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opencc-zeroDec 2021View details →

Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis

The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain, and could be impacted by continued fishing and bycatch pressure and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6,350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes, and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity, and pH. The paucity of well annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour, and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.

opencc-by-4.0Dec 2021View details →

Map 1 in Clusia falcata (Clusiaceae), an endangered species with exceptionally narrow leaves endemic to Chiapas, Mexico

Map 1. Distribution map of Clusia falcata in Chiapas, Mexico.

opencc-zeroJan 2022View details →

Ignorance is not bliss: Evolutionary naïveté in an endangered desert fish and implications for conservation

Predator naiveté has been invoked to explain the impacts of non-native predators on isolated populations that evolved with limited predation. Such impacts have been repeatedly observed for the endangered Pahrump poolfish, Empetrichthys latos, a desert fish species that evolved in isolation since the end of the Pleistocene. We tested Pahrump poolfish anti-predator responses to conspecific chemical alarm cues released from damaged epidermal tissue in terms of fish activity and water column position. Pahrump poolfish behavioural responses to conspecific alarm cues did not differ from responses to a dechlorinated tap water control. As a positive control, the well-studied fathead minnow, Pimephales promelas, showed significant alarm cue responses in terms of reduced activity and lowered water column position. The density of epidermal club cells, the presumptive source of alarm cues, was significantly lower in Pahrump poolfish relative to fathead minnows. Therefore, anti-predator competence mediated by conspecific alarm cues does not seem to be a component of the ecology of Pahrump poolfish. These findings provide a proximate mechanism for the vulnerability of Pahrump poolfish to non-native predators, with implications for conservation and management of insular species.

opencc-zeroDec 2016View details →

Data from: Genetic diversity and divergence in the fountain darter (Etheostoma fonticola): implications for conservation of an endangered species

The endangered fountain darter Etheostoma fonticola is found only in the Comal and San Marcos rivers in the Guadalupe River basin in central Texas, USA. Comal River fountain darters were believed to be extir- pated following a severe drought in the 1950s and were reintroduced in the early 1970s using 457 darters from the San Marcos River. In this study we used 23 microsatellite loci to describe and evaluate the genetic diversity, population structure and effective population size (Ne) of fountain darters. We also evaluated the genetic effect of the Comal River reintroduction and the influence of low-head dams (dams) on dispersal in both rivers. Bayesian analysis of individual genotypes and Analysis of Molecular Variation supported two distinct populations concordant with the two rivers. Estimates of Ne were much smaller (<10 %) than census size (Nc) in both rivers but did not indicate the populations are at risk of an immediate and rapid loss of genetic diversity. Coalescent-based estimates of the genetically effective number of founders (Nf) for the Comal River averaged about 49 darters and, together with the indices of genetic diversity and the bottleneck test (heterozygosity excess) results, were consistent with a founder event following the reintroduction in the Comal River. Finally, our results regarding the influence of dams on fountain darter dispersal were equivocal and did not support a conclusion. We recommend this issue be examined further as part of the fountain darter recovery program.

opencc-by-4.0Feb 2023View details →

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

Binned microsatelite data of the peninsular pronghorn subspecies (Antilocapra americana peninsularis). Data is organized in by year manner. Each population correspond to the year samples were collected from, for example Pop_09 corresponds to samples collected from year 2009, whereas Pop_21 corresponds to the samples collected from year 2021.

opencc-by-4.0Feb 2022View details →

Fig. 6 in Two new remarkable and endangered catfish species of the genus Cambeva (Siluriformes, Trichomycteridae) from southern Brazil

Fig. 6. Type locality of Cambeva betabelardense sp. nov.

opencc-by-4.0Feb 2022View details →

Fig. 4 in Two new remarkable and endangered catfish species of the genus Cambeva (Siluriformes, Trichomycteridae) from southern Brazil

Fig. 4. Type locality of Cambeva alphabelardense sp. nov.

opencc-zeroJun 2022View details →

High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal

Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.

