Niche Contractions in Declining Species: Mechanisms and Consequences

Ecological dynamics of moa extinctions reveal convergent refugia that today harbour flightless birds

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 called moa that were endemic to New Zealand. Here 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 range contraction from an extensive fossil record. These process-based simulations revealed important interspecific differences in the ecological and demographic attributes of moa and established how these differences influenced likely trajectories of geographic and demographic declines of moa following Polynesian colonization of New Zealand. We show that despite these interspecific differences in extinction dynamics, the spatial patterns of geographic range collapse of moa species were probably similar. It is most likely that the final populations of all moa species persisted in suboptimal habitats in cold, mountainous areas that were generally last and least impacted by people. We find that these refugia for the last populations of moa continue to serve as isolated sanctuaries for New Zealand's remaining flightless birds, providing fresh insights for conserving endemic species in the face of current and future threats.

Climate change may reveal currently unavailable parts of species' ecological niches

The ability of climatic niche models to predict species extinction risks can be hampered if niches are incompletely quantified. This can occur when niches are estimated considering only currently available climatic conditions, disregarding the fact that climate change can open up portions of the fundamental niche that are currently inaccessible to species. Using a new metric, we estimate the prevalence of potential situations of fundamental niche truncation by measuring whether current ecological niche limits are contiguous to the boundaries of currently available climatic conditions for 24,944 species at the global scale in both terrestrial and marine realms and including animals and plants. We show that 12,172 (~49%) species are showing niche contiguity, particularly those inhabiting tropical ecosystems and the marine realm. Using niche expansion scenarios, we find that 86% of species showing niche contiguity could have a fundamental niche potentially expanding beyond current climatic limits, resulting in lower-yet still alarming-rates of predicted biodiversity loss, particularly within the tropics. Caution is therefore advised when forecasting future distributions of species presenting niche contiguity, particularly towards climatic limits that are predicted to expand in the future.

Climatically robust multiscale species distribution models to support pronghorn recovery in California

We combined two climate-based distribution models with three finer-scale suitability models to identify habitat for pronghorn recovery in California now and into the future. We used a consensus approach to identify areas of suitable climate now and future for pronghorn in California. We compared the results of climate models from two separate hypotheses about their historical ecology in the state. Under the migration hypothesis, pronghorn were expected to be limited climatically by extreme cold in winter and extreme heat in summer; under the niche reduction hypothesis, historical pronghorn of distribution would have better represented the climatic limitations of the species. We combined occurrences from GPS collars distributed across three populations of pronghorn in the state to create three distinct habitat suitability models: (1) an ensemble model using random forests, Maxent, classification and regression Trees, and a generalized linear model; (2) a step selection function; and (3) an expert-driven model. We evaluated consensus among both the climate models and the suitability models to prioritize areas for, and evaluate the prospects of, pronghorn recovery. Climate suitability for pronghorn in the future depends heavily on model assumptions. Under the migration hypothesis, our model predicted that there will be no suitable climate in California in the future. Under the niche reduction hypothesis, by contrast, suitable climate will expand. Habitat suitability also depended on the methods used, but areas of consensus among all three models exist in large patches throughout the state. Identifying habitat for a species which has undergone extreme range collapse, and which has very fine scale habitat needs, presents novel challenges for spatial ecologists. Our multimethod, multihypothesis approach can allow habitat modelers to identify areas of consensus and, perhaps more importantly, fill critical knowledge gaps that could resolve disagreements among the models. For pronghorn, a better understanding of their upper thermal tolerances and whether historical populations migrated will be crucial to their potential recovery in California and throughout the arid Southwest.

