Population decline assessment, historical baselines, and conservation

The potential of historical spy-satellite imagery to support research in ecology and conservation

Remote sensing data are important for assessing ecological change, but their value is often restricted by their limited temporal coverage. Major historical events that affected the environment, such as those associated with colonial history, World War II, or the Green Revolution are not captured by modern remote sensing. In the present article, we highlight the potential of globally available black-and-white satellite photographs to expand ecological and conservation assessments back to the 1960s and to illuminate ecological concepts such as shifting baselines, time-lag responses, and legacy effects. This historical satellite photography can be used to monitor ecosystem extent and structure, species' populations and habitats, and human pressures on the environment. Even though the data were declassified decades ago, their use in ecology and conservation remains limited. But recent advances in image processing and analysis can now unlock this research resource. We encourage the use of this opportunity to address important ecological and conservation questions.

100 years of anthropogenic impact causes changes in freshwater functional biodiversity

Despite efforts from scientists and regulators, biodiversity is declining at an alarming rate. Unless we find transformative solutions to preserve biodiversity, future generations may not be able to enjoy nature's services. We have developed a conceptual framework that establishes the links between biodiversity dynamics and abiotic change through time and space using artificial intelligence. Here, we apply this framework to a freshwater ecosystem with a known history of human impact and study 100 years of community-level biodiversity, climate change and chemical pollution trends. We apply explainable network models with multimodal learning to community-level functional biodiversity measured with multilocus metabarcoding, to establish correlations with biocides and climate change records. We observed that the freshwater community assemblage and functionality changed over time without returning to its original state, even if the lake partially recovered in recent times. Insecticides and fungicides, combined with extreme temperature events and precipitation, explained up to 90% of the functional biodiversity changes. The community-level biodiversity approach used here reliably explained freshwater ecosystem shifts. These shifts were not observed when using traditional quality indices (e.g. Trophic Diatom Index). Our study advocates the use of high-throughput systemic approaches on long-term trends over species-focused ecological surveys to identify the environmental factors that cause loss of biodiversity and disrupt ecosystem functions.

180 years of marine animal diversity as perceived by public media in southern Brazil

Commoditization of marine resources has dramatically increased anthropogenic footprints on coastal and ocean systems, but the scale of these impacts remain unclear due to a pervasive lack of historical baselines. Through the analysis of historical newspapers, this paper explores changes in marine animals (vertebrates and invertebrates) targeted by historical fisheries in southern Brazil since the late 19th century. The investigation of historical newspaper archives revealed unprecedented information on catch composition, and perceived social and economic importance of key species over decades, predating official national-level landing records. We show that several economically and culturally important species have been under persistent fishing pressure at least since the first national-scale subsidies were introduced for commercial fisheries in Brazil in the late 19th and early 20th centuries. Our work expands the current knowledge on historical fish catch compositions in the southwestern Atlantic Ocean, while advocating for the integration of historical data in ocean sustainability initiatives.

Factors Affecting Habitat Selection of Endangered Steppe Eagle (Aquila nipalensis) in Pakistan: Implications for Raptors Conservation

The steppe eagle (Aquila nipalensis) is an endangered migratory raptor species that migrates in winter to Pakistan and neighbouring countries. In Pakistan, the species migrate at the end of autumn and utilise different habitats across the country. Very little information is available about the species’ population status, distribution, and factors affecting its distribution in Pakistan. In the present study, we predicted the distribution of steppe eagles in Pakistan associated with different environmental variables. We used 149 presence points of the species from an online source (GBIF), published literature, and wildlife photographers. The MaxEnt analysis showed that highly suitable habitats were mostly present in Azad Jammu and Kashmir (AJK), federally administered areas and surrounding areas, southern areas of Sindh Province, and some parts of Khyber Pakhtunkhwa (KP) Province. In addition, some patches were also predicted by MaxEnt in Balochistan Province. Human population density (27.0%), chicken density (16.6%), temperature seasonality (11.1%), and rivers (10.3%) were identified as the main environmental factors that affect the habitat distribution of steppe eagle in Pakistan. Only a small percentage (2.62%) of the total Pakistan area was estimated to be a highly suitable area for steppe eagles, while 20.58% and 7.46% were identified as the least and moderately suitable areas, respectively. Conservation of identified habitats and mitigation of anthropogenic impacts to conserve this endangered eagle species are recommended for immediate and long-term conservation across Pakistan.

