifically, we used annual (1985-2018) Landsat data and land-cover classification and habitat degradation analyses across different internal time series slices to simulate range-based RLS assessments for our case study taxa to explore potential assessment uncertainty arising from temporal SRS data set coverage, incorporating proxies of (change in) habitat quality, and assumptions on spatial scaling of habitat extent for RLS parameter generation. We found extensive variation in simulated species-specific range-based RLS assessments, and this variation was mostly associated with the time series over which parameters were estimated. However, results of some species-specific assessments differed by up to 3 categories (near threatened to critically endangered) within the same time series, due to the effects of incorporating habitat quality and the spatial scaling used in RLS parameter estimation. Our results showed that a one-size-fits-all approach to incorporating SRS information in RLS assessment is inappropriate, and we urge caution in conducting range-based assessments with SRS for species for which habitat dependence on specific ecosystem types is incompletely understood. We propose novel revisions to parameter spatial scaling guidelines to improve integration of existing time series data on ecosystem change into the RLS assessment process., (© 2021 The Authors. Conservation Biology published by Wiley Periodicals LLC on behalf of Society for Conservation Biology.)

Establishing protected areas (PAs) is an essential strategy to reduce biodiversity loss. However, many PAs do not provide adequate protection due to poor funding, inadequate staffing and equipment, and ineffective management. As part of China's recent economic growth, the Chinese government has significantly increased investment in nature reserves over the past 20 years, providing a unique opportunity to evaluate whether PAs can protect threatened species effectively. We compiled data from published literature on populations of gibbons (Hylobatidae), a threatened taxon with cultural significance, that occurred in Chinese reserves after 1980. We evaluated the ability of these PAs to maintain gibbon habitat and populations by comparing forest cover and human disturbance between reserves and their surrounding areas and modeling the impact of reserve characteristics on gibbon population trends. We also assessed the perspective of reserve staff concerning PA management effectiveness through an online survey. Reserves effectively protected gibbon habitat by reducing forest loss and human disturbance; however, half the reserves lost their gibbon populations since being established. Gibbons were more likely to survive in reserves established more recently, at higher elevation, with less forest loss and lower human impact, and that have been relatively well studied. A larger initial population size in the 1980s was positively associated with gibbon persistence. Although staff of all reserves reported increased investment and improved management over the past 20-30 years, no relationship was found between management effectiveness and gibbon population trends. We suggest early and emphatic intervention is critical to stop population decline and prevent extinction., (© 2020 Society for Conservation Biology.)

The Lesser Antillean island chain in the eastern Caribbean formerly supported a diverse rodent fauna including multiple endemic genera of oryzomyine rice rats. The Caribbean rice rats are now all extinct, with most island populations known only from Holocene palaeontological and zooarchaeological material and with many remaining taxonomically undescribed. Rice rat material is reported from several pre-Columbian Ceramic Age (late Holocene) archaeological sites on the Grenada Bank, including sites on Grenada and Carriacou, but the taxonomic identity and diversity of the Grenada Bank rice rats has remained uncertain. We provide a morphology-based description of rice rats from Grenada and Carriacou, and analyze their phylogenetic and biogeographical affinities to other Caribbean and mainland Neotropical oryzomyines. We recognize two taxa from the Grenada Bank: we describe the new species Megalomys camerhogne from Pearls (Grenada), representing the largest-bodied member of the extinct endemic Caribbean genus Megalomys, and we refer smaller-bodied oryzomyine material from Pearls and Sabazan (Carriacou) to the widespread extant Neotropical species Zygodontomys brevicauda. Body size variation within Megalomys correlates with island bank area and might thus reflect historical rather than modern biogeography. Zygodontomys specimens from the Grenada Bank fall within the upper end of size variation in extant populations and may constitute an example of 'island gigantism', but it is possible that occurrence of this widespread species on the Grenada Bank might reflect prehistoric human-mediated translocation. We predict further endemic Caribbean rice rat taxa remain to be discovered, including a possible species of Megalomys on the neighbouring island of St. Vincent.