Niche-based approach to explore the impacts of environmental disturbances on biodiversity

Globally, species are increasingly at risk from compounding threatening processes, an increasingly prominent driver of which is environmental disturbances. To facilitate effective conservation efforts following such events, methods that evaluate potential impacts across multiple species and provide landscape-scale information are needed to guide targeted responses. Often, the geographic overlap between a disturbance and species' distribution is calculated and then used as a proxy for potential impact. However, such methods do not account for the important influence of environmental heterogeneity throughout species' ranges. To address this shortcoming, we quantified the effects of environmental disturbances on species' environmental niche space. Using the Australian 2019 and 2020 Black Summer fires as a case study, we applied a niche-centric approach to examine the potential impacts of these fires on 387 vertebrate species. We examined the utility of established and novel niche metrics to assess the potential impacts of large-scale disturbance events on species by comparing the potential effects of the fires as determined by our various niche measures to those derived from geographic-based measures of impact. We examined the quality of environmental space affected by the disturbance by quantifying the position in niche space where the disturbance occurred (center or margin), the uniqueness of the environmental space that was burned, and the degree to which the remaining, unburned portion of the niche differed from a species' original prefire niche. There was limited congruence between the proportion of geographic and niche space affected, which showed that geographic-based approaches in isolation may have underestimated the impact of the fires for 56% of modeled species. For each species, when combined, these metrics provided a greater indication of postdisturbance recovery potential than geographic-based measures alone. Accordingly, the integration of niche-based analyses into conservation assessments following large-scale disturbance events will lead to a more nuanced understanding of potential impacts and guide more informed and effective conservation actions.

Potential sources of time lags in calibrating species distribution models

The Anthropocene is characterized by a rapid pace of environmental change and is causing a multitude of biotic responses, including those that affect the spatial distribution of species. Lagged responses are frequent and species distributions and assemblages are consequently pushed into a disequilibrium state. How the characteristics of environmental change-for example, gradual 'press' disturbances such as rising temperatures due to climate change versus infrequent 'pulse' disturbances such as extreme events-affect the magnitude of responses and the relaxation times of biota has been insufficiently explored. It is also not well understood how widely used approaches to assess or project the responses of species to changing environmental conditions can deal with time lags. It, therefore, remains unclear to what extent time lags in species distributions are accounted for in biodiversity assessments, scenarios and models; this has ramifications for policymaking and conservation science alike. This perspective piece reflects on lagged species responses to environmental change and discusses the potential consequences for species distribution models (SDMs), the tools of choice in biodiversity modelling. We suggest ways to better account for time lags in calibrating these models and to reduce their leverage effects in projections for improved biodiversity science and policy.

Global erosion of terrestrial environmental space by artificial light at night

Artificial light at night (ALAN) disrupts natural light cycles, with biological impacts that span from behaviour of individual organisms to ecosystem functions, and across bacteria, fungi, plants and animals. Global consequences have almost invariably been inferred from the geographic distribution of ALAN. How ALAN is distributed in environmental space, and the extent to which combinations of environmental conditions with natural light cycles have been lost, is also key. Globally (between 60°N and 56°S), we ordinated four bioclimatic variables at 1.61 * 1.21 km resolution to map the position and density of terrestrial pixels within nighttime environmental space. We then used the Black Marble Nighttime Lights product to determine where direct ALAN emissions were present in environmental space in 2012 and how these had expanded in environmental space by 2022. Finally, we used the World Atlas of Artificial Sky Brightness to determine the proportion of environmental space that is unaffected by ALAN across its spatial distribution. We found that by 2012 direct ALAN emissions occurred across 71.9 % of possible nighttime terrestrial environmental conditions, with temperate nighttime environments and highly modified habitats disproportionately impacted. From 2012 to 2022 direct ALAN emissions primarily grew within 34.4 % of environmental space where it was already present, with this growth concentrated in tropical environments. Additionally considering skyglow, just 13.2 % of environmental space now only experiences natural light cycles throughout its distribution. With opportunities to maintain much of environmental space under such cycles fast disappearing, the removal, reduction and amelioration of ALAN from areas of environmental space in which it is already widespread is critical.

Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot

Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity-abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity.

An invasive pathogen drives directional niche contractions in amphibians

Global change is causing an unprecedented restructuring of ecosystems, with the spread of invasive species being a key driver. While population declines of native species due to invasives are well documented, much less is known about whether new biotic interactions reshape niches of native species. Here we quantify geographic range and realized-niche contractions in Australian frog species following the introduction of amphibian chytrid fungus Batrachochytrium dendrobatidis, a pathogen responsible for catastrophic amphibian declines worldwide. We show that chytrid-impacted species experienced proportionately greater contractions in niche breadth than geographic distribution following chytrid emergence. Furthermore, niche contractions were directional, with contemporary distributions of chytrid-impacted species characterized by higher temperatures, lower diurnal temperature range, higher precipitation and lower elevations. Areas with these conditions may enable host persistence with chytrid through lower pathogenicity of the fungus and/or greater demographic resilience. Nevertheless, contraction to a narrower subset of environmental conditions could increase host vulnerability to other threatening processes and should be considered in assessments of extinction risk and during conservation planning. More broadly, our results emphasize that biotic interactions can strongly shape species realized niches and that large-scale niche contractions due to new species interactions-particularly emerging pathogens-could be widespread.