The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn

Endangered species with small population sizes are susceptible to genetic erosion, which can be detrimental to long-term persistence. Consequently, monitoring and mitigating the loss of genetic diversity are essential for conservation. The Peninsular pronghorn (Antilocapra americana peninsularis) is an endangered pronghorn subspecies that is almost entirely held in captivity. Captive breeding has increased the number of pronghorns from 25 founders in 1997 to around 700 individuals today, but it is unclear how the genetic diversity of the captive herd may have changed over time. We therefore generated and analysed data for 16 microsatellites spanning 2009-2021. We detected a decline in heterozygosity and an increase in the proportion of inbred individuals over time. However, these trends appear to have been partially mitigated by a genetically informed breeding management attempt that was implemented in 2018. We also reconstructed the recent demographic history of the Peninsular pronghorn, revealing two sequential population declines putatively linked to the desertification of the Baja California peninsula around 6000 years ago, and hunting and habitat loss around 500 years ago, respectively. Our results provide insights into the genetic diversity of an endangered antelope and indicate the potential for genetically informed management to have positive conservation outcomes.

Quantifying the impacts of 166 years of land cover change on lowland bird communities

Land cover change for agriculture is thought to be a major threat to global biodiversity. However, its ecological impact has rarely been quantified in the Northern Hemisphere, as broad-scale conversion to farmland mainly occurred until the 1400s-1700s in the region, limiting the availability of sufficient data. The Ishikari Lowland in Hokkaido, Japan, offers an excellent opportunity to address this issue, as hunter-gatherer lifestyles dominated this region until the mid-nineteenth century and land cover maps are available for the period of land cover changes (i.e. 1850-2016). Using these maps and a hierarchical community model of relationships between breeding bird abundance and land cover types, we estimated that broad-scale land cover change over a 166-year period was associated with more than 70% decline in both potential species richness and abundance of avian communities. We estimated that the abundance of wetland and forest species declined by greater than 88%, whereas that of bare-ground/farmland species increased by more than 50%. Our results suggest that broad-scale land cover change for agriculture has led to drastic reductions in wetland and forest species and promoted changes in community composition in large parts of the Northern Hemisphere. This study provides potential baseline information that could inform future conservation policies.

Reconstructing Long-Term Changes in Avian Populations Using Lake Sediments: Opening a Window Onto the Past

The lack of long-term monitoring data for many wildlife populations is a limiting factor in establishing meaningful and achievable conservation goals. Even for well-monitored species, time series are often very short relative to the timescales required to understand a population’s baseline conditions before the contemporary period of increased human impacts. To fill in this critical information gap, techniques have been developed to use sedimentary archives to provide insights into long-term population dynamics over timescales of decades to millennia. Lake and pond sediments receiving animal inputs (e.g., feces, feathers) typically preserve a record of ecological and environmental information that reflects past changes in population size and dynamics. With a focus on bird-related studies, we review the development and use of several paleolimnological proxies to reconstruct past colony sizes, including trace metals, isotopes, lipid biomolecules, diatoms, pollen and non-pollen palynomorphs, invertebrate sub-fossils, pigments, and others. We summarize how animal-influenced sediments, cored from around the world, have been successfully used in addressing some of the most challenging questions in conservation biology, namely: How dynamic are populations on long-term timescales? How may populations respond to climate change? How have populations responded to human intrusion? Finally, we conclude with an assessment of the current state of the field, challenges to overcome, and future potential for research.

Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species

Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.