Preventing extinctions requires understanding macroecological patterns of vulnerability or persistence. However, correlates of risk can be nonlinear, within-species risk varies geographically, and current-day threats cannot reveal drivers of past losses. We investigated factors that regulated survival or extinction in Caribbean mammals, which have experienced the globally highest level of human-caused postglacial mammalian extinctions, and included all extinct and extant Holocene island populations of non-volant species (219 survivals or extinctions across 118 islands). Extinction selectivity shows a statistically detectable and complex body mass effect, with survival probability decreasing for both mass extremes, indicating that intermediate-sized species have been more resilient. A strong interaction between mass and age of first human arrival provides quantitative evidence of larger mammals going extinct on the earliest islands colonized, revealing an extinction filter caused by past human activities. Survival probability increases on islands with lower mean elevation (mostly small cays acting as offshore refugia) and decreases with more frequent hurricanes, highlighting the risk of extreme weather events and rising sea levels to surviving species on low-lying cays. These findings demonstrate the interplay between intrinsic biology, regional ecology and specific local threats, providing insights for understanding drivers of biodiversity loss across island systems and fragmented habitats worldwide.

Reconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging from ∼0.1 to 200 kg and traditionally classified into three higher-order taxa (Capromyidae/Capromyinae, Heteropsomyinae, and Heptaxodontidae). Few species survive today, and the evolutionary affinities of living and extinct Caribbean caviomorphs to each other and to mainland taxa are unclear: Are they monophyletic, polyphyletic, or paraphyletic? We use ancient DNA techniques to present the first genetic data for extinct heteropsomyines and heptaxodontids, as well as for several extinct capromyids, and demonstrate through analysis of mitogenomic and nuclear data sets that all sampled Caribbean caviomorphs represent a well-supported monophyletic group. The remarkable morphological and ecological variation observed across living and extinct caviomorphs from Cuba, Hispaniola, Jamaica, Puerto Rico, and other islands was generated through within-archipelago evolutionary radiation following a single Early Miocene overwater colonization. This evolutionary pattern contrasts with the origination of diversity in many other Caribbean groups. All living and extinct Caribbean caviomorphs comprise a single biologically remarkable subfamily (Capromyinae) within the morphologically conservative living Neotropical family Echimyidae. Caribbean caviomorphs represent an important new example of insular mammalian adaptive radiation, where taxa retaining "ancestral-type" characteristics coexisted alongside taxa occupying novel island niches. Diversification was associated with the greatest insular body mass increase recorded in rodents and possibly the greatest for any mammal lineage., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

One of the most striking human impacts on global biodiversity is the ongoing depletion of large vertebrates from terrestrial and aquatic ecosystems. Recent work suggests this loss of megafauna can affect processes at biome or Earth system scales with potentially serious impacts on ecosystem structure and function, ecosystem services, and biogeochemical cycles. We argue that our contemporary approach to biodiversity conservation focuses on spatial scales that are too small to adequately address these impacts. We advocate a new global approach to address this conservation gap, which must enable megafaunal populations to recover to functionally relevant densities. We conclude that re-establishing biome and Earth system functions needs to become an urgent global priority for conservation science and policy., (Crown Copyright © 2020. Published by Elsevier Ltd. All rights reserved.)

To understand the current biodiversity crisis, it is crucial to determine how humans have affected biodiversity in the past. However, the extent of human involvement in species extinctions from the Late Pleistocene onward remains contentious. Here, we apply Bayesian models to the fossil record to estimate how mammalian extinction rates have changed over the past 126,000 years, inferring specific times of rate increases. We specifically test the hypothesis of human-caused extinctions by using posterior predictive methods. We find that human population size is able to predict past extinctions with 96% accuracy. Predictors based on past climate, in contrast, perform no better than expected by chance, suggesting that climate had a negligible impact on global mammal extinctions. Based on current trends, we predict for the near future a rate escalation of unprecedented magnitude. Our results provide a comprehensive assessment of the human impact on past and predicted future extinctions of mammals., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).)