Modeling the Wintering Habitat Distribution of the Black Stork in Shaanxi, China: A Hierarchical Integration of Climate and Land Use/Land Cover Data

Species distribution models (SDMs) are effective tools for wildlife conservation and management, as they employ the quantification of habitat suitability and environmental niches to evaluate the patterns of species distribution. The utilization of SDMs at various scales in a hierarchical approach can provide additional and complementary information, significantly improving decision-making in local wildlife conservation initiatives. In this study, we considered the appropriate spatial scale and data resolution to execute species distribution modeling, as these factors greatly influence the modeling procedures. We developed SDMs for wintering black storks at both the regional and local scales. At the regional scale, we used climatic and climate-driven land use/land cover (LULC) variables, along with wintering occurrence points, to develop models for mainland China. At the local scale, we used local environmental variables and locally gathered wintering site data to develop models for Shaanxi province. The predictions from both the regional and local models were then combined at the provincial level by overlapping suitable areas based on climatic and local conditions. We compared and evaluated the resulting predictions using seven statistical metrics. The national models provide information on the appropriate climatic conditions for the black stork during the wintering period throughout China, while the provincial SDMs capture the important local ecological factors that influence the suitability of habitats at a finer scale. As anticipated, the national SDMs predict a larger extent of suitable areas compared to the provincial SDMs. The hierarchical prediction approach is considered trustworthy and, on average, yields better outcomes than non-hierarchical methods. Our findings indicate that human-driven LULC changes have a significant and immediate impact on the wintering habitat of the black stork. However, the effects of climate change seem to be reducing the severity of this impact. The majority of suitable wintering habitats lie outside the boundaries of protected areas, highlighting the need for future conservation and management efforts to prioritize addressing these conservation gaps and focusing on the protection of climate refuges.

How does spatial extent and environmental limits affect the accuracy of species richness estimates from ecological niche models? A case study with North American Pinaceae and Cactaceae

Measuring species richness at varying spatial extents can be challenging, especially at large extents where exhaustive species surveys are difficult or impossible. Our work aimed at determining the reliability of species richness estimates from stacked ecological niche models at different spatial extents for taxonomic groups with vastly different environmental dependencies and interactions. To accomplish this, we generated ecological niche models for the species of Cactaceae and Pinaceae that occur within 180 published floras from North America north of Mexico. We overlaid or stacked the resulting species' potential distribution estimates over the bounding boxes representing each of the 180 floras to generate predictions of species richness. In general, our stacked models of Cactaceae and Pinaceae were poor predictors of species richness. The relationships between observed and predicted values improved noticeably with the size of spatial extents. However, the stacked models tended to overpredict the richness of Cactaceae and over- and underpredict the richness of Pinaceae. Cactaceae stacked models showed higher sensitivity and lower specificity than those for Pinaceae. We conclude that stacked ecological niche models may be somewhat poor predictors of species richness at smaller spatial extents and should be used with caution for this purpose. Perhaps more importantly, abilities to compensate for their limitations or apply corrections to their reliability may vary with taxonomic groups.

Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia

Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.

Increases in intraspecific body size variation are common among North American mammals and birds between 1880 and 2020

Many studies have documented the average body size of animals declining over time. Compared to mean body size, less is known about long-term changes in intraspecific trait variation (ITV), which is also important to understanding species' ability to cope with environmental challenges. On the basis of 393,499 specimen records from 380 species collected in North America between 1880 and 2020, we found that body size ITV increased by 9.59% for mammals (n = 302) and 30.67% for birds (n = 78); human-harvested species had higher probability of ITV increase. The observed increasing ITV in many species suggests possible niche expansion and potential buffering effects against downsizing but it risks increased maladaptation to rapidly changing environments. The results demonstrate that trait mean and variance do not necessarily respond in similar ways to anthropogenic pressures and both should be considered.