Strong isolation by distance among local populations of an endangered butterfly species (Euphydryas aurinia)

The marsh fritillary (Euphydryas aurinia) is a critically endangered butterfly species in Denmark known to be particularly vulnerable to habitat fragmentation due to its poor dispersal capacity. We identified and genotyped 318 novel SNP loci across 273 individuals obtained from 10 small and fragmented populations in Denmark using a genotyping-by-sequencing (GBS) approach to investigate its population genetic structure. Our results showed clear genetic substructuring and highly significant population differentiation based on genetic divergence (FST) among the 10 populations. The populations clustered in three overall clusters and due to further substructuring among these, it was possible to clearly distinguish six clusters in total. We found highly significant deviations from Hardy-Weinberg equilibrium due to heterozygote deficiency within every population investigated which indicates substructuring and/or inbreeding (due to mating among closely related individuals). The stringent filtering procedure that we have applied to our genotype quality could have overestimated the heterozygote deficiency and the degree of substructuring of our clusters but is allowing relative comparisons of the genetic parameters among clusters. Genetic divergence increased significantly with geographic distance, suggesting limited gene flow at spatial scales comparable to the dispersal distance of individual butterflies and strong isolation by distance. Altogether, our results clearly indicate that the marsh fritillary populations are genetically isolated. Further, our results highlight that the relevant spatial scale for conservation of rare, low mobile species may be smaller than previously anticipated.

Data for: Modeling the distribution of the endangered Jemez Mountains salamander (Plethodon neomexicanus) in relation to geology, topography, and climate

The Jemez Mountains salamander (Plethodon neomexicanus; hereafter JMS) is an endangered salamander restricted to the Jemez Mountains in north-central New Mexico, United States. This strictly terrestrial species requires moist surface conditions for mating and foraging. Threats to its current habitat include fire suppression and ensuing severe fires, changes in forest composition, habitat fragmentation, and climate change. Forest composition changes resulting from reduced fire frequency and increased tree density suggest that its current aboveground habitat does not mirror its historically successful habitat regime. We hypothesized that geology and topography might play a significant role in the current distribution of the salamander. We modeled the distribution of the JMS using a machine learning algorithm to assess how geology, topography, and climate variables influence its distribution. Our habitat suitability map reveals low uncertainty in model predictions, and we found slight discrepancies between the designated critical habitat and the most suitable areas for the JMS. Because geological features are important to its distribution, we recommend that geological and topographical data are considered, both during survey design and in the description of localities of JMS records once detected.

Give and take: Effects of genetic admixture on mutation load in endangered Florida panthers

Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.

Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan

Demographic events can shape genetic diversity through genetic drift, often leaving a persistent signal in the genetic characteristics of species. Rhodeus atremius suigensis is an endangered bitterling fish endemic to the Okayama Plain, Japan. In this study, we inferred its demographic history and genetic structure using a comprehensive analysis of the mtDNA ND1 gene, microsatellite markers (MS) and MHC class IIB gene. Based on mtDNA, R. a. suigensis included two sublineages; A and B. While <a name="OLE_LINK85"></a><a name="OLE_LINK88"></a>the former was widely distributed, the latter was restricted to eastern populations<a name="OLE_LINK11"></a><a name="OLE_LINK12"></a> that were monomorphic in MHC. Phylogenetic analysis revealed that R. a. suigensis, together with R. a. atremius, experienced a substantial bottleneck in the middle Pleistocene. In MS and MHC, genetic diversity was low in all populations; ranked as the lowest among bitterling species. Bayesian clustering suggested that two clusters of MS had been widely introgressed in the centre of its distribution. These clusters seem to have been formed by the disruption of the distribution in the last Pleistocene, and later admixed by a large-scale reclamation in the Okayama Plain since the 16th century, which triggered a decline in effective population size (Ne) in many populations. Based on coalescence analysis, all populations reached their lowest Ne around the middle of the 20th century. Accordingly, R. a. suigensis seems to have experienced two large bottlenecks in the past. While the first bottleneck was probably due to climatic changes in the middle Pleistocene, the second is due to anthropogenic degradation and fragmentation of habitats in recent years.

Data: Detecting preservation and reintroduction sites for endangered plant species using a two-step modelling and field approach

To withstand the surge of species loss worldwide, (re)introduction of endangered plant species has become an increasingly common technique in conservation biology. Successful (re)introduction plans, however, require identifying sites that provide the optimal ecological conditions for the target species to thrive. In this study, we propose a two-step approach to identify appropriate (re)introduction sites. The first step involves modelling the niche and distribution of the species with bioclimatic and topographical predictors, both at continental and at national scales. The second step consists of refining these bioclimatic predictions by analysing stationary ecological parameters, such as soil conditions, and relating them to population-level fitness values. We demonstrate this methodology using Swiss populations of the lady's slipper orchid (Cypripedium calceolus L., Orchidaceae), for which conservation plans have existed for years but have generally been unfruitful. Our workflow identified sites for future (re)introductions based on the species requirements for mid-to-sunny light conditions and specific soil physico-chemical properties, such as basic to neutral pH and low soil organic matter content. Our findings show that by combining wide-scale bioclimatic modelling with fine scale field measurements it is possible to carefully identify the ecological requirements of a target species for successful (re)introductions.

Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow

Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (Siphateles bicolor snyderi), which has been rendered endangered by introgression from the introduced Lahontan Tui Chub (Siphateles bicolor obesa). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both the native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake vs. stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic-lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.

opencc-by-4.0Feb 2022View details →

Figure 5 in A New Coccidian (Apicomplexa: Eimeriidae) in the Critically Endangered Central American River Turtle (Dermatemys Mawii) in Belize

Figure 5. Composite line drawing of a sporulated mitra-shaped oocyst of Eimeria grayi n. sp.

opencc-by-4.0Oct 2022View details →

Conservation implications of herbicides on seagrasses: sublethal glyphosate exposure decreases fitness in the endangered Zostera capensis

Dataset containing morphological, biomass and chlorophyll responses of the seagrass, Zostera capensis, to sublethal glyphosate exposure over a 3 week exposure period.

opencc-by-nc-4.0Oct 2021View details →

Figure 5 in Agricultural activities and threat to fauna in Brazil: an analysis of the Red Book of Endangered Brazilian Fauna

Figure 5. Number of species affected by isolation, in each group, compared to the number of species affected by habitat reduction and habitat fragmentation.

opencc-zeroMay 2024View details →

Data from: Reproductive ecology of the critically endangered pancake tortoise (Malacochersus tornieri) in the wild

Reproduction of the pancake tortoise in the wild has remained poorly known over the decades. This study fills the knowledge gap by investigating the reproductive ecology of the species in its natural habitats in Kenya. Data were collected using the time-constrained search-and-seize method, group-level scan sampling, radio tracking, and camera-trapping. Our observations revealed a total of 19 mating events that occurred between December and April, predominantly during the rainy seasons. Mating duration averaged 15.2±2.4 minutes. Male-male aggression was observed during the mating season, with the dominant male keeping off all other males and mating with the resident females. Nest preparation events occurred between April and June. Nine nesting events were recorded, but in only five of them was an egg deposited. The nests were dug in loose soil, appeared almost circular, and measured 8.4±0.9 cm wide and 7.0±0.1 cm deep (n=7). The average clutch size was one egg. The eggs were white, hard-shelled, oval, and elongated measuring 4.4±0.4 cm long, 2.7±0.04 cm wide and weighed 17±0.6 g (n=3). Incubation period lasted 177± 5.7 days (n=2), and hatching coincided with the onset of the short rainy season in November, aligned with the availability of abundant food for the tortoises. The hatchlings were minimally wider than long, having an average straight carapace length of 4.5±0.6 cm, an average width of 4.5±0.4 cm, and on average weighed 14.7±3.7g, (N=9). They remained near the nest site for 4-5 days before relocating to tiny rock crevices away from the adult tortoise crevices. Egg and hatchling predation was high, with four of the total of six eggs, observed after they were laid, being destroyed. Three juveniles, out of nine, were also eaten by predators. These findings contribute useful information for the formulation of effective conservation and management strategies for this critically endangered species.

opencc-zeroJun 2024View details →

Data from: Consequences of repeated sarcoptic mange outbreaks in an endangered mammal population

Diseases and parasites are important drivers of population dynamics in wild mammal populations. Small and endangered populations that overlap with larger, reservoir populations are particularly vulnerable to diseases and parasites, especially in ecosystems highly influenced by climate change. Sarcoptic mange, caused by a parasitic mite (Sarcoptes scabiei), constitutes a severe threat to many wildlife populations and is today considered a panzootic. The Scandinavian arctic fox (Vulpes lagopus) is endangered with a fragmented distribution and is threatened by e.g., red fox (Vulpes vulpes) expansion, prey scarcity and inbreeding depression. Moreover, one of the subpopulations in Scandinavia has suffered from repeated outbreaks of sarcoptic mange during the past decade, most likely spread by red foxes. This was first documented in 2013 and then again 2014, 2017, 2019, 2020 and 2021. We used field inventories and wildlife cameras to follow the development of sarcoptic mange outbreaks in this arctic fox subpopulation with specific focus on disease transmission and consequences for reproductive output. In 2013-14, we documented visual symptoms of sarcoptic mange in about 30% of the total population. Despite medical treatment, we demonstrate demographic consequences where the number of arctic fox litters plateaued and litter size was reduced after the introduction of S. scaibei. Furthermore, we found indications that mange likely was transmitted by a few arctic foxes travelling between several dens, i.e., "super-spreaders". This study highlights sarcoptic mange as a severe threat to small populations and can put the persistence of the entire Scandinavian arctic fox population at risk.