Trophy quality trends and hunting effort of selected big game in Chewore South Safari Area, northern Zimbabwe, 2009-2012

This study was based on a temporal analysis of trophy quality trends and hunting effort in Chewore South Safari Area (CSSA), Zimbabwe, for the period 2009–2012. We selected four of the big five species, namely; buffalo (Syncerus caffer), elephant (Loxodonta africana), the leopard (Panthera pardus) and lion (Panthera leo) for analysis. Existing database of 188 trophies from 2009 to 2011 was reviewed and recorded using the Safari Club International (SCI) scoring system. Further, 50 trophies for 2012 were measured and recorded based on the SCI scoring system. Local ecological knowledge on trophy quality and hunting effort in CSSA was obtained through semi-structured questionnaires from 22 conveniently selected professional hunters in 2012. The results indicated no significant change in trophy quality trends of buffalo, leopard and lion (p > 0.05) over the study period. In contrast, there was a significant decline in elephant trophy quality trend over the same period (p < 0.05). The results showed no significant change in hunting effort over the study period for all the four study species (p > 0.05). Furthermore, seventy-two percent (72%, n = 13) of the professional hunters confirmed that elephant population was declining in CSSA and this was likely due to poaching. Professional hunters perceived trophy hunting as a source of financial capital generation for wildlife conservation (61%, n = 11), as well as positively contributing to the local economy (56%, n = 10). It was concluded that hunting has limited negative impact on species trophy quality trends when a sustainable hunting system is consistently followed in CSSA. CSSA management need to continuously monitor trophy hunting, animal populations and employ adaptive management approach to quota setting and species conservation.

Reference state and benchmark concepts for better biodiversity conservation in contemporary ecosystems

Measuring the status and trends of biodiversity is critical for making informed decisions about the conservation, management or restoration of species, habitats and ecosystems. Defining the reference state against which status and change are measured is essential. Typically, reference states describe historical conditions, yet historical conditions are challenging to quantify, may be difficult to falsify, and may no longer be an attainable target in a contemporary ecosystem. We have constructed a conceptual framework to help inform thinking and discussion around the philosophical underpinnings of reference states and guide their application. We characterize currently recognized historical reference states and describe them as Pre-Human, Indigenous Cultural, Pre-Intensification and Hybrid-Historical. We extend the conceptual framework to include contemporary reference states as an alternative theoretical perspective. The contemporary reference state framework is a major conceptual shift that focuses on current ecological patterns and identifies areas with higher biodiversity values relative to other locations within the same ecosystem, regardless of the disturbance history. We acknowledge that past processes play an essential role in driving contemporary patterns of diversity. The specific context for which we design the contemporary conceptual frame is underpinned by an overarching goal-to maximize biodiversity conservation and restoration outcomes in existing ecosystems. The contemporary reference state framework can account for the inherent differences in the diversity of biodiversity values (e.g. native species richness, habitat complexity) across spatial scales, communities and ecosystems. In contrast to historical reference states, contemporary references states are measurable and falsifiable. This 'road map of reference states' offers perspective needed to define and assess the status and trends in biodiversity and habitats. We demonstrate the contemporary reference state concept with an example from south-eastern Australia. Our framework provides a tractable way for policy-makers and practitioners to navigate biodiversity assessments to maximize conservation and restoration outcomes in contemporary ecosystems.

Estimating biodiversity changes in the Camargue wetlands: An expert knowledge approach

Mediterranean wetlands are critical strongholds for biodiversity and the provision of ecosystem functions and services; yet, they are being severely degraded by a number of socio-economic drivers and pressures, including climate change. Moreover, we still lack comprehensive understanding of the extent to which biodiversity loss in Mediterranean wetlands will accelerate change in ecosystem processes. Here, we evaluate how changes in biodiversity can alter the ecosystem of the Camargue (southern France). We collected data on species presence/absence, trends and abundance over a 40-year period by combining observations from the scholarly literature with insights derived from expert knowledge. In total, we gathered more than 1500 estimates of presence/absence, over 1400 estimates of species abundance, and about 1400 estimates of species trends for eight taxonomic groups, i.e. amphibians, reptiles, breeding birds, fish, mammals, dragonflies (odonates), orthopterans and vascular plants. Furthermore, we used information on recently arrived species and invasive species to identify compositional changes across multiple taxa. Complementing targeted literature searches with expert knowledge allowed filling important gaps regarding the status and trends of biodiversity in the Camargue. Species trend data revealed sharp population declines in amphibians, odonates and orthopterans, while birds and plants experienced an average increase in abundance between the 1970s and the 2010s. The general increasing trends of novel and invasive species is suggested as an explanation for the changing abundance of birds and plants. While the observed declines in certain taxa reflect the relative failure of the protection measures established in the Camargue, the increasing exposure to novel and invasive species reveal major changes in the community structure of the different taxonomic groups. This study is the first attempt to assess changes in biodiversity in the Camargue using an expert knowledge approach, and can help manage the uncertainties and complexities associated with rapid social-ecological change in other Mediterranean wetlands.