Effects of climate and land-cover change on the conservation status of gibbons

Species shift their distribution in response to climate and land-cover change, which may result in a spatial mismatch between currently protected areas (PAs) and priority conservation areas (PCAs). We examined the effects of climate and land-cover change on potential range of gibbons and sought to identify PCAs that would conserve them effectively. We collected global gibbon occurrence points and modeled (ecological niche model) their current and potential 2050s ranges under climate-change and different land-cover-change scenarios. We examined change in range and PA coverage between the current and future ranges of each gibbon species. We applied spatial conservation prioritization to identify the top 30% PCAs for each species. We then determined how much of the PCAs are conserved in each country within the global range of gibbons. On average, 31% (SD 22) of each species' current range was covered in PAs. PA coverage of the current range of 9 species was <30%. Nine species lost on average 46% (SD 29) of their potential range due to climate change. Under climate-change with an optimistic land-cover-change scenario (B1), 12 species lost 39% (SD 28) of their range. In a pessimistic land-cover-change scenario (A2), 15 species lost 36% (SD 28) of their range. Five species lost significantly more range under the A2 scenario than the B1 scenario (p = 0.01, SD 0.01), suggesting that gibbons will benefit from effective management of land cover. PA coverage of future range was <30% for 11 species. On average, 32% (SD 25) of PCAs were covered by PAs. Indonesia contained more species and PCAs and thus has the greatest responsibility for gibbon conservation. Indonesia, India, and Myanmar need to expand their PAs to fulfill their responsibility to gibbon conservation. Our results provide a baseline for global gibbon conservation, particularly for countries lacking gibbon research capacity.

Primates facing climate crisis in a tropical forest hotspot will lose climatic suitable geographical range

Global climate changes affect biodiversity and cause species distribution shifts, contractions, and expansions. Climate change and disease are emerging threats to primates, and approximately one-quarter of primates' ranges have temperatures over historical ones. How will climate changes influence Atlantic Forest primate ranges? We used habitat suitability models and measured potential changes in area and distributions shifts. Climate change expected in 2100 may change the distribution area of Atlantic Forest primates. Fourteen species (74%) are predicted to lose more than 50% of their distribution, and nine species (47%) are predicted to lose more than 75% of their distribution. The balance was negative, indicating a potential future loss, and the strength of the reduction in the distribution is related to the severity of climate change (SSP scenarios). Directional shifts were detected to the south. The projected mean centroid latitudinal shift is ~ 51 km to the south for 2100 SSP5-8.5 scenario. The possibility of dispersal will depend on suitable routes and landscape configuration. Greenhouse gas emissions should be urgently reduced. Our results also emphasize that no more forest loss is acceptable in Atlantic Forest, and restoration, canopy bridges, friendly agroecosystems, and monitoring of infrastructure projects are urgent to enable dealing with climate change.

Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.

Environmental factors influencing the distribution of the Kangaroo Island dunnart (Sminthopsis fuliginosus aitkeni)

Determining the factors that drive the distributions of threatened species is often critical for informing effective conservation management actions. Species distribution models can be used to distinguish common habitat features shared by limited historical records and identify other areas where a species might persist. In this study, we built a species distribution model for the Endangered and cryptic Kangaroo Island dunnart (Sminthopsis fuliginosus aitkeni). We fitted generalised linear models using incidental records and presence-absence data from surveys between 1969 and 2018. In the models we included the variables rainfall, percentage native vegetation in the surrounding 2 km2, and post-fire vegetation age. The modelling suggested that rainfall and to a lesser extent post-fire vegetation age are good predictors of dunnart occurrence, with dunnart occurrence greatest in areas of high rainfall (&gt;600 mm) and vegetation age classes &lt;30 years post fire. Potentially suitable habitat for the KI dunnart was predicted to be on the central-western side of Kangaroo Island. These results suggest that careful fire management could benefit the dunnart, and that decreased rainfall (as projected by Australian climate models), will be a threat in the long term. Extensive recent fires on western Kangaroo Island suggest that climate-related threats are already being realised.

