Population genomics for wildlife conservation and management

Local adaptation has a role in reducing vulnerability to climate change in a widespread Amazonian forest lizard

The extant genetic variation within and among taxa reflects a long history of diversification and adaptive mechanisms in response to climate change and landscape alterations. However, the velocity of current anthropogenic changes poses an imminent threat to global biodiversity. Understanding how species and populations might respond to global climate change provides valuable information for conservation in the face of these impacts. Here, we use genomic data to observe candidate loci under climate selection and test for genetic vulnerability to climate change in a widespread Amazonian ombrophilous lizard population. We found nine populations across Amazonia with a considerable amount of admixture among them. Distinct approaches of genome-environment association analyses revealed 56 candidate single-nucleotide polymorphisms (SNPs) under climatic selection, showing an east-west gradient in the adaptive landscape and a signal of local climate adaptation across the species range. According to our results, signals of local adaptation indicate that the species may not respond equally throughout its range, with some populations facing higher extinction risks. Genomic offset analysis predicts the southern and central portions of Amazonia to have a higher vulnerability to future climate change. Our findings highlight the importance of considering spatially explicit contexts with a large sampling coverage to evaluate how local adaptation and climatic vulnerability affect Amazonian forest ectothermic fauna.

Submerged Corridors of Ancient Gene Flow in an Island Amphibian

Many island archipelagos sit on shallow continental shelves, and during the Pleistocene, these islands were often connected as global sea levels dropped following glaciation. Given a continental shelf only 30-60 m below sea level, the terrestrial biota of the Seychelles Archipelago likely dispersed amongst now isolated islands during the Pleistocene. Hypogeophis rostratus is an egg-laying, direct-developing caecilian amphibian found on 10 islands in the granitic Seychelles. Despite the seemingly limited dispersal abilities of this salt-intolerant amphibian, its distribution on multiple islands suggests likely historic dispersal across now submerged continental shelf corridors. We tested for the genetic signature of these historic corridors using fine-scale genomic data (ddRADseq). We found that genomic clusters often did not correspond to islands in the archipelago and that isolation-by-distance patterns were more consistent with gene flow across a continuous landscape than with isolated island populations. Using effective migration surfaces and ancestral range expansion prediction, we found support for contemporary populations originating near the large southern island of Mahé and dispersing to northern islands via the isolated Frégate island, with additional historic migration across the flat expanse of the Seychelles bank. Collectively