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Data from: "Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015
Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus tephrosceles), which is a highly threatened monkey due to habitat loss. We analyzed blood samples from 24 individuals from Kibale National Park (Uganda) using single-end RAD sequencing. We obtained 70,773,857 reads, of which 58,814,906 passed the filtering steps. Using the program STACKS v. 1.11 we identified 113,376 loci, of which 50,558 were polymorphic and had a mean observed heterozygosity of 0.25. These data will be used to study the effects of habitat fragmentation on genomic diversity, dispersal, and disease transmission in this species. Our approach provides a good example of the potential of RAD sequencing in studies of wild primate populations.
Data from: Genetic structure and demographic history of the endangered tree species Dysoxylum malabaricum (Meliaceae) in Western Ghats, India: implications for conservation in a biodiversity hotspot
The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, one of the world's eight most important biodiversity hotspots. As D. malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-wide genetic structure of twelve D. malabaricum populations was evaluated to assess the impact of human activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (FIS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred before the last glacial maximum. Finally we discussed the implications of these results, in particular the presence of a clear pattern of historical genetic subdivision, on conservation policies.
Data from: Successive invasion-mediated interspecific hybridizations and population structure in the endangered cichlid Oreochromis mossambicus
Hybridization between invasive and native species accounts among the major and pernicious threats to biodiversity. The Mozambique tilapia Oreochromis mossambicus, a widely used freshwater aquaculture species, is especially imperiled by this phenomenon since it is recognized by the IUCN as an endangered taxon due to genetic admixture with O. niloticus an invasive congeneric species. The Lower Limpopo and the intermittent Changane River (Mozambique) drain large wetlands of potentially great importance for conservation of O. mossambicus, but their populations have remained unstudied until today. Therefore we aimed (1) to estimate the autochthonous diversity and population structure among genetically pure O. mossambicus populations to provide a baseline for the conservation genetics of this endangered species, (2) to quantify and describe genetic variation of the invasive populations and investigate the most likely factors influencing their spread, (3) to identify O. mossambicus populations unaffected by hybridization. Bayesian assignment tests based on 423 AFLP loci and the distribution of 36 species-specific mitochondrial haplotypes both indicate a low frequency of invasive and hybrid genotypes throughout the system, but nevertheless reveal evidence for limited expansion of two alien species (O. niloticus and O. andersonii) and their hybrids in the Lower Limpopo. O. mossambicus populations with no traces of hybridization are identified. They exhibit a significant genetic structure. This contrasts with previously published estimates and provides rather promising auspices for the conservation of O. mossambicus. Especially, parts of the Upper Changane drainage and surrounding wetlands are identified as refugial zones for O. mossambicus populations. They should therefore receive high conservation priority and could represent valuable candidates for the development of aquaculture strains based on local genetic resources.
Data from: Genetic rescue increases fitness and aids rapid recovery of an endangered marsupial population
Genetic rescue has now been attempted in several threatened species, but the contribution of genetics per se to any increase in population health can be hard to identify. Rescue is expected to be particularly useful when individuals are introduced into small isolated populations with low levels of genetic variation. Here we consider such a situation by documenting genetic rescue in the mountain pygmy possum, Burramys parvus. Rapid population recovery occurred in the target population after the introduction of a small number of males from a large genetically diverged population. Initial hybrid fitness was more than two-fold higher than non-hybrids; hybrid animals had a larger body size, and female hybrids produced more pouch young and lived longer. Genetic rescue likely contributed to the largest population size ever being recorded at this site. These data point to genetic rescue as being a potentially useful option for the recovery of small threatened populations.