Untapped potential of physiology, behaviour and immune markers to predict range dynamics and marginality

Linking environmental conditions to the modulators of individual fitness is necessary to predict long-term population dynamics, viability, and resilience. Functional physiological, behavioral, and reproductive markers can provide this mechanistic insight into how individuals perceive physiological, psychological, chemical, and physical environmental challenges through physiological and behavioral responses that are fitness proxies. We propose a Functional Marginality framework where relative changes in allostatic load, reproductive health, and behavior can be scaled up to evidence and establish causation of macroecological processes such as local extirpation, colonization, population dynamics, and range dynamics. To fully exploit functional traits, we need to move beyond single biomarker studies to develop an integrative approach that models the interactions between extrinsic challenges, physiological, and behavioral pathways and their modulators. In addition to providing mechanistic markers of range dynamics, this approach can also serve as a valuable conservation tool for evaluating individual- and population-level health, predicting responses to future environmental change and measuring the impact of interventions. We highlight specific studies that have used complementary biomarkers to link extrinsic challenges to population performance. These frameworks of integrated biomarkers have untapped potential to identify causes of decline, predict future changes, and mitigate against future biodiversity loss.

Niche lability mitigates the impact of invasion but not urbanization

Native species can coexist with invasive congeners by partitioning niche space; however, impacts from invasive species often occur alongside other disturbances. Native species' responses to the interactions of multiple disturbances remain poorly understood. Here we study the impacts of urbanization and an invasive congener on a native species. Using abundance (catch-per-unit effort) and vertical distribution of native green anoles (Anolis carolinensis) and invasive brown anoles (Anolis sagrei) across a gradient of natural-to-urban forests, we ask if niche shifting (lability) is occurring, and if it can mitigate impacts from one or both disturbances. We use generalized linear models to relate species abundances across the landscape to urbanization, forest structural complexity, and congener abundances (i.e., A. sagrei); and test for an interaction between urbanization and congener abundance. Our data show that A. sagrei presence results in a 17-fold upward shift in vertical niche of A. carolinensis-an 8.3 m shift in median perch height, and models reveal urbanization also drives an increase in A. carolinensis perch height. A. carolinensis and A. sagrei abundances negatively and positively correlate with urbanization, respectively, and neither species' abundance correlate with congener abundance. Despite a positive correlation between A. sagrei abundance and urbanization, our results do not show evidence of this interaction affecting A. carolinensis. Instead, niche lability appears to enable the native species to mitigate the impact of one driver of decline (invasive competition) while our data suggest it declines with the second (urbanization).

Species co-occurrence and management intensity modulate habitat preferences of forest birds

Background

Species co-occurrences can have profound effects on the habitat use of species, and therefore habitat structure alone cannot fully explain observed abundances. To account for this aspect of community organization, we developed multi-species abundance models, incorporating the local effect of co-occurring and potentially associated species, alongside with environmental predictors, linked mainly to forest management intensity. We coupled it with a landscape-scale analysis to further examine the role of management intensity in modifying the habitat preferences in connection with the landscape context. Using empirical data from the Black Forest in southern Germany, we focused on the forest bird assemblage and in particular on the cavity-nesting and canopy-foraging guilds. We included in the analysis species that co-occur and for which evidence suggests association is likely.

Results

Our findings show that the local effect of species associations can mitigate the effects of management intensity on forest birds. We also found that bird species express wider habitat preferences in forests under higher management intensity, depending on the landscape context.

Conclusions

We suspect that species associations may facilitate the utilization of a broader range of environmental conditions under intensive forest management, which benefits some species over others. Networks of associations may be a relevant factor in the effectiveness of conservation-oriented forest management.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01136-8.

Declining amphibians might be evolving increased reproductive effort in the face of devastating disease

The devastating infectious disease chytridiomycosis has caused declines of amphibians across the globe, yet some populations are persisting and even recovering. One understudied effect of wildlife disease is changes in reproductive effort. Here, we aimed to understand if the disease has plastic effects on reproduction and if reproductive effort could evolve with disease endemism. We compared the effects of experimental pathogen exposure (trait plasticity) and population-level disease history (evolution in trait baseline) on reproductive effort using gametogenesis as a proxy in the declining and endangered frog Litoria verreauxii alpina. We found that unexposed males from disease-endemic populations had higher reproductive effort, which is consistent with an evolutionary response to chytridiomycosis. We also found evidence of trait plasticity, where males and females were affected differently by infection: pathogen exposed males had higher reproductive effort (larger testes), whereas females had reduced reproductive effort (smaller and fewer developed eggs) regardless of the population of origin. Infectious diseases can cause plastic changes in the reproductive effort at an individual level, and population-level disease exposure can result in changes to baseline reproductive effort; therefore, individual- and population-level effects of disease should be considered when designing management and conservation programs for threatened and declining species.