Climate, Fascism, and Ibex: Experiments in Using Population Dynamics Modeling as a Historiographical Tool

In the interwar years the Gran Paradiso ibex population followed two subsequent, contrasting trends: a steady rise once the national park was established in 1922, followed by a precipitous fall after the Fascist regime took direct control of conservation in 1934, which almost led to the colony's extinction. This paper addresses the issue of how models taken from population ecology may inform historical narratives. The data for the interwar years were analyzed using a statistical model based on climate and population density, which has proved reliable for most of the post-World War II period. The article highlights the pivotal role of anthropic variables in determining the inter-war trends and how these are best analyzed using historical scholarship.

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

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.

Collapse of a desert bird community over the past century driven by climate change

Deserts, already defined by climatic extremes, have warmed and dried more than other regions in the contiguous United States due to climate change. Our resurveys of sites originally visited in the early 20th century found Mojave Desert birds strongly declined in occupancy and sites lost nearly half of their species. Declines were associated with climate change, particularly decreased precipitation. The magnitude of the decline in the avian community and the absence of species that were local climatological “winners” are exceptional. Our results provide evidence that bird communities in the Mojave Desert have collapsed to a new, lower baseline. Declines could accelerate with future climate change, as this region is predicted to become drier and hotter by the end of the century.

Climate change has caused deserts, already defined by climatic extremes, to warm and dry more rapidly than other ecoregions in the contiguous United States over the last 50 years. Desert birds persist near the edge of their physiological limits, and climate change could cause lethal dehydration and hyperthermia, leading to decline or extirpation of some species. We evaluated how desert birds have responded to climate and habitat change by resurveying historic sites throughout the Mojave Desert that were originally surveyed for avian diversity during the early 20th century by Joseph Grinnell and colleagues. We found strong evidence of an avian community in collapse. Sites lost on average 43% of their species, and occupancy probability declined significantly for 39 of 135 breeding birds. The common raven was the only native species to substantially increase across survey sites. Climate change, particularly decline in precipitation, was the most important driver of site-level persistence, while habitat change had a secondary influence. Habitat preference and diet were the two most important species traits associated with occupancy change. The presence of surface water reduced the loss of site-level richness, creating refugia. The collapse of the avian community over the past century may indicate a larger imbalance in the Mojave and provide an early warning of future ecosystem disintegration, given climate models unanimously predict an increasingly dry and hot future.

Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

Ecosystems have been modified by human activities for millennia, and insights about ecology and extinction risk based only on recent data are likely to be both incomplete and biased. We synthesize multiple long-term archives (over 250 archaeological and palaeontological sites dating from the early Holocene to the Ming Dynasty and over 4400 historical records) to reconstruct the spatio-temporal dynamics of Holocene–modern range change across China, a megadiverse country experiencing extensive current-day biodiversity loss, for 34 mammal species over three successive postglacial time intervals. Our combined zooarchaeological, palaeontological, historical and current-day datasets reveal that both phylogenetic and spatial patterns of extinction selectivity have varied through time in China, probably in response both to cumulative anthropogenic impacts (an ‘extinction filter’ associated with vulnerable species and accessible landscapes being affected earlier by human activities) and also to quantitative and qualitative changes in regional pressures. China has experienced few postglacial global species-level mammal extinctions, and most species retain over 50% of their maximum estimated Holocene range despite millennia of increasing regional human pressures, suggesting that the potential still exists for successful species conservation and ecosystem restoration. Data from long-term archives also demonstrate that herbivores have experienced more historical extinctions in China, and carnivores have until recently displayed greater resilience. Accurate assessment of patterns of biodiversity loss and the likely predictive power of current-day correlates of faunal vulnerability and resilience is dependent upon novel perspectives provided by long-term archives.

