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Abstract Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.

Abstract Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across institutions and countries in access to technologies, funding, and training. Consequently, in many cases, more accessible traditional genetic data (e.g., microsatellites) are still utilized for making conservation decisions. Conservation approaches need to be pragmatic by tackling clearly defined management questions and using the most appropriate methods available, while maximizing the use of limited resources. Here we present some key questions to consider when applying the molecular toolbox for accessible and actionable conservation management. Finally, we highlight a number of important steps to be addressed in a collaborative way, which can facilitate the broad integration of molecular data into conservation.

Animal husbandry is one of man’s oldest occupations. It began with the domestication of animals and developed continuously, in parallel with the evolution of human society. The selection and improvement of goats in Romania was not a clearly defined objective until around 1980. In recent years, with the increasing economic value given to goats, breeding programs are becoming established. In Romania, a few goat genetic studies using microsatellites and mtDNA have been carried out; however, a systematic characterization of the country’s goat genomic resources remains missing. In this study, we analyzed the genetic variability of Carpatina goats from four distinct geographical areas (northern, north-eastern, eastern and southern Romania), using the Illumina OvineSNP60 (RefSeq ARS1) high-density chip for 67 goats. Heterozygosity values, inbreeding coefficients and effective population size across all autosomes were calculated for those populations that inhabit high- and low-altitude and high- and low-temperature environments. Diversity, as measured by expected heterozygosity (HE), ranged from 0.413 in the group from a low-temperature environment to 0.420 in the group from a high-temperature environment. Within studied groups, the HT (high temperature) goats were the only group with a positive but low average inbreeding coefficient value, which was 0.009. After quality control (QC) analysis, 46,965 SNPs remained for analysis (MAF < 0.01). LD was calculated for each chromosome separately. The Ne has been declining since the time of domestication, having recently reached 123, 125, 185 and 92 for the HA (high altitude), LA (low altitude), HT (high temperature) and LT (low temperature) group, respectively. Our study revealed a low impact of inbreeding in the Carpatina population, and the Ne trend also indicated a steep decline in the last hundred years. These results will contribute to the genetic improvement of the Carpatina breed.

Abstract Avian diet can be affected by site‐specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi‐marker fecal metabarcoding to provide in‐depth dietary analysis of a declining passerine in the UK, the Hawfinch (Coccothraustes coccothraustes). We collected fecal samples from (n = 262) UK Hawfinches prior to, and during, the breeding seasons in 2016–2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilize multiple resources within their foraging environments.

Knowledge of diet and dietary selectivity is vital, especially for the conservation of declining species. Accurately obtaining this information, however, is difficult, especially if the study species feeds on a wide range of food items within heterogeneous and inaccessible environments, such as the tree canopy. Hawfinches (Coccothraustes coccothraustes), like many woodland birds, are declining for reasons that are unclear. We investigated the possible role that dietary selection may have in these declines in the UK. Here, we used a combination of high-throughput sequencing of 261 hawfinch faecal samples assessed against tree occurrence data from quadrats sampled in three hawfinch population strongholds in the UK to test for evidence of selective foraging. This revealed that hawfinches show selective feeding and consume certain tree genera disproportionally to availability. Positive selection was shown for beech (Fagus), cherry (Prunus), hornbeam (Carpinus), maples (Acer) and oak (Quercus), while Hawfinch avoided ash (Fraxinus), birch (Betula), chestnut (Castanea), fir (Abies), hazel (Corylus), rowan (Sorbus) and lime (Tilia). This approach provided detailed information on hawfinch dietary choice and may be used to predict the effects of changing food resources on other declining passerines populations in the future.