Novel Conditions in Conservation Translocations: A Conservative-Extrapolative Strategic Framework

In response to anthropogenic threats, conservation translocations are increasingly used to combat species' population and range declines. However, moving animals outside of their current distribution can mean introducing them to novel conditions, even in the case of reintroductions to formerly inhabited areas due to ecosystem changes following extirpation. This exposure to novel conditions introduces uncertainty that can undermine decision making for species conservation. Here we propose two strategies, which we define as conservative and extrapolative, for approaching and managing novelty and the resulting uncertainty in conservation translocations. Conservative strategies are characterised by the avoidance and removal of novel conditions as much as possible, whereas extrapolative strategies are more experimental, allowing exposure to novel conditions and monitoring outcomes to increase understanding of a species' ecology. As each strategy carries specific risks and opportunities, they will be applicable in different scenarios. Extrapolative strategies suit species in recovery which can afford some experimental management, or species facing novel and emerging threats which require less traditional translocations, such as assisted colonisations. We provide examples, applying our framework to two endemic New Zealand species with long histories of translocation management: tuatara (Sphenodon punctatus), a reptile and takahē (Porphyrio hochstetteri), a flightless bird.

Population genomics and conservation management of a declining tropical rodent

Conservation management is improved by incorporating information about the spatial distribution of population genetic diversity into planning strategies. Northern Australia is the location of some of the world's most severe ongoing declines of endemic mammal species, yet we have little genetic information from this regional mammal assemblage to inform a genetic perspective on conservation assessment and planning. We used next-generation sequencing data from remnant populations of the threatened brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of genomic diversity and differentiation across the landscape and investigate standardised hierarchical genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We found strong population structuring, with high levels of differentiation between populations (F_ST = 0.21-0.78). Two distinct genomic lineages between the Tiwi Islands and mainland are also present. Prioritisation analysis showed that one population in both lineages would need to be conserved to retain at least ~80% of alleles for the species. Analysis of standardised genomic diversity metrics showed that approximately half of the total diversity occurs among lineages (δ = 0.091 from grand total γ = 0.184). We suggest that a focus on conserving remnant island populations may not be appropriate for the preservation of species-level genomic diversity and adaptive potential, as these populations represent a small component of the total diversity and a narrow subset of the environmental conditions in which the species occurs. We also highlight the importance of considering both genomic and ecological differentiation between source and receiving populations when considering translocations for conservation purposes.

Human-modified landscapes narrow the isotopic niche of neotropical birds

Deforestation and habitat loss resulting from land use changes are some of the utmost anthropogenic impacts that threaten tropical birds in human-modified landscapes (HMLs). The degree of these impacts on birds' diet, habitat use, and ecological niche can be measured by isotopic analysis. We investigated whether the isotopic niche width, food resources, and habitat use of bird trophic guilds differed between HMLs and natural landscapes (NLs) using stable carbon (δ¹³C) and nitrogen isotopes (δ¹⁵N). We analyzed feathers of 851 bird individuals from 28 landscapes in the Brazilian Atlantic Forest. We classified landscapes into two groups according to the percentage of forest cover (HMLs ≤ 30%; NLs ≥ 47%), and compared the isotopic niche width and mean values of δ¹³C and δ¹⁵N for each guild between landscape types. The niches of frugivores, insectivores, nectarivores, and omnivores were narrower in HMLs, whereas granivores showed the opposite pattern. In HMLs, nectarivores showed a reduction of 44% in niche width, while granivores presented an expansion of 26%. Individuals in HMLs consumed more resources from agricultural areas (C₄ plants), but almost all guilds showed a preference for forest resources (C₃ plants) in both landscape types, except granivores. Degraded and fragmented landscapes typically present a lower availability of habitat and food resources for many species, which was reflected by the reduction in niche width of birds in HMLs. Therefore, to protect the diversity of guilds in HMLs, landscape management strategies that offer birds more diverse habitats must be implemented in tropical regions.