Data from: Evaluating anthropogenic threats to endangered killer whales to inform effective recovery plans
Understanding cumulative effects of multiple threats is key to guiding effective management to conserve endangered species. The critically endangered, Southern Resident killer whale population of the northeastern Pacific Ocean provides a data-rich case to explore anthropogenic threats on population viability. Primary threats include: limitation of preferred prey, Chinook salmon; anthropogenic noise and disturbance, which reduce foraging efficiency; and high levels of stored contaminants, including PCBs. We constructed a population viability analysis to explore possible demographic trajectories and the relative importance of anthropogenic stressors. The population is fragile, with no growth projected under current conditions, and decline expected if new or increased threats are imposed. Improvements in fecundity and calf survival are needed to reach a conservation objective of 2.3% annual population growth. Prey limitation is the most important factor affecting population growth. However, to meet recovery targets through prey management alone, Chinook abundance would have to be sustained near the highest levels since the 1970s. The most optimistic mitigation of noise and contaminants would make the difference between a declining and increasing population, but would be insufficient to reach recovery targets. Reducing acoustic disturbance by 50% combined with increasing Chinook by 15% would allow the population to reach 2.3% growth.
Data from: Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken
The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity-related genes or both. Here, we tested whether genome-wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie-chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive-bred birds was related to alleles of the innate (Toll-like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome-wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome-wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome-wide heterozygosity.
Data from: Satellite tracking reveals novel migratory patterns and the importance of seamounts for endangered South Pacific humpback whales
The humpback whale population of New Caledonia appears to display a novel migratory pattern characterized by multiple directions, long migratory paths and frequent pauses over seamounts and other shallow geographical features. Using satellite-monitored radio tags, we tracked 34 whales for between 5 and 110 days, travelling between 270 and 8540 km on their southward migration from a breeding ground in southern New Caledonia. Mean migration speed was 3.53±2.22 km h−1, while movements within the breeding ground averaged 2.01±1.63 km h−1. The tag data demonstrate that seamounts play an important role as offshore habitats for this species. Whales displayed an intensive use of oceanic seamounts both in the breeding season and on migration. Seamounts probably serve multiple and important roles as breeding locations, resting areas, navigational landmarks or even supplemental feeding grounds for this species, which can be viewed as a transient component of the seamount communities. Satellite telemetry suggests that seamounts represent an overlooked cryptic habitat for the species. The frequent use by humpback whales of such remote locations has important implications for conservation and management.
Persistence of an endangered native duck, feral mallards, and multiple hybrid swarms across the main Hawaiian Islands
Interspecific hybridization is recognized as an important process in the evolutionary dynamics of both speciation and the reversal of speciation. However, our understanding of the spatial and temporal patterns of hybridization that erode versus promote species boundaries is incomplete. The endangered, endemic koloa maoli (or Hawaiian duck, Anas wyvilliana) is thought to be threatened with genetic extinction through ongoing hybridization with an introduced congener, the feral mallard (A. platyrhynchos). We investigated spatial and temporal variation in hybrid prevalence in populations throughout the main Hawaiian Islands, using genomic data to characterize population structure of koloa, quantify the extent of hybridization, and compare hybrid proportions over time. To accomplish this, we genotyped 3,308 double-digest restriction-site-associated DNA (ddRAD) loci in 425 putative koloa, mallards, and hybrids from populations across the main Hawaiian Islands. We found that despite a population decline in the last century, koloa genetic diversity is high. There were few hybrids on the island of Kauaʻi, home to the largest population of koloa. By contrast, we report that sampled populations outside of Kauaʻi can now be characterized as hybrid swarms, in that all individuals sampled were of mixed koloa × mallard ancestry. Further, there is some evidence that these swarms are stable over time. These findings demonstrate spatial variation in the extent and consequences of interspecific hybridization, and highlight how islands or island-like systems with small population sizes may be especially prone to genetic extinction when met with a congener that is not reproductively isolated.
Data from: Introgression threatens the survival of the critically endangered freshwater crayfish Cherax tenuimanus (Decapoda : Parastacidae) in the wild
Hybridization and genetic introgression following the introduction of exotic species can pose a significant threat to the survival of geographically restricted species. A remnant population of the critically endangered freshwater crayfish Cherax tenuimanus in the upper reaches of the Margaret River in southwestern Australia is under threat following the introduction and spread of its congener Cherax cainii. Here, we examine the extent of hybridization and introgression between the two species using twelve polymorphic microsatellite loci. Our study reveals there are three times more C. cainii than C. tenuimanus at our study site in the upper reaches of the Margaret River. There is also evidence of hybridization and introgression between C. tenuimanus and C. cainii at this site, with F1, F2 and backcrossed individuals identified. While interbreeding was confirmed in this study, our simulations suggest that the levels of introgression are much lower than would be expected under random mating, indicating partial reproductive barriers exist. Nevertheless, it is apparent that hybridization and introgression with C. cainii pose a serious threat to C. tenuimanus and their survival in the wild will require active adaptive management and continued genetic monitoring to evaluate management effectiveness.