The Madagascan endemic subfamily Cophylinae in the family Microhylidae, is an example of a taxonomic group for which much is still to be discovered. Indeed, the cophyline frogs present a large portion of Madagascar’s cryptic and microendemic amphibian diversity, yet they remain understudied. A new red-bellied species of the microhylid frog genus Stumpffia is described from the central plateau of Madagascar. Visual encounter surveys in Ambohitantely and Anjozorobe in 2019 and 2020 identified this previously unknown Stumpffia species, which closely resembles Stumpffia kibomena known from Andasibe in the east. Stumpffia lynnae sp. nov. adds another species to the red-bellied species complex, differing from S. kibomena by genetic differentiation in the mitochondrial 16S rRNA gene (3.6–3.9%) and distinct nuclear RAG1 haplotypes, as well as strongly by its advertisement call. The new species is known from across Ambohitantely Special Reserve and Anjozorobe Angavo protected area, but is known only from one complete specimen and eight individual tissue samples. Based on the rarity of the species, the small number of locations in which it has been found, and its disappearing forest habitat, its IUCN Red List classification is suggested as “Endangered”. This species is the first Stumpffia described from Madagascar’s central plateau, highlighting the importance of conserving the remnant forest fragments in this area and the ongoing need to survey and protect this threatened habitat type.

Abstract Erymnochelys madagascariensis is a Critically Endangered turtle endemic to Madagascar. Anthropogenic activity has depleted the wild population by 70% in the last century, and effective conservation management is essential to ensuring its persistence. Captive breeding was implemented to augment depleted populations in the southern part of Ankarafantsika National Park (ANP), when no genetic data were available for E. madagascariensis. It is unknown how much of the natural population’s diversity is encapsulated in captivity. We used eight microsatellite loci and fragments of two mitochondrial genes to identify the genetic structure of E. madagascariensis in the wild. Captive bred turtles were compared with wild populations in order to assess the representativeness of this ex situ conservation strategy for ANP. Six microsatellite clusters, ten cytochrome b, and nine COI haplotypes were identified across wild populations, with high genetic divergence found between populations in two groups of watersheds. Captive bred individuals represent three out of six sampled microsatellite clusters found in the wild and just one mitochondrial haplotype, possibly due to genetic drift. To improve genetic representation, the strategy of frequent interchange between captive and wild breeders within ANP should be revitalised and, as originally planned, hatchlings or juveniles should not be released beyond ANP.

Abstract Spiders are among the dominant invertebrate predators in agricultural systems and are significant regulators of insect pests. The precise dynamics of biocontrol of pests in the field are, however, poorly understood. This study investigates how density‐independent prey choice, taxonomy, life stage, sex, and web characteristics affect spider diet and biocontrol. We collected spiders in four genera of Linyphiidae (i.e., Bathyphantes, Erigone, Tenuiphantes, and Microlinyphia), and individuals from the Lycosidae genus Pardosa, and their proximate prey communities from barley fields in Wales, UK between April and September 2018. We analyzed the gut contents of 300 individual spiders using DNA metabarcoding. From the 300 spiders screened, 89 prey taxa were identified from 45 families, including a wide range of pests and predators. Thrips were the dominant prey, present in over a third of the spiders sampled, but a type IV functional response appears to reduce their predation at peak abundances. Spider diets significantly differed based on web characteristics, but this depended on the genus and sex of the spider and it was not the principal separating factor in the trophic niches of linyphiids and lycosids. Diets significantly differed between spider genera and life stages, reflected in different propensities for intraguild predation and pest predation. Adult spiders predated a greater diversity of other predators, and juveniles predated a greater diversity of pests. Overall, Tenuiphantes spp. and Bathyphantes spp. exhibited the greatest individual potential for biocontrol of the greatest diversity of pest genera. The greater trophic niche complementarity of Pardosa spp. and Erigone spp., however, suggests that their complementary predation of different pests might be of greater overall benefit to biocontrol. Sustainable agriculture should aim to optimize conditions throughout the cropping cycle for effective biocontrol, prioritizing provision for a diversity of spiders which predate a complementary diversity of pest species.