Effects of climate change and land cover on the distributions of a critical tree family in the Philippines

Southeast Asian forests are dominated by the tree family Dipterocarpaceae, whose abundance and diversity are key to maintaining the structure and function of tropical forests. Like most biodiversity, dipterocarps are threatened by deforestation and climate change, so it is crucial to understand the potential impacts of these threats on current and future dipterocarp distributions. We developed species distribution models (SDMs) for 19 species of dipterocarps in the Philippines, which were projected onto current and two 2070 representative concentration pathway (RCP) climate scenarios, RCP 4.5 and 8.5. Current land cover was incorporated as a post-hoc correction to restrict projections onto intact habitats. Land cover correction alone reduced current species distributions by a median 67%, and within protected areas by 37%. After land cover correction, climate change reduced distributions by a median 16% (RCP 4.5) and 27% (RCP 8.5) at the national level, with similar losses in protected areas. There was a detectable upward elevation shift of species distributions, consisting of suitable habitat losses below 300 m and gains above 600 m. Species-rich stable areas of continued habitat suitability (i.e., climate macrorefugia) fell largely outside current delineations of protected areas, indicating a need to improve protected area planning. This study highlights how SDMs can provide projections that can inform protected area planning in the tropics.

Hidden invasion and niche contraction revealed by herbaria specimens in the fungal complex causing oak powdery mildew in Europe

Deciphering the dynamics involved in past microbial invasions has proven difficult due to the inconspicuous nature of microbes and their still poorly known diversity and biogeography. Here we focus on powdery mildew, a common disease of oaks which emerged in Europe at the beginning of the twentieth century and for which three closely related Erysiphe species are mainly involved. The study of herbaria samples combined with an experimental approach of interactions between Erysiphe species led us to revisit the history of this multiple invasion. Contrary to what was previously thought, herbaria sample analyses very strongly suggested that the currently dominant species, E. alphitoides, was not the species which caused the first outbreaks and was described as a new species at that time. Instead, E. quercicola was shown to be present since the early dates of disease reports and to be widespread all over Europe in the beginning of the twentieth century. E. alphitoides spread and became progressively dominant during the second half of the twentieth century while E. quercicola was constrained to the southern part of its initial range, corresponding to its current distribution. A competition experiment provided a potential explanation of this over-invasion by demonstrating that E. alphitoides had a slight advantage over E. quercicola by its ability to infect leaves during a longer period during shoot development. Our study is exemplary of invasions with complexes of functionally similar species, emphasizing that subtle differences in the biology of the species, rather than strong competitive effects may explain patterns of over-invasion and niche contraction.

Nest-site selection of a subarctic-breeding shorebird: evidence for tree avoidance without fitness consequences

Vegetation communities in the subarctic are at risk of change due to climate-driven tree and shrub encroachment. Vegetation change may lead to unsuitable habitat for arctic-breeding birds, many of whom are declining. Although many possible factors are contributing to their decline, loss of breeding habitat could be a major contributor. We examined nest-site selection in Dunlin (Calidris alpina hudsonia (Todd, 1953)), a shorebird that nests in open fen habitats in the Churchill, Manitoba, Canada, region. Our objective was to determine whether this species avoids treed habitats and the possible fitness consequences for this. We examined the role of vegetative horizontal and vertical concealments on nest-site selection and nest fate. Dunlin selected nest sites with lower densities of trees than present at unused sites (40 m radius). Both horizontal and vertical concealments were significantly greater at nests than at unused sites, and horizontal concealment was greatest in the north. No measure of tree density or height, or concealment, significantly predicted nest fate. Although Dunlin appear to select nest sites that may minimize exposure to northerly winds and that may provide cover against potential predators, the current nest-site characteristics are not reinforced by contemporary selection.