Background: The Caribbean offers a unique opportunity to study evolutionary dynamics in insular mammals. However, the recent extinction of most Caribbean non-volant mammals has obstructed evolutionary studies, and poor DNA preservation associated with tropical environments means that very few ancient DNA sequences are available for extinct vertebrates known from the region's Holocene subfossil record. The endemic Caribbean eulipotyphlan family Nesophontidae ("island-shrews") became extinct ~ 500 years ago, and the taxonomic validity of many Nesophontes species and their wider evolutionary dynamics remain unclear. Here we use both morphometric and palaeogenomic methods to clarify the status and evolutionary history of Nesophontes species from Hispaniola, the second-largest Caribbean island., Results: Principal component analysis of 65 Nesophontes mandibles from late Quaternary fossil sites across Hispaniola identified three non-overlapping morphometric clusters, providing statistical support for the existence of three size-differentiated Hispaniolan Nesophontes species. We were also able to extract and sequence ancient DNA from a ~ 750-year-old specimen of Nesophontes zamicrus, the smallest non-volant Caribbean mammal, including a whole-mitochondrial genome and partial nuclear genes. Nesophontes paramicrus (39-47 g) and N. zamicrus (~ 10 g) diverged recently during the Middle Pleistocene (mean estimated divergence = 0.699 Ma), comparable to the youngest species splits in Eulipotyphla and other mammal groups. Pairwise genetic distance values for N. paramicrus and N. zamicrus based on mitochondrial and nuclear genes are low, but fall within the range of comparative pairwise data for extant eulipotyphlan species-pairs., Conclusions: Our combined morphometric and palaeogenomic analyses provide evidence for multiple co-occurring species and rapid body size evolution in Hispaniolan Nesophontes, in contrast to patterns of genetic and morphometric differentiation seen in Hispaniola's extant non-volant land mammals. Different components of Hispaniola's mammal fauna have therefore exhibited drastically different rates of morphological evolution. Morphological evolution in Nesophontes is also rapid compared to patterns across the Eulipotyphla, and our study provides an important new example of rapid body size change in a small-bodied insular vertebrate lineage. The Caribbean was a hotspot for evolutionary diversification as well as preserving ancient biodiversity, and studying the surviving representatives of its mammal fauna is insufficient to reveal the evolutionary patterns and processes that generated regional diversity.

Comparative assessment of the relative information content of different independent spatial data types is necessary to evaluate whether they provide congruent biogeographic signals for predicting species ranges. Opportunistic occurrence records and systematically collected survey data are available from the Dominican Republic for Hispaniola's surviving endemic non-volant mammals, the Hispaniolan solenodon ( Solenodon paradoxus ) and Hispaniolan hutia ( Plagiodontia aedium ); opportunistic records (archaeological, historical and recent) exist from across the entire country, and systematic survey data have been collected from seven protected areas. Species distribution models were developed in maxent for solenodons and hutias using both data types, with species habitat suitability and potential country-level distribution predicted using seven biotic and abiotic environmental variables. Three different models were produced and compared for each species: (a) opportunistic model, with starting model incorporating abiotic-only predictors; (b) total survey model, with starting model incorporating biotic and abiotic predictors; and (c) reduced survey model, with starting model incorporating abiotic-only predictors to allow further comparison with the opportunistic model. All models predict suitable environmental conditions for both solenodons and hutias across a broadly congruent, relatively large area of the Dominican Republic, providing a spatial baseline of conservation-priority landscapes that might support native mammals. Correlation between total and reduced survey models is high for both species, indicating the substantial explanatory power of abiotic variables for predicting Hispaniolan mammal distributions. However, correlation between survey models and opportunistic models is only moderately positive. Species distribution models derived from different data types can provide different predictions about habitat suitability and conservation-priority landscapes for threatened species, likely reflecting incompleteness and bias in spatial sampling associated with both data types. Models derived using both opportunistic and systematic data must therefore be applied critically and cautiously., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Palaeontologists often ask identical questions to those asked by ecologists. Despite this, ecology is considered a core discipline of conservation biology, while palaeontologists are rarely consulted in the protection of species, habitats and ecosystems. The recent emergence of conservation palaeobiology presents a big step towards better integration of palaeontology in conservation science, although its focus on historical baselines may not fully capture the potential contributions of geohistorical data to conservation science. In this essay we address previously defined priority questions in conservation and consider which of these questions may be answerable using palaeontological data. Using a statistical assessment of surveys, we find that conservation biologists and younger scientists have a more optimistic view of potential palaeontological contributions to the field compared to experienced palaeontologists. Participants considered questions related to climate change and marine ecosystems to be the best addressable with palaeontological data. As these categories are also deemed most relevant by ecologists and receive the greatest research effort in conservation, they are the natural choice for future academic collaboration. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Long-term baselines on biodiversity change through time are crucial to inform conservation decision-making in biodiversity hotspots, but environmental archives remain unavailable for many regions. Extensive palaeontological, zooarchaeological and historical records and indigenous knowledge about past environmental conditions exist for China, a megadiverse country experiencing large-scale biodiversity loss, but their potential to understand past human-caused faunal turnover is not fully assessed. We investigate a series of complementary environmental archives to evaluate the quality of the Holocene-historical faunal record of Hainan Island, China's southernmost province, for establishing new baselines on postglacial mammalian diversity and extinction dynamics. Synthesis of multiple archives provides an integrated model of long-term biodiversity change, revealing that Hainan has experienced protracted and ongoing human-caused depletion of its mammal fauna from prehistory to the present, and that past baselines can inform practical conservation management. However, China's Holocene-historical archives exhibit substantial incompleteness and bias at regional and country-wide scales, with limited taxonomic representation especially for small-bodied species, and poor sampling of high-elevation landscapes facing current-day climate change risks. Establishing a clearer understanding of the quality of environmental archives in threatened ecoregions, and their ability to provide a meaningful understanding of the past, is needed to identify future conservation-relevant historical research priorities. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Long-term faunal data are needed to track biodiversity change and extinction over wide spatio-temporal scales. The Holocene record is a particularly rich and well-resolved resource for this purpose but nonetheless represents a biased subset of the original faunal composition, both at the site-level assemblage and when data are pooled for wider-scale analysis. We investigated patterns and potential sources of taxonomic, spatial and temporal bias in two Holocene datasets of mammalian occurrence and abundance, one at the global species level and one at the continental population-level. Larger-bodied species are disproportionately abundant in the Holocene fossil record, but this varies according to trophic level, probably owing to past patterns of human subsistence and exploitation. Despite the uneven spatial distribution of mammalian occurrence records, we found no specific source of sampling bias, suggesting that this error type can be avoided by intensive data collection protocols. Faunal assemblages are more abundant and precisely dated nearer to the present as a consequence of taphonomy, past human demography and dating methods. Our study represents one of the first attempts to quantify incompleteness and bias in the Holocene mammal record, and failing to critically assess the quality of long-term faunal datasets has major implications for understanding species decline and extinction risk. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