Anilany helenae is a Critically Endangered frog native to the central highlands of Madagascar. Due to ongoing habitat loss of its known range, this species’ population is considered declining, while little is known about its ecology, behavior, and taxonomy. Within the context of developing tools that can aid the conservation of Madagascar’s amphibian fauna, and add to the continued understanding of their taxonomy, we assembled its complete mitochondrial genome (Genbank Accession number MZ751042). This contributes the first complete mitochondrial genome of a microhylid from Madagascar, despite there being over 100 species in the Cophylinae subfamily alone. Anilany helenae’s circular mitochondrial genome is 17,519 bp long, contains 37 genes, and exhibits differences in gene arrangement compared with other microhylids, including the placement of protein coding genes nad1 and nad2. A phylogeny of the 13 protein coding genes of the few Madagascan anuran mitogenomes available, along with species from Africa and East Asia, places A. helenae along with the New Guinean Mantophryne lateralis in a basal position with respect to the other microhylids in the tree.

Abstract Background The lack of an understanding about the genomic architecture underpinning parental behaviour in subsocial insects displaying simple parental behaviours prevents the development of a full understanding about the evolutionary origin of sociality. Lethrus apterus is one of the few insect species that has biparental care. Division of labour can be observed between parents during the reproductive period in order to provide food and protection for their offspring. Results Here, we report the draft genome of L. apterus, the first genome in the family Geotrupidae. The final assembly consisted of 286.93 Mbp in 66,933 scaffolds. Completeness analysis found the assembly contained 93.5% of the Endopterygota core BUSCO gene set. Ab initio gene prediction resulted in 25,385 coding genes, whereas homology-based analyses predicted 22,551 protein coding genes. After merging, 20,734 were found during functional annotation. Compared to other publicly available beetle genomes, 23,528 genes among the predicted genes were assigned to orthogroups of which 1664 were in species-specific groups. Additionally, reproduction related genes were found among the predicted genes based on which a reduction in the number of odorant- and pheromone-binding proteins was detected. Conclusions These genes can be used in further comparative and functional genomic researches which can advance our understanding of the genetic basis and hence the evolution of parental behaviour.

Abstract The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.

Abstract Background Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals. To fill this gap in knowledge, we used nuclear and mitochondrial DNA markers to assess genetic diversity, gene flow and the genetic structure in the Bornean tree shrew, Tupaia longipes, that inhabits forest fragments of the Lower Kinabatangan Wildlife Sanctuary, Sabah. Furthermore, we used these markers to assess dispersal regimes in male and female T. longipes. Results In addition to the Kinabatangan River, a known barrier for dispersal in tree shrews, the heterogeneous landscape along the riverbanks affected the genetic structure in this species. Specifically, while in larger connected forest fragments along the northern riverbank genetic connectivity was relatively undisturbed, patterns of genetic differentiation and the distribution of mitochondrial haplotypes in a local scale indicated reduced migration on the strongly fragmented southern riverside. Especially, oil palm plantations seem to negatively affect dispersal in T. longipes. Clear sex-biased dispersal was not detected based on relatedness, assignment tests, and haplotype diversity. Conclusion This study revealed the importance of landscape connectivity to maintain migration and gene flow between fragmented populations, and to ensure the long-term persistence of species in anthropogenically disturbed landscapes.

Abstract The Asian water monitor lizard, Varanus salvator, is one of the largest predators in Southeast Asia which persists in human‐dominated landscapes and, as such, is a suitable model to understand the behavioral plasticity of generalists in anthropogenic landscapes. We used Local Convex Hull with adaptive algorithm to estimate the home range size of 14 GPS‐tagged individuals, followed by a MAXENT approach and community prey composition to understand the habitat preferences within the landscape. We estimated larger home ranges in forest than in oil palm plantations, as well as a larger diversity and abundance of mammals. Core home ranges were always linked to water bodies. However, the use of underproductive oil palm, freshwater swamp forest, and degraded forest by monitor lizards were higher than other kind of vegetation. This suitable habitat is proportionally larger in forest (73.7%) than in oil palm plantations (39.6%). Generalized estimation equation models showed that, while full home range size was negatively associated with the abundance of mammals, core areas depicted a positive association with mammal abundance, as well as with the proportion of suitable habitat within the home range. Besides having smaller home ranges in oil palm plantations, our findings suggest that limited suitable habitat availability forces the Asian water monitor lizard's population to establish only one or very few core areas. Contrastingly, under the protection of forest, they have more core areas, widely dispersed within larger home ranges. We conclude that regardless the plasticity of the species, human‐dominated landscapes are altering natural patterns of home range establishment in the monitor lizard's population, creating a potential ecological trap where conditions may not remain favorable for them in the long run. A deeper understanding of the ecological implications on the species and the prey community is advisable.