Imperial trophy or island relict? A new extinction paradigm for Père David's deer: a Chinese conservation icon

Determining the 'dynamic biogeography' of range collapse in threatened species is essential for effective conservation, but reconstruction of spatio-temporal patterns of population vulnerability and resilience can require use of non-standard ecological data such as historical archives. Père David's deer or milu, one of the few living mammal species that has become extinct in the wild, is historically known only from a small captive herd of unknown provenance that survived until 1900 in the Imperial Hunting Park near Beijing, from which all living individuals are descended. Using ancient DNA analysis, we demonstrate that two fawns collected in 1868 from Hainan Island, off the southern Chinese mainland, represent the only known wild milu specimens and were sampled from probably the last wild population. The Hainan milu population shows extremely low genetic differentiation from descendants of the Beijing herd, suggesting that this now-extinct population may have been the source of the captive herd. This revised extinction model refutes the supposed long-term survival of a captive milu herd for centuries or millennia after final extinction of wild populations, highlighting the vulnerability of remnant mammal populations in the absence of proactive management and the importance of historical museum collections for providing unique new insights on evolution, biogeography and conservation. Milu experienced a pattern of final population persistence on an island at the periphery of their former range, consistent with the 'range eclipse' or 'contagion' model of range collapse, and matching the spatial extinction dynamics of other extinct mammals such as the thylacine and woolly mammoth.

Setting temporal baselines for biodiversity: the limits of available monitoring data for capturing the full impact of anthropogenic pressures

Temporal baselines are needed for biodiversity, in order for the change in biodiversity to be measured over time, the targets for biodiversity conservation to be defined and conservation progress to be evaluated. Limited biodiversity information is widely recognized as a major barrier for identifying temporal baselines, although a comprehensive quantitative assessment of this is lacking. Here, we report on the temporal baselines that could be drawn from biodiversity monitoring schemes in Europe and compare those with the rise of important anthropogenic pressures. Most biodiversity monitoring schemes were initiated late in the 20^th century, well after anthropogenic pressures had already reached half of their current magnitude. Setting temporal baselines from biodiversity monitoring data would therefore underestimate the full range of impacts of major anthropogenic pressures. In addition, biases among taxa and organization levels provide a truncated picture of biodiversity over time. These limitations need to be explicitly acknowledged when designing management strategies and policies as they seriously constrain our ability to identify relevant conservation targets aimed at restoring or reversing biodiversity losses. We discuss the need for additional research efforts beyond standard biodiversity monitoring to reconstruct the impacts of major anthropogenic pressures and to identify meaningful temporal baselines for biodiversity.

Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene

The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18 700 mammalian zooarchaeological records for the last 11 700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of ‘static’ past baselines to inform current-day environmental management and restoration.

When Common Birds Became Rare: Historical Records Shed Light on Long-Term Responses of Bird Communities to Global Change in the Largest Wetland of France

Many species have suffered large population declines due to the anthropogenic influence on ecosystems. Understanding historical population trends is essential for informing best efforts to preserve species. We propose a new method to reconstruct the past structure of a regional species pool, based on historical naturalist literature. Qualitative information collected from annotated checklists and reports can be relevant to identify major long-term community changes. We reviewed ornithological literature on the Camargue, the largest wetland in France. We reconstructed the entire breeding bird community from 1830 to 2009 and translated historical data into semi-quantitative data. This data permitted a calculation of a Community Commonness Index to measure the average level of abundance of species in a community. The Community Specialization and Community Temperature Indices were used to evaluate the potential long-term impact of land-use and climate changes on the composition of the regional bird species pool. We found a decrease in average abundance and specialization between 1950 and 1989, suggesting that changes in land-use negatively impacted the structure and composition of the local bird community by reducing species abundance and removing habitat-specialists (e.g. Southern Grey Shrike, Greater Short-toed Lark). These results are likely to be linked with a major loss of natural habitats in the Camargue between 1942 and 1984 when natural areas and traditional farmland were converted into intensive cultivated lands. We also found fluctuations among species with high versus low temperature preference. However, long-term effects of climate change on the bird community might be blurred by the impact of land-use changes. Overall, our results contrast with those obtained from well-monitored colonial waterbirds showing long-term increases. Our results plead for a more regular use of historical naturalist data when examining long-term changes in species communities as they allow the establishment of an older temporal point of reference and consideration of species not covered by traditional monitoring schemes.