How does past evolutionary performance impact future evolutionary performance? This is an important question not just for macroevolutionary biologists who wish to chart the phenomena that describe deep-time changes in biodiversity but also for conservation biologists, as evolutionarily distinct species-which may be deemed 'low-performing' in our current era-are increasingly the focus of conservation efforts. Contrasting hypotheses exist to account for the history and future of evolutionarily distinct species: on the one hand, they may be relicts of large radiations, potentially 'doomed' to extinction; or they may be slow-evolving, 'living fossils', likely neither to speciate nor go extinct; or they may be seeds of future radiations. Here, we attempt to test these hypotheses in Mammalia by combining a molecular phylogenetic supertree with fossil record occurrences and measuring change in evolutionary distinctness (ED) at different time slices. With these time slices, we modelled future ED as a function of past ED. We find that past evolutionary performance does indeed have an impact on future evolutionary performance: the most evolutionarily isolated clades tend to become more evolutionarily distinct with time, indicating that low-performing clades tend to remain low-performing throughout their evolutionary history. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Ecological baselines-reference states of species' distributions and abundances-are key to the scientific arguments underpinning many conservation and management interventions, as well as to the public support to such interventions. Yet societal as well as scientific perceptions of these baselines are often based on ecosystems that have been deeply transformed by human actions. Despite increased awareness about the pervasiveness and implications of this shifting baseline syndrome, ongoing global assessments of the state of biodiversity do not take into account the long-term, cumulative, anthropogenic impacts on biodiversity. Here, we propose a new framework for documenting such impacts, by classifying populations according to the extent to which they deviate from a baseline in the absence of human actions. We apply this framework to the bowhead whale ( Balaena mysticetus ) to illustrate how it can be used to assess populations with different geographies and timelines of known or suspected impacts. Through other examples, we discuss how the framework can be applied to populations for which there is a wide diversity of existing knowledge, by making the best use of the available ecological, historical and archaeological data. Combined across multiple populations, this framework provides a standard for assessing cumulative anthropogenic impacts on biodiversity. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon ( Solenodon paradoxus ). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 ( KLK1 ) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1 s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions., Competing Interests: The authors declare no competing interest., (Copyright © 2019 the Author(s). Published by PNAS.)