Predicting the distribution of a rare chipmunk (Neotamias quadrivittatus oscuraensis): comparing MaxEnt and occupancy models

Species distribution models (SDMs) use presence records to determine the relationship between species occurrence and various environmental variables to create predictive maps describing the species’ distribution. The Oscura Mountains Colorado chipmunk (Neotamias quadrivittatus oscuraensis) occurs in central New Mexico and is of conservation concern due to its relict distribution and threats to habitat. We previously created an occupancy model for this taxon, but were concerned that the model may not have adequately captured the ecological factors influencing the chipmunk’s distribution because of the data hungry nature of occupancy modeling. MaxEnt is another SDM method that is particularly effective at testing large numbers of variables and handling small sample sizes. Our goal was to create a MaxEnt model for the Oscura Mountains Colorado chipmunk and to compare it with our previous occupancy model for this taxon, either to strengthen our original assessment of the relevant ecological factors or identify additional factors that were not captured by our occupancy model. We created MaxEnt models using occurrence records from baited camera traps and opportunistic surveys. We adjusted model complexity using a novel method for tuning both the regularization multiplier and feature class parameters while also performing variable selection. We compared the distribution maps and variables selected by MaxEnt to the results of our occupancy model for this taxon. The MaxEnt and occupancy models selected similar environmental variables and the overall spatial pattern of occurrence was similar for each model. Likelihood of occurrence was positively related to elevation, piñon woodland vegetation type, and topographic variables associated with escarpments. The overall similarities between the MaxEnt and occupancy models increased our confidence of the ecological factors influencing the distribution of the chipmunk. We conclude that MaxEnt offers advantages for predicting the distribution of rare species, which can help inform conservation actions.

Niche Models Differentiate Potential Impacts of Two Aquatic Invasive Plant Species on Native Macrophytes

Potamogeton crispus (curlyleaf pondweed) and Myriophyllum spicatum (Eurasian watermilfoil) are widely thought to competitively displace native macrophytes in North America. However, their perceived competitive superiority has not been comprehensively evaluated. Coexistence theory suggests that invader displacement of native species through competitive exclusion is most likely where high niche overlap results in competition for limiting resources. Thus, evaluation of niche similarity can serve as a starting point for predicting the likelihood of invaders having direct competitive impacts on resident species. Across two environmental gradients structuring macrophyte communities—water depth and light availability—both P. crispus and M. spicatum are thought to occupy broad niches. For a third dimension, phenology, the annual growth cycle of M. spicatum is typical of other species, whereas the winter-ephemeral phenology of P. crispus may impart greater niche differentiation and thus lower risk of native species being competitively excluded. Using an unprecedented dataset comprising 3404 plant surveys from Minnesota collected using a common protocol, we modeled niches of 34 species using a probabilistic niche framework. Across each niche dimension, P. crispus had lower overlap with native species than did M. spicatum; this was driven in particular by its distinct phenology. These results suggest that patterns of dominance seen in P. crispus and M. spicatum have likely arisen through different mechanisms, and that direct competition with native species is less likely for P. crispus than M. spicatum. This research highlights the utility of fine-scale, abundance-based niche models for predicting invader impacts.

Global conservation of species' niches

Environmental change is rapidly accelerating, and many species will need to adapt to survive¹. Ensuring that protected areas cover populations across a broad range of environmental conditions could safeguard the processes that lead to such adaptations^1-3. However, international conservation policies have largely neglected these considerations when setting targets for the expansion of protected areas⁴. Here we show that-of 19,937 vertebrate species globally^5-8-the representation of environmental conditions across their habitats in protected areas (hereafter, niche representation) is inadequate for 4,836 (93.1%) amphibian, 8,653 (89.5%) bird and 4,608 (90.9%) terrestrial mammal species. Expanding existing protected areas to cover these gaps would encompass 33.8% of the total land surface-exceeding the current target of 17% that has been adopted by governments. Priority locations for expanding the system of protected areas to improve niche representation occur in global biodiversity hotspots⁹, including Colombia, Papua New Guinea, South Africa and southwest China, as well as across most of the major land masses of the Earth. Conversely, we also show that planning for the expansion of protected areas without explicitly considering environmental conditions would marginally reduce the land area required to 30.7%, but that this would lead to inadequate niche representation for 7,798 (39.1%) species. As the governments of the world prepare to renegotiate global conservation targets, policymakers have the opportunity to help to maintain the adaptive potential of species by considering niche representation within protected areas^1,2.