Data from: An empirical and mechanistic explanation of abundance-occupancy relationships for a critically endangered nomadic migrant
The positive abundance-occupancy relationship (AOR) is a pervasive pattern in macroecology. Similarly, the association between occupancy (or probability of occurrence) and abundance is also usually assumed to be positive and in most cases constant. Examples of AORs for nomadic species with variable distributions are extremely rare. Here we examined temporal and spatial trends in the AOR over seven years for a critically endangered nomadic migrant which relies on dynamic pulses in food availability to breed. We predicted a negative temporal relationship, where local mean abundances increase when the number of occupied sites decreases, and a positive relationship between local abundances and the probability of occurrence. We also predicted that these patterns are largely attributable to spatiotemporal variation in food abundance. The temporal AOR was significantly negative and annual food availability was significantly positively correlated with the number of occupied sites, but negatively correlated with abundance. Thus, as food availability decreased, local densities of birds increased, and vice-versa. The abundance - probability of occurrence relationship was positive and non-linear, but varied between years due to differing degrees of spatial aggregation caused by changing food availability. Importantly, high abundance (or occupancy) did not necessarily equate to high quality habitat and may be indicative of resource bottlenecks or exposure to other processes affecting vital rates. Our results provide a rare empirical example that highlights the complexity of AORs for species that target aggregated food resources in dynamic environments.
Data from: Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph
Understanding reproduction and mating systems is important for managers tasked with conserving vulnerable species. Genetic tools allow biologists to investigate reproduction and mating systems with high resolution and are particularly useful for species that are otherwise difficult to study in their natural environments. We conducted parentage analyses using 19 nuclear DNA microsatellite loci to assess the influence of population density, genetic diversity, and ancestry on reproduction, and to examine the mating system of pygmy rabbits (Brachylagus idahoensis) bred in large naturalized enclosures for the reintroduction and recovery of the endangered distinct population in central Washington, USA. Reproductive output for females and males decreased as population density and individual homozygosity increased. We identified an interaction indicating that male reproductive output decreased as genetic diversity declined at high population densities, but there was no effect at low densities. Males with high amounts (>50%) of Washington ancestry had higher reproductive output than the other ancestry groups, while reproductive output was decreased for males with high northern Utah/Wyoming ancestry and females with high Oregon/Nevada ancestry. Females and males bred with an average of 3.8 and 3.6 mates per year, respectively, and we found no evidence of positive or negative assortative mating with regards to ancestry. Multiple paternity was confirmed in 81% of litters, and we report the first documented cases of juvenile breeding by pygmy rabbits. This study demonstrates how variation in population density, genetic diversity, and ancestry impact fitness for an endangered species being bred for conservation. Our results advance understanding of basic life history characteristics for a cryptic species that is difficult to study in the wild, and provide lessons for managing populations of vulnerable species in captive and free-ranging populations.
Figure 5 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 5. Megophrys frigida sp. nov. in preservative: (a) dorsal view (holotype of VNMN 010948); (b) ventral view (holotype of VNMN 010948); (c) lateral view of head (holotype of VNMN 010948); (d) palmar surface of left hand (holotype of VNMN 010948); (e) plantar surface of left foot (holotype of VNMN 010948); (f, g, h) dorsal, ventral and profile view of Megophrys frigida sp. nov. paratype (AMS R186131). Scale bars: 10 mm.