Samuel Turvey and Jennifer Crees introduce the effects of humans on biodiversity., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Inaccurate taxonomic assessment of threatened populations can hinder conservation prioritization and management, with human-mediated population movements obscuring biogeographic patterns and confounding reconstructions of evolutionary history. Giant salamanders were formerly distributed widely across China, and are interpreted as a single species, Andrias davidianus . Previous phylogenetic studies have identified distinct Chinese giant salamander lineages but were unable to associate these consistently with different landscapes, probably because population structure has been modified by human-mediated translocations for recent commercial farming. We investigated the evolutionary history and relationships of allopatric Chinese giant salamander populations with Next-Generation Sequencing methods, using historical museum specimens and late 20th-century samples, and retrieved partial or near-complete mitogenomes for 17 individuals. Samples from populations unlikely to have been affected by translocations form three clades from separate regions of China, spatially congruent with isolation by either major river drainages or mountain ranges. Pliocene-Pleistocene divergences for these clades are consistent with topographic modification of southern China associated with uplift of the Qinghai-Tibet Plateau. General Mixed Yule Coalescent model analysis indicates that these clades represent separate species: Andrias davidianus (Blanchard, 1871) (northern Yangtze/Sichuan), Andrias sligoi (Boulenger, 1924) (Pearl/Nanling), and an undescribed species (Huangshan). Andrias sligoi is possibly the world's largest amphibian. Inclusion of additional reportedly wild samples from areas of known giant salamander exploitation and movement leads to increasing loss of biogeographic signal. Wild Chinese giant salamander populations are now critically depleted or extirpated, and conservation actions should be updated to recognize the existence of multiple species., Competing Interests: None declared., (© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Humans are implicated as a major driver of species extinctions from the Late Pleistocene to the present. However, our predictive understanding of human-caused extinction remains poor due to the restricted temporal and spatial scales at which this process is typically assessed, and the risks of bias due to "extinction filters" resulting from a poor understanding of past species declines. We develop a novel continent-wide data set containing country-level last-occurrence records for 31 European terrestrial mammals across the Holocene (c.11,500 yr BP to present), an epoch of relative climatic stability that captures major transitions in human demography. We analyze regional extirpations against a high-resolution database of human population density (HPD) estimates to identify species-specific tolerances to changing HPD through the Holocene. Mammalian thresholds to HPD scale strongly with body mass, with larger-bodied mammals experiencing regional population losses at lower HPDs than smaller-bodied mammals. Our analysis enables us to identify levels of tolerance to HPD for different species, and therefore has wide applicability for determining biotic vulnerability to human impacts. This ecological pattern is confirmed across wide spatiotemporal scales, providing insights into the dynamics of prehistoric extinctions and the modern biodiversity crisis, and emphasizing the role of long-term archives in understanding human-caused biodiversity loss., (© 2019 by the Ecological Society of America.)

The Hispaniolan solenodon, Solenodon paradoxus , and Hispaniolan hutia, Plagiodontia aedium , are the Dominican Republic's only surviving endemic non-volant land mammals, and are high priorities for conservation. The country has an extensive protected area (PA) network designed to maintain habitats and benefit biodiversity, but which faces significant anthropogenic threats likely to detrimentally impact both species. We examined how differences in habitats, forest structure, topography, and human activity influence presence of solenodons and hutias across the Dominican Republic. Systematic surveys of seven PAs were undertaken to record indirect signs, with presence-absence data analyzed using a multi-model inference approach incorporating ecological variables from both field and GIS data. Solenodons were detected relatively frequently, whereas detections of hutias were uncommon. Lower elevations, increased surrounding tree cover, canopy closure, and reduced levels of low vegetation are all associated with increased probability of detecting solenodons, whereas agriculture and mangrove represent poor-quality habitat. Increased canopy closure, tree basal area (indicating older-growth forest), and increased rock substrate (providing more den sites) are associated with increased probability of detecting hutias. Our findings indicated that human activities within PAs are likely to negatively affect both species, and conservation activities should focus on preventing encroachment and conversion of forest to agriculture to maintain high-quality forest habitats. El solenodonte de la Hispaniola, Solenodon paradoxus , y la hutia de la Hispaniola, Plagiodontia aedium , son los únicos mamíferos endémicos terrestres no voladores que sobreviven en la República Dominicana, su conservación es de alta prioridad. El país tiene una extensa red de áreas protegidas (AP) diseñada para mantener hábitats y beneficiar la biodiversidad, pero se enfrenta a amenazas antropogénicas. Sin embargo, no existen datos cuantitativos para evaluar las presiones antropogénicas que amenazan a los solenodontes y las hutias. Examinamos cómo las diferencias en los hábitats, la estructura del bosque, la topografía y la actividad humana influyen la presencia de solenodontes y hutias en toda la República Dominicana. Se realizaron encuestas sistemáticas de siete AP para registrar los signos indirectos de ambas especies, los datos de presencia/ausencia fueron analizados mediante inferencia multimodelo que incorpora variables ecológicas de los datos de campo y Sistema de Información Geográfica. Los Solenodontes se detectaron relativamente frecuentemente, mientras que las detecciones de hutias fueron menos comunes. Las elevaciones más bajas, el aumento de la cubierta arbórea circundante, el cierre del dosel y los niveles reducidos de vegetación baja se asocian con una mayor probabilidad de detectar solenodones. Mientras que la agricultura y los manglares representan un hábitat de mala calidad para el solenodonte. Aumento del cierre del dosel, área basal del árbol (que indica un bosque más antiguo) y un sustrato con mayor proporcion de roca (que proporciona más sitios para madrigueras) se asocian con una mayor probabilidad de detectar hutias. Nuestros hallazgos indican que las actividades humanas dentro de las AP pueden afectar negativamente a ambas especies. Las actividades de conservación deberían enfocarse en mantener hábitats forestales de alta calidad por medio de prevenir la invasión y la conversión de los bosques a agricultura.