First estimates of the probability of survival in a small-bodied, high-elevation frog (Boreal Chorus Frog, Pseudacris maculata), or how historical data can be useful

In an era of shrinking budgets yet increasing demands for conservation, the value of existing (i.e., historical) data are elevated. Lengthy time series on common, or previously common, species are particularly valuable and may be available only through the use of historical information. We provide first estimates of the probability of survival and longevity (0.67–0.79 and 5–7 years, respectively) for a subalpine population of a small-bodied, ostensibly common amphibian, the Boreal Chorus Frog (Pseudacris maculata (Agassiz, 1850)), using historical data and contemporary, hypothesis-driven information–theoretic analyses. We also test a priori hypotheses about the effects of color morph (as suggested by early reports) and of drought (as suggested by recent climate predictions) on survival. Using robust mark–recapture models, we find some support for early hypotheses regarding the effect of color on survival, but we find no effect of drought. The congruence between early findings and our analyses highlights the usefulness of historical information in providing raw data for contemporary analyses and context for conservation and management decisions.

Pushing back the baseline: a novel approach to detect long-term changes in terrestrial faunal abundance using historical qualitative descriptions

Studies that examine changes in the populations of flora and fauna often do so against a baseline of relatively recent distribution data. It is much rarer to see evaluations of population change over the longer–term in order to extend the baseline back in time. Here, we use two methods (regression analysis and line of equality) to identify long-term differences in abundance derived from qualitative descriptions, and we test the efficacy of this approach by comparison with contemporary data. We take descriptions of bird population abundance in Cambridgeshire, UK, from the first half of the 19th century and compare these with more recent estimates by converting qualitative descriptions to an ordinal scale. We show, first, that the ordinal scale of abundance corresponds well to quantitative estimates of density and range size based on current data, and, second, that the two methods of comparison revealed both increases and declines in species, some of which were consistent using both approaches but others showed differing responses. We also show that the regional rates of extinction (extirpation) for birds are twice as high as equivalent rates for plants. These data extend analyses of avifaunal change back to a baseline 160-190 years before present, thus bringing a novel perspective on long-term change in populations and categories of conservation concern (e.g., Amber- or Red-lists) based on recent data. Changes in status are discussed in relation to various factors, although perhaps the most pervasive were of anthropogenic origin.

Please don't misuse the museum: 'declines' may be statistical

Detecting declines in populations at broad spatial scales takes enormous effort, and long-term data are often more sparse than is desired for estimating trends, identifying drivers for population changes, framing conservation decisions, or taking management actions. Museum records and historic data can be available at large scales across multiple decades, and are therefore an attractive source of information on the comparative status of populations. However, changes in populations may be real (e.g. in response to environmental covariates) or resulting from variation in our ability to observe the true population response (also possibly related to environmental covariates). This is a (statistical) nuisance in understanding the true status of a population. Evaluating statistical hypotheses alongside more interesting ecological ones is important in the appropriate use of museum data. Two statistical considerations are generally applicable to use of museum records: first without initial random sampling, comparison with contemporary results cannot provide inference to the entire range of a species, and second the availability of only some individuals in a population may respond to environmental changes. Changes in the availability of individuals may reduce the proportion of the population that is present and able to be counted on a given survey event, resulting in an apparent decline even when population size is stable.

Maximum-likelihood inference of population size contractions from microsatellite data

Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MSVAR) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared with alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that the violations of a single step mutation assumption induce very high bias toward false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the MIGRAINE software package.