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.

New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today’s KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse.

The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.

The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.

In Borneo, oil palm plantations have replaced much of natural resources, where generalist species tend to be the principal beneficiaries, due to the abundant food provided by oil palm plantations. Here, we analyse the distribution of the Asian water monitor lizard (Varanus salvator) population within an oil palm-dominated landscape in the Kinabatangan floodplain, Malaysian Borneo. By using mark-recapture methods we estimated its population size, survival, and growth in forest and plantation habitats. We compared body measurements (i.e. body weight and body length) of individuals living in forest and oil palm habitats as proxy for the population's health status, and used general least squares estimation models to evaluate its response to highly fragmented landscapes in the absence of intensive hunting pressures. Contrary to previous studies, the abundance of lizards was higher in the forest than in oil palm plantations. Recruitment rates were also higher in the forest, suggesting that these areas may function as a source of new individuals into the landscape. While there were no morphometric differences among plantation sites, we found significant differences among forested areas, where larger lizards were found inhabiting forest adjacent to oil palm plantations. Although abundant in food resources, the limited availability of refugia in oil palm plantations may intensify intra-specific encounters and competition, altering the body size distribution in plantation populations, contrary to what happens in the forest. We conclude that large patches of forest, around and within oil palm plantations, are essential for the dynamics of the monitor lizard population in the Kinabatangan floodplain, as well as a potential source of individuals to the landscape. We recommend assessing this effect in other generalist species, as well as the impact on the prey communities, especially to reinforce the establishment of buffer zones and corridors as a conservation strategy within plantations.

Stress experienced during early life may have lasting effects on the immune system, with impacts on health and disease dependent on the nature and duration of the stressor. The epigenome is especially sensitive to environmental stimuli during early life and represents a potential mechanism through which stress may cause long-lasting health effects. However, the extent to which the epigenome responds differently to chronic vs acute stressors is unclear, especially for non-mammalian species. We examined the effects of acute stress (cold-shock during embryogenesis) and chronic stress (absence of tank enrichment during larval-stage) on global gene expression (using RNA-seq) and DNA methylation (using RRBS) in the gills of Atlantic salmon (Salmo salar) four months after hatching. Chronic stress induced pronounced transcriptional differences, while acute stress caused few lasting transcriptional effects. However, both acute and chronic stress caused lasting and contrasting changes in the methylome. Crucially, we found that acute stress enhanced transcriptional immune response to a pathogenic challenge (bacterial lipopolysaccharide, LPS), while chronic stress suppressed it. We identified stress-induced changes in promoter and gene-body methylation that were associated with altered expression for a small proportion of immune-related genes, and evidence of wider epigenetic regulation within signalling pathways involved in immune response. Our results suggest that stress can affect immuno-competence through epigenetic mechanisms, and highlight the markedly different effects of chronic larval and acute embryonic stress. This knowledge could be used to harness the stimulatory effects of acute stress on immunity, paving the way for improved stress and disease management through epigenetic conditioning.

Abstract Background Captive animal populations, be it for food production or conservation programmes, are often maintained at densities far beyond those in natural environments, which can have profound effects on behaviour, immune and stress levels, and ultimately welfare. How such alterations impact transcriptional responses to pathogen infection is a ‘different kettle of fish’ and remains poorly understood. Here, we assessed survival and gene expression profiles of infected fish reared at two different densities to elucidate potential functional genomic mechanisms for density-related differences in disease susceptibility. Results Utilising a whole-transcriptome sequencing (RNAseq) approach, we demonstrate that rearing density in tilapia (Oreochromis niloticus) significantly impacts susceptibility to the oomycete Saprolegnia parasitica, via altered transcriptional infection responses. Tilapia held at low densities have increased expression of genes related to stress, likely due to increased aggressive interactions. When challenged with Saprolegnia, low-density fish exhibit altered expression of inflammatory gene responses and enhanced levels of adaptive immune gene suppression compared to fish reared at higher density, resulting in significantly increased mortality rates. In addition, Saprolegnia infection substantially perturbs expression of circadian clock genes, with fish reared at low-density having higher levels of molecular clock dysregulation. Conclusions Our results reveal the wide-scale impact of stocking density on transcriptional responses to infection and highlight the need to incorporate circadian biology into our understanding of disease dynamics in managed animals.