The insular Caribbean until recently contained a diverse mammal fauna including four endemic platyrrhine primate species, all of which died out during the Holocene. Previous morphological studies have attempted to establish how these primates are related to fossil and extant platyrrhines, whether they represent ancient or recent colonists, and whether they constitute a monophyletic group. These efforts have generated multiple conflicting hypotheses, from close sister-taxon relationships with several different extant platyrrhines to derivation from a stem platyrrhine lineage outside the extant Neotropical radiation. This diversity of opinion reflects the fact that Caribbean primates were morphologically extremely unusual, displaying numerous autapomorphies and apparently derived conditions present across different platyrrhine clades. Here we report ancient DNA data for an extinct Caribbean primate: a limited-coverage entire mitochondrial genome and seven regions of nuclear genome for the most morphologically derived taxon, the Jamaican monkey Xenothrix mcgregori We demonstrate that Xenothrix is part of the existing platyrrhine radiation rather than a late-surviving stem platyrrhine, despite its unusual adaptations, and falls within the species-rich but morphologically conservative titi monkey clade (Callicebinae) as sister to the newly recognized genus Cheracebus These results are not congruent with previous morphology-based hypotheses and suggest that even morphologically conservative lineages can exhibit phenetic plasticity in novel environments like those found on islands. Xenothrix and Cheracebus diverged ca. 11 Ma, but primates have been present in the Caribbean since 17.5-18.5 Ma, indicating that Caribbean primate diversity was generated by multiple over-water colonizations., Competing Interests: The authors declare no conflict of interest.

Madagascar's now-extinct radiation of large-bodied ratites, the elephant birds (Aepyornithidae), has been subject to little modern research compared to the island's mammalian megafauna and other Late Quaternary giant birds. The family's convoluted and conflicting taxonomic history has hindered accurate interpretation of morphological diversity and has restricted modern research into their evolutionary history, biogeography and ecology. We present a new quantitative analysis of patterns of morphological diversity of aepyornithid skeletal elements, including material from all major global collections of aepyornithid skeletal remains, and constituting the first taxonomic reassessment of the family for over 50 years. Linear morphometric data collected from appendicular limb elements, and including nearly all type specimens, were examined using multivariate cluster analysis and the Bayesian information criterion, and with estimation of missing data using multiple imputation and expectation maximization algorithms. These analyses recover three distinct skeletal morphotypes within the Aepyornithidae. Two of these morphotypes are associated with the type specimens of the existing genera Mullerornis and Aepyornis , and represent small-bodied and medium-bodied aepyornithids, respectively. Aepyornis contains two distinct morphometric subgroups, which are identified as the largely allopatric species A. hildebrandti and A. maximus. The third morphotype, which has not previously been recognized as a distinct genus, is described as the novel taxon Vorombe titan . Vorombe represents the largest-bodied aepyornithid and is the world's largest bird, with a mean body mass of almost 650 kg. This new taxonomic framework for the Aepyornithidae provides an important new baseline for future studies of avian evolution and the Quaternary ecology of Madagascar., Competing Interests: The authors have no competing interests.