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Fig. 5 in New data on the early stages and behaviour of the endangered species Callophrys mystaphia (Lepidoptera: Lycaenidae) and its first larval parasitoid, Cotesia sp. (Hymenoptera: Braconidae)
Fig. 5. Larvae of Callophrys mystaphia Miller, 1913 forming 'feeding windows' on the host plant.
Navigating agricultural landscapes: Responses of critically endangered giant tortoises to farmland vegetation and infrastructure
<p><strong>Context</strong>: Interactions between wildlife and anthropogenic infrastructure, such as roads, fences, and dams, can influence wildlife movement, and potentially cause human-wildlife conflict. In the Galapagos archipelago, two species of critically endangered giant tortoise encounter infrastructure and human-modified vegetation in farms, which could influence movement choices.</p> <p><strong>Objectives</strong>: We investigated factors influencing tortoise movement and habitat selection in the agricultural landscape of Santa Cruz Island, Galapagos.</p> <p><strong>Methods</strong>: We examined the movement of 27 tortoises collected using GPS tracking between 2014 and 2020, in relation to the location of vegetation, ponds, fences, and roads.</p> <p><strong>Results:</strong> We found that tortoises preferred pasture over native vegetation, but there was little difference among their preferences for native vegetation, crops, or invasive vegetation. Tortoises also travelled slower in pasture, and faster in invasive vegetation, compared to crops and native vegetation. Tortoises were more likely to be found closer to ponds than predicted by chance. Our results indicated that most fences were porous to tortoises, with limited impact on their movement. Tortoises were more likely to use areas near roads with low-traffic.</p> <p><strong>Conclusions</strong>: Pastures and ponds are important habitats for tortoises in farms and are likely to be used preferentially by tortoises. Overall, fences and roads did not strongly obstruct tortoise movements, however, this may lead to potential injury to tortoises on roads and property damage for farmers. To best identify priority areas for managing wildlife on farms, we recommend evaluating the combined effects of multiple anthropogenic landscape features on wildlife movements.</p>
Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago
<p><strong>Aim</strong>: The biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (<em>Sus verrucosus</em>) and Bawean (<em>S. blouchi</em>) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation.</p> <p><strong>Location</strong>: Malay Archipelago, with focus on Bawean and Java.</p> <p><strong>Methods</strong>: We employed genome-wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times, and to perform demographic model selection.</p> <p><strong>Results</strong>: In contrast to the hypothesis of recent divergence during the last glacial maximum, <em>S. blouchi</em> was found to have diverged from <em>S. verrucosus</em> at least 166k years ago following a founder event. The contemporary <em>S. blouchi</em> population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of <em>S. blouchi</em>, as was previously proposed based on morphometrics. The demographic history of <em>S. verrucosus</em> showed evidence of secondary contact with the sympatric banded pig (<em>S. scrofa vittatus</em>) that colonised Java 70k years ago.</p> <p><strong>Main</strong> <strong>conclusions</strong>: While the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both <em>S. verrucosus</em> and <em>S. blouchi</em>. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.</p>
Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse
<p>The population of the Yellow-breasted Bunting <em>Emberiza aureola</em>, a formerly widely distributed and abundant songbird of northern Eurasia, suffered a catastrophic decline and a strong range contraction between 1980 and 2013. There is evidence that the decline was driven by illegal trapping during migration, but potential contributions of other factors to the decline, such as land-use change, have not yet been evaluated. Before effects of land-use change can be evaluated, a basic understanding of the ecological requirements of the species is needed. We therefore compared habitat use in ten remaining breeding regions across the range, from European Russia to Japan and the Russian Far East. We also assessed large-scale variation in habitat parameters across the breeding range.</p> <p>We found large variation in habitat use, within and between populations. Differences were related to the cover and height of trees and shrubs at Yellow-breasted Bunting territories. In many regions, Yellow-breasted Buntings occupied early successional stages, including anthropogenic habitats characterized by mowing, grazing or fire regimes. We found that the probability of presence can be best predicted with the cover of shrubs, herbs and grasses. Highest probabilities were found at shrub cover values of 40 to 70 %.</p> <p>Differences in habitat use along a longitudinal gradient were small, but we found strong differences across latitudes, possibly related to habitat availability. We conclude that the remaining Yellow-breasted Bunting populations are not limited to specific habitat types. Our results provide important baseline information to model the range-wide distribution of this critically endangered species and to guide targeted conservation measures.</p>
Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird
<p>Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (<em>Pardalotus</em> <em>quadragintus</em>), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.</p>
DaRT-seq raw data of Eucalyptus spp for the genetic assessment of the value of restoration planting within an endangered eucalypt woodland
<p>Assessment of woodland restoration often focusses on stand demographics, but genetic factors likely influence long-term stand viability. We examined the genetic composition of Yellow Box (<em>Eucalyptus melliodora</em>) trees in endangered Box-Gum Grassy Woodland in SE Australia, some 30 years after planting with seeds of reportedly local provenance. Using DArT sequencing for 1406 SNPs, we compared genetic diversity and population structure of planted <em>E. melliodora</em> trees with remnant bushland trees, paddock trees, and natural recruits. Genetic patterns imply that natural stands and paddock trees had historically high gene flow (among group pairwise FST = 0.04–0.10). Genetic diversity was highest among relictual paddock trees (He = 0.17), while diversity of revegetated trees was identical to natural bushland trees (He = 0.14). Bayesian clustering placed the revegetated trees into six genetic groups with four corresponding to genotypes from paddock trees, indicating that revegetated stands are mainly of genetically diverse, local provenance. Natural recruits were largely derived from paddock trees with some contribution from planted trees. A few trees have likely hybridised with other local eucalypt species which are unlikely to compromise stand integrity. We show that paddock trees have high genetic diversity and capture historic genetic variety and provide important foci for natural recruitment of genetically diverse and outcrossed seedlings.</p>
Adapting camera-trap placement based on animal behaviour for rapid detection: a focus on the Endangered, white-bellied pangolin (Phataginus tricuspis)
<p>Table containing detection data of species using two camera trap placement strategies (log vs non-log)</p>
Fig. 1 in Ex-situ conservation of the critically endangered swamp forest crab Parathelphusa reticulata Ng, 1990 (Decapoda: Brachyura: Gecarcinucidae): observations on its reproduction and biology in captivity
Fig. 1. Captive breeding facility in the Singapore Botanic Gardens. Photograph: Daniel J. J. Ng.
Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA
<p><span>Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (</span><span><em>Salmo</em> <em>salar</em></span><span>) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer.</span></p>
Historical DNA reveals climate adaptation in an endangered songbird
<p>To cope with climate change, species may shift their distributions or adapt <em>in situ</em> to changing environmental conditions. However, clear examples of genetic changes via adaptation are limited. We explore evolutionary responses to climate change in the endangered southwestern willow flycatcher (<em>Empidonax</em> <em>trailli</em> <em>extimus</em>) through whole-genome comparisons between historical specimens, collected from 1888–1909 near San Diego, CA, and contemporary individuals from across the breeding range. Genomic analyses revealed that introgression into San Diego increased adaptive potential over time and shifted genome-wide population structure towards that of neighboring populations. In contrast, loci linked to climate (dew point temperature and precipitation) shifted away from neighboring populations and in a direction consistent with adaptation to climate change in southern CA. This research highlights the role of admixture in facilitating adaptive shifts through its impact on genome-wide genetic variation and represents one of the few studies to document climate adaptation in a wild population.</p>
Genomic Signatures of Disease Resistance in Endangered Staghorn Corals
<p>White Band Disease (WBD) has caused unprecedented declines in the Caribbean <em>Acropora</em> corals, which are now listed as critically endangered species. Highly disease resistant <em>Acropora</em> <em> cervicornis</em> genotypes exist, but we lack understanding of the genetic underpinnings of disease resistance. Using transmission experiments, a newly assembled genome, and whole genome resequencing of 76 <em>A. cervicornis</em> genotypes from Florida and Panama, we identified ten genomic regions and 73 single-nucleotide polymorphisms (SNPs) that are strongly associated with disease resistance and that include functional, protein coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that simple genetic screens can predict <em>A. cervicornis</em> disease resistance and that adaptive polygenic variation can be used to improve disease resistance in wild and nursery stocks of <em>A. cervicornis</em> across the Caribbean.</p>
Genetic erosion in an endangered desert fish during a multi-decadal megadrought despite long-term supportive breeding
<p>Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande Silvery Minnow. This species experiences 'boom-and-bust' population dynamics where large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We leveraged demographic and genetic data from wild and hatchery individuals to understand the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's <em>d</em>=1.34) and remains low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size (N<sub>eD</sub>) were positively associated (<em>r</em>=0.53) with wild/total abundance, but as the proportion of hatchery-origin spawners increased, N<sub>eD</sub> was reduced (N<sub>eD</sub> <em>r</em>= -0.55). Megadrought limits wild spawner abundance and precludes refreshment of hatchery brood stocks with wild fish, hence we predict an increasingly hatchery-dominated population, and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.</p>
Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake
<p class="MsoNormal">Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (<em>Sistrurus catenatus</em>) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.</p>
Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink
<p>The application of next‐generation sequencing (NGS) to non‐invasive samples is one of the most promising methods in conservation genomics, but these types of samples present significant challenges for NGS. The European mink (<em>Mustela lutreola</em>) is critically endangered throughout its range. However, important aspects such as census size and inbreeding remain still unknown in many populations, so it is crucial to develop new methods to monitor this species. In this work, we placed hair tubes along riverbanks in a border area of the Iberian population, which allowed the genetic identification of 76 European mink hair samples. We then applied a reduced representation genomic sequencing (ddRAD) technique to a subset of these samples to test whether we could extract sufficient genomic information from them. We show that several problems with the DNA, including contamination, fragmentation, oxidation, and possibly sample mixing, affected the samples. Using various bioinformatic techniques to reduce these problems, we were able to unambiguously genotype 19 hair samples belonging to six individuals. This small number of individuals showed that the demographic status of the species in this peripheral population is worse than expected. The data obtained also allowed us to perform preliminary analyses of relatedness and inbreeding. Although further improvements in sampling and analysis are needed, the application of the ddRAD technique to non‐invasively obtained hairs represents a significant advance in the genomic study of endangered species.</p>
Landscape genetics of an endangered salt marsh endemic: identifying population continuity and barriers to dispersal
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Navigating agricultural landscapes: Responses of critically endangered giant tortoises to farmland vegetation and infrastructure
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Data from: Artificial refuges to combat habitat loss for an endangered marsupial predator: how do they measure up?
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Data on range-wide breeding habitat use of the critically endangered Yellow-breasted Bunting Emberiza aureola after population collapse
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Genetic differentiation and overexploitation history of the critically endangered Lehmann’s Poison Frog: Oophaga lehmanni
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Data from: Connections across open water: A bi-organelle, genomics-scale assessment of Atlantic-wide population dynamics in a pelagic, endangered apex predator shark (Isurus oxyrinchus)
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.