Figure 1 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 1. Distribution of Megophrys frigida sp. nov. in the Hoang Lien Range, north-west Vietnam. The solid blue area represents the presumed area where the habitat is within the species' estimated elevation range, covered with forest, and not separated from known localities by any continuous stretch of unsuitable habitat by a distance equal to or greater than 1 km. The blue cross-hatching denotes areas where this species may be extant in China (potential range). The light blue outline indicates the Extent Of Occurrence (EOO).
Figure 7 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 7. Megophrys frigida sp. nov. in life in situ at Mount Ky Quan San, Bat Xat District, Lao Cai Province, Vietnam, 2668 m above sea level: (a) holotype (VNMN 010948); (b) unvouchered individual.
Figure 9 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 9. Comparison of advertisement calls of Megophrys frigida sp. nov. holotype (VNMN 010948: a–c) recorded at 16.0°C and M. fansipanensis (AMS R186115: d–f) recorded at 15.3°C: (a, d) 30 s waveform of relative amplitude (Rel. amp.) over time for several call groups; (b, e) 5 s waveform of Rel. amp. over time for one call group; (c, f) 1 s waveform and spectrogram of Rel. amp. and frequency for calls.
Figure 3. A in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 3. A BI phylogenetic tree for a 647-bp section of CO1 (mtDNA) gene for Megophrys frigida sp. nov., along with representatives of all Panophrys species for which comparative sequences are available. Numbers at terminals correspond to Sample IDs in Supplementary information II. Bayesian posterior probability and ML bootstrap support for nodes are indicated on the tree: <95, not given; ≥ 95, orange dot; 100%, black dot. Coloured bars denote subgenera. The outgroup (Leptobrachium boringii) is not shown.
Figure 4 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 4. (a) Discriminant analysis of morphometric characters of male Panophrys in the Hoang Lien Range, with 95% ellipses. Blue = Megophrys fansipanensis (lateral view of AMS R186113 in life); red = Megophrys hoanglienensis (dorsolateral view of AMS R186122 in life); purple = Megophrys jingdongensis (dorsolateral view of AMS R185924 in life); orange = Megophrys rubrimera (lateral view of HNLP2016062200001 in life) and green = Megophrys frigida sp. nov. (dorsolateral view of AMS R186131 in life). Canonical axes 1 and 2 are linear combinations of the variables. Images of frogs are approximately to scale. (b) Boxplots of snout-to-vent length among adult male Megophrys species from the Hoang Lien Range. (c) Body weight differentiation (mg/mm). Horizontal lines within each box represent the median and boxes encompass the 75th and 25th quartiles.
Figure 2. A in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 2. A BI phylogenetic tree for a 1353-bp section of 12S–16S (mtDNA) gene of Megophrys frigida sp. nov., along with representatives of all Panophrys species for which comparative sequences are available. Numbers at terminals correspond to Sample IDs in Supplementary information II. Bayesian posterior probability and ML bootstrap support for nodes are indicated on the tree: <95, not indicated; ≥ 95, orange dot; 100%, black dot. Coloured bars denote subgenera. Outgroups (Leptobrachella oshanensis and Leptobrachium boringii) are not shown.
Figure 8 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 8. Megophrys frigida sp. nov. habitat: (a) view of the type locality on Mount Ky Quan San, Bat Xat District, Lao Cai Province, Vietnam, from 2700 m above sea level (asl); (b) type locality, 2668 m asl; (c) heavily grazed and deforested area very close to the type locality.
Figure 6 in A new potentially Endangered species of Megophrys (Amphibia: Megophryidae) from Mount Ky Quan San, north-west Vietnam
Figure 6. Megophrys frigida sp. nov. in life: (a, b) dorsal and ventral view of holotype VNMN 010948 under sedation; (c, d) dorsal and ventral view of referred specimen HLNP 20170910 00006 under sedation; (e, f) dorsal and ventral view of paratype AMS R186131 under sedation; (g, h) dorsal and ventral view of paratype AMS R186132 under sedation; (i) dorsolateral view of holotype VNMN 010948; (j) dorsolateral view of paratype AMS R186131; (k) cloaca and femoral glands of holotype VNMN 010948; (l) cloaca and femoral glands of paratype AMS R186132. Not to scale.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.