Backcasting the decline of a vulnerable Great Plains reproductive ecotype: identifying threats and conservation priorities

Conservation efforts for threatened or endangered species are challenging because the multi-scale factors that relate to their decline or inhibit their recovery are often unknown. To further exacerbate matters, the perceptions associated with the mechanisms of species decline are often viewed myopically rather than across the entire species range. We used over 80 years of fish presence data collected from the Great Plains and associated ecoregions of the United States, to investigate the relative influence of changing environmental factors on the historic and current truncated distributions of the Arkansas River shiner Notropis girardi. Arkansas River shiner represent a threatened reproductive ecotype considered especially well adapted to the harsh environmental extremes of the Great Plains. Historic (n = 163 records) and current (n = 47 records) species distribution models were constructed using a vector-based approach in MaxEnt by splitting the available data at a time when Arkansas River shiner dramatically declined. Discharge and stream order were significant predictors in both models; however, the shape of the relationship between the predictors and species presence varied between time periods. Drift distance (river fragment length available for ichthyoplankton downstream drift before meeting a barrier) was a more important predictor in the current model and indicated river segments 375-780 km had the highest probability of species presence. Performance for the historic and current models was high (area under the curve; AUC > 0.95); however, forecasting and backcasting to alternative time periods suggested less predictive power. Our results identify fragments that could be considered refuges for endemic plains fish species and we highlight significant environmental factors (e.g., discharge) that could be manipulated to aid recovery.

Shifting baselines and the extinction of the Caribbean monk seal

The recent extinction of the Caribbean monk seal Monachus tropicalis has been considered an example of a human-caused extinction in the marine environment, and this species was considered a driver of the changes that have occurred in the structure of Caribbean coral reef ecosystems since colonial times. I searched archaeological records, historical data, and geographic names (used as a proxy of the presence of seals) and evaluated the use and quality of these data to conclude that since prehistoric times the Caribbean monk seal was always rare and vulnerable to human predation. This finding supports the hypothesis that in AD 1500, the Caribbean monk seal persisted as a small fragmented population in which individuals were confined to small keys, banks, or isolated islands in the Gulf of Mexico and the Caribbean Sea. This hypothesis is contrary to the assumption that the species was widespread and abundant historically. The theory that the main driver of monk seal extinction was harvesting for its oil for use in the sugar cane industry of Jamaica during the 18th century is based primarily on anecdotal information and is overemphasized in the literature. An analysis of reported human encounters with this species indicates monk seal harvest was an occasional activity, rather than an ongoing enterprise. Nevertheless, given the rarity of this species and its restricted distribution, even small levels of hunting or specimen collecting must have contributed to its extinction, which was confirmed in the mid-20th century. Some sources had been overlooked or only partially reviewed, others misinterpreted, and a considerable amount of anecdotal information had been uncritically used. Critical examination of archaeological and historical records is required to infer accurate estimations of the historical abundance of a species. In reconstructing the past to address the shifting baseline syndrome, it is important to avoid selecting evidence to confirm modern prejudices.

Inferring recent historic abundance from current genetic diversity

Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.

Reliability of genetic bottleneck tests for detecting recent population declines

The identification of population bottlenecks is critical in conservation because populations that have experienced significant reductions in abundance are subject to a variety of genetic and demographic processes that can hasten extinction. Genetic bottleneck tests constitute an appealing and popular approach for determining if a population decline has occurred because they only require sampling at a single point in time, yet reflect demographic history over multiple generations. However, a review of the published literature indicates that, as typically applied, microsatellite-based bottleneck tests often do not detect bottlenecks in vertebrate populations known to have experienced declines. This observation was supported by simulations that revealed that bottleneck tests can have limited statistical power to detect bottlenecks largely as a result of limited sample sizes typically used in published studies. Moreover, commonly assumed values for mutation model parameters do not appear to encompass variation in microsatellite evolution observed in vertebrates and, on average, the proportion of multi-step mutations is underestimated by a factor of approximately two. As a result, bottleneck tests can have a higher probability of 'detecting' bottlenecks in stable populations than expected based on the nominal significance level. We provide recommendations that could add rigor to inferences drawn from future bottleneck tests and highlight new directions for the characterization of demographic history.