The sheep and goat were domesticated ~10,500 years ago in the same region of the Middle-East. Here, Alberto et al compare the genomes of wild Asiatic mouflon and Bezoar ibex with that of domestics from local, traditional and improved breeds and find common targets of selection related to domestication and improvement in sheep and goats.

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.

Abstract Mouflon (Ovis aries musimon) became extinct from mainland Europe after the Neolithic, but remnant populations from the Mediterranean islands of Corsica and Sardinia have been used for reintroductions across Europe since the 19th-century. Mouflon x sheep hybrids are larger-bodied than mouflon, potentially showing increased male reproductive success, but little is known about genomic levels of admixture, or about the adaptive significance of introgression between resident mouflon and local sheep breeds. Here we analysed Ovine medium-density SNP array genotypes of 92 mouflon from six geographic regions, along with data from 330 individuals of 16 domestic sheep breeds. We found lower levels of genetic diversity in mouflon than in domestic sheep, consistent with past bottlenecks in mouflon. Introgression signals were bidirectional and affected most mouflon and sheep populations, being strongest in one Sardinian mouflon population. Developing and using a novel approach to identify chromosomal regions with consistent introgression signals, we infer adaptive introgression from mouflon to domestic sheep related to immunity mechanisms, but not in the opposite direction. Further, we infer that Soay and Sarda sheep carry introgressed mouflon alleles involved in bitter taste perception and/or innate immunity. Our results illustrate the potential for adaptive introgression even among recently diverged populations.

The vicuña (Vicugna vicugna) is the most representative wild ungulate of the high Andes of South America with two recognized morphological subspecies, V. v. mensalis in the north and V. v. vicugna in the south of its distribution. Current vicuña population size (460,000–520,000 animals) is the result of population recovery programs established in response to 500 years of overexploitation. Despite the vicuña’s ecosystemic, economic and social importance, studies about their genetic variation and history are limited and geographically restricted. Here, we present a comprehensive assessment of the genetic diversity of vicuña based on samples collected throughout its distribution range corresponding to eleven localities in Peru and five in Chile representing V. v. mensalis, plus four localities each in Argentina and Chile representing V. v. vicugna. Analysis of mitochondrial DNA and microsatellite markers show contrasting results regarding differentiation between the two vicuña types with mitochondrial haplotypes supporting subspecies differentiation, albeit with only a few mutational steps separating the two subspecies. In contrast, microsatellite markers show that vicuña genetic variation is best explained as an isolation by distance pattern where populations on opposite ends of the distribution present different allelic compositions, but the intermediate populations present a variety of alleles shared by both extreme forms. Demographic characterization of the species evidenced a simultaneous and strong reduction in the effective population size in all localities supporting the existence of a unique, large ancestral population (effective size ∼50,000 individuals) as recently as the mid-Holocene. Furthermore, the genetic variation observed across all localities is better explained by a model of gene flow interconnecting them rather than only by genetic drift. Consequently, we propose space “continuous” Management Units for vicuña as populations exhibit differentiation by distance and spatial autocorrelation linked to sex biased dispersal instead of population fragmentation or geographical barriers across the distribution.

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.

The domestication of wild vicuña and guanaco by early pre-Inca cultures is an iconic example of wildlife management and domestication in the Americas. Although domestic llamas and alpacas were clearly selected for key, yet distinct, phenotypic traits, the relative patterns and direction of selection and domestication have not been confirmed using genetic approaches. However, the detailed archaeological records from the region suggest that domestication was a process carried out under significant control and planning, which would have facilitated coordinated and thus extremely effective selective pressure to achieve and maintain desired phenotypic traits. Here we link patterns of sequence variation in two well-characterised genes coding for colour variation in vertebrates and interpret the results in the context of domestication in guanacos and vicuñas. We hypothesise that colour variation in wild populations of guanacos and vicunas were strongly selected against. In contrast, variation in coat colour variation in alpaca was strongly selected for and became rapidly fixed in alpacas. In contrast, coat colour variants in llamas were of less economic value, and thus were under less selective pressure. We report for the first time the full sequence of MC1R and 3 exons of ASIP in 171 wild specimens from throughout their distribution and which represented a range of commonly observed colour patterns. We found a significant difference in the number of non-synonymous substitutions, but not synonymous substitutions among wild and domestics species. The genetic variation in MC1R and ASIP did not differentiate alpaca from llama due to the high degree of reciprocal introgression, but the combination of 11 substitutions are sufficient to distinguish domestic from wild animals. Although there is gene flow among domestic and wild species, most of the non-synonymous variation in MC1R and ASIP was not observed in wild species, presumably because these substitutions and the associated colour phenotypes are not effectively transmitted back into wild populations. Therefore, this set of substitutions unequivocally differentiates wild from domestic animals, which will have important practical application in forensic cases involving the poaching of wild vicuñas and guanacos. These markers will also assist in identifying and studying archaeological remains pre- and post-domestication.

Geographic Information Systems (GIS) are becoming increasingly popular in the context of molecular ecology and conservation biology thanks to their display options efficiency, flexibility and management of geodata. Indeed, spatial data for wildlife and livestock species is becoming a trend with many researchers publishing genomic data that is specifically suitable for landscape studies. GIS uniquely reveal the possibility to overlay genetic information with environmental data and, as such, allow us to locate and analyze genetic boundaries of various plant and animal species or to study gene-environment associations (GEA). This means that, using GIS, we can potentially identify the genetic bases of species adaptation to particular geographic conditions or to climate change. However, many biologists are not familiar with the use of GIS and underlying concepts and thus experience difficulties in finding relevant information and instructions on how to use them. In this paper, we illustrate the power of free and open source GIS approaches and provide essential information for their successful application in molecular ecology. First, we introduce key concepts related to GIS that are too often overlooked in the literature, for example coordinate systems, GPS accuracy and scale. We then provide an overview of the most employed open-source GIS-related software, file formats and refer to major environmental databases. We also reconsider sampling strategies as high costs of Next Generation Sequencing (NGS) data currently diminish the number of samples that can be sequenced per location. Thereafter, we detail methods of data exploration and spatial statistics suited for the analysis of large genetic datasets. Finally, we provide suggestions to properly edit maps and to make them as comprehensive as possible, either manually or trough programming languages.

Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10-20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.

Morphological consistency in metazoans is remarkable given the pervasive occurrence of genetic variation, environmental effects, and developmental noise. Developmental stability, the ability to reduce developmental noise, is a fundamental property of multicellular organisms, yet its genetic bases remains elusive. Imperfect bilateral symmetry, or fluctuating asymmetry, is commonly used to estimate developmental stability. We observed that Drosophila melanogaster overexpressing Cyclin G (CycG) exhibit wing asymmetry clearly detectable by sight. Quantification of wing size and shape using geometric morphometrics reveals that this asymmetry is a genuine-but extreme-fluctuating asymmetry. Overexpression of CycG indeed leads to a 40-fold increase of wing fluctuating asymmetry, which is an unprecedented effect, for any organ and in any animal model, either in wild populations or mutants. This asymmetry effect is not restricted to wings, since femur length is affected as well. Inactivating CycG by RNAi also induces fluctuating asymmetry but to a lesser extent. Investigating the cellular bases of the phenotypic effects of CycG deregulation, we found that misregulation of cell size is predominant in asymmetric flies. In particular, the tight negative correlation between cell size and cell number observed in wild-type flies is impaired when CycG is upregulated. Our results highlight the role of CycG in the control of developmental stability in D. melanogaster. Furthermore, they show that wing developmental stability is normally ensured via compensatory processes between cell growth and cell proliferation. We discuss the possible role of CycG as a hub in a genetic network that controls developmental stability.

Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θ(Watterson), θ(π), and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data.