The Complete Mitogenome of the Mountain Chicken Frog, Leptodactylus fallax

The mountain chicken frog (Leptodactylus fallax) is a critically endangered frog native to the Caribbean islands of Dominica and Montserrat. Over the past 25 years their populations have declined by over 85%, largely due to a chytridiomycosis outbreak that nearly wiped out the Montserratian population. Within the context of developing tools that can aid in the conservation of the mountain chicken frog, we assembled its complete mitochondrial genome, contributing the first complete mitogenome of the genus Leptodactylus (Genbank Accession number MW260634). The circular genome is 18,669 bp long and contains 37 genes. A phylogenetic analysis reveals that L. fallax forms a clade with Leptodactylus melanonotus, highlighting the close relationship of Leptodactylus spp. relative to other species from the superfamily Hyloidea included in the analysis

The Complete Mitogenome of the Mountain Chicken Frog, Leptodactylus fallax

The mountain chicken frog (Leptodactylus fallax) is a critically endangered frog native to the Caribbean islands of Dominica and Montserrat. Over the past 25 years their populations have declined by over 85%, largely due to a chytridiomycosis outbreak that nearly wiped out the Montserratian population. Within the context of developing tools that can aid in the conservation of the mountain chicken frog, we assembled its complete mitochondrial genome, contributing the first complete mitogenome of the genus Leptodactylus (Genbank Accession number MW260634). The circular genome is 18,669 bp long and contains 37 genes. A phylogenetic analysis reveals that L. fallax forms a clade with Leptodactylus melanonotus, highlighting the close relationship of Leptodactylus spp. relative to other species from the superfamily Hyloidea included in the analysis

Using DNA metabarcoding to explore spatial variation in diet across European Hawfinch populations

The investigation of diet in avian species is essential for understanding their ecology and local adaptations, as well as long-term conservation. This can be particularly challenging because of the wide distribution and high ecological plasticity of many bird species. Here, we focused on the Hawfinch (Coccothraustes coccothraustes), which has shown variation in population trends. Across Europe, central and eastern European populations are moderately declining while western European populations are moderately increasing. Ecological drivers behind these differing trends are still unknown; one possibility is differences in diet, yet little research has been conducted into Hawfinch diet in mainland Europe or elsewhere. Dietary richness and variation are under-studied in woodland bird species, due primarily to challenges in accurately identifying plant and invertebrate taxa consumed. This study presents the first molecular dietary analysis of Hawfinch populations across two European countries. Faecal samples were collected between January and July of 2019 from Hawfinch caught at six artificial feed sites: two in Denmark and four in Germany. We successfully extracted DNA from 80 samples by amplifying plant Internal Transcribed Spacer 2 (ITS2) and invertebrate Cytochrome Oxidase Subunit 1 (COI) barcodes. A total of 35 plant and 37 invertebrate taxa were found, with plant and insect orders Fagales and Lepidoptera, respectively, the most frequently detected. Hawfinch dietary composition differed significantly between European countries, suggesting Hawfinch can make use of available food resources that are likely to differ spatially. Our study shows how DNA metabarcoding can be used to provide novel ecological information associated with under-studied bird species, thus providing essential information for future management and conservation of Hawfinch and their habitats

Money spider dietary choice in pre- and post-harvest cereal crops using metabarcoding

Money spiders (Linyphiidae) are an important component of conservation biological control in cereal crops, but they rely on alternative prey when pests are not abundant, such as between cropping cycles. To optimally benefit from these generalist predators, prey choice dynamics must first be understood. Money spiders and their locally available prey were collected from cereal crops 2 weeks pre‐ and post‐harvest. Spider gut DNA was amplified with two novel metabarcoding primer pairs designed for spider dietary analysis, and sequenced. The combined general and spider‐exclusion primers successfully identified prey from 15 families in the guts of the 46 linyphiid spiders screened, whilst avoiding amplification of Erigone spp. The primers show promise for application to the diets of other spider families such as Agelenidae and Pholcidae. Distinct invertebrate communities were identified pre‐ and post‐harvest, and changes in spider diet and, to a lesser extent, prey choice reflected this. Spiders were found to consume one another more than expected, indicating their propensity towards intraguild predation, but also consumed common pest families. Changes in spider prey choice may redress prey community changes to maintain a consistent dietary intake. Consistent provision of alternative prey via permanent refugia should be considered to sustain effective conservation biocontrol

Dynamics and genetics of a disease-driven species decline to near extinction:lessons for conservation

Amphibian chytridiomycosis has caused precipitous declines in hundreds of species worldwide. By tracking mountain chicken (Leptodactylus fallax) populations before, during and after the emergence of chytridiomycosis, we quantified the real-time species level impacts of this disease. We report a range-wide species decline amongst the fastest ever recorded, with a loss of over 85% of the population in fewer than 18 months on Dominica and near extinction on Montserrat. Genetic diversity declined in the wild, but emergency measures to establish a captive assurance population captured a representative sample of genetic diversity from Montserrat. If the Convention on Biological Diversity's targets are to be met, it is important to evaluate the reasons why they appear consistently unattainable. The emergence of chytridiomycosis in the mountain chicken was predictable, but the decline could not be prevented. There is an urgent need to build mitigation capacity where amphibians are at risk from chytridiomycosis.</p

Innate and adaptive immune genes associated with MERS-CoV infection in dromedaries

The recent SARS-CoV-2 pandemic has refocused attention to the betacoronaviruses, only eight years after the emergence of another zoonotic betacoronavirus, the Middle East respiratory syndrome coronavirus (MERS-CoV). While the wild source of SARS-CoV-2 may be disputed, for MERS-CoV, dromedaries are considered as source of zoonotic human infections. Testing 100 immune-response genes in 121 dromedaries from United Arab Emirates (UAE) for potential association with present MERS-CoV infection, we identified candidate genes with important functions in the adaptive, MHC-class I (HLA-A-24-like) and II (HLA-DPB1-like), and innate immune response (PTPN4, MAGOHB), and in cilia coating the respiratory tract (DNAH7). Some of these genes previously have been associated with viral replication in SARS-CoV-1/-2 in humans, others have an important role in the movement of bronchial cilia. These results suggest similar host genetic pathways associated with these betacoronaviruses, although further work is required to better understand the MERS-CoV disease dynamics in both dromedaries and humans

No signs of inbreeding despite long-term isolation and habitat fragmentation in the critically endangered Montseny brook newt (Calotriton arnoldi)

Endemic species with restricted geographic ranges potentially suffer the highest risk of extinction. If these species are further fragmented into genetically isolated subpopulations, the risk of extinction is elevated. Habitat fragmentation is generally considered to have negative effects on species survival, despite some evidence for neutral or even positive effects. Typically, non-negative effects are ignored by conservation biology. The Montseny brook newt (Calotriton arnoldi) has one of the smallest distribution ranges of any European amphibian (8 km2) and is considered critically endangered by the International Union for Conservation of Nature. Here we apply molecular markers to analyze its population structure and find that habitat fragmentation owing to a natural barrier has resulted in strong genetic division of populations into two sectors, with no detectable migration between sites. Although effective population size estimates suggest low values for all populations, we found low levels of inbreeding and relatedness between individuals within populations. Moreover, C. arnoldi displays similar levels of genetic diversity to its sister species Calotriton asper, from which it separated around 1.5 million years ago and which has a much larger distribution range. Our extensive study shows that natural habitat fragmentation does not result in negative genetic effects, such as the loss of genetic diversity and inbreeding on an evolutionary timescale. We hypothesize that species in such conditions may evolve strategies (for example, special mating preferences) to mitigate the effects of small population sizes. However, it should be stressed that the influence of natural habitat fragmentation on an evolutionary timescale should not be conflated with anthropogenic habitat loss or degradation when considering conservation strategies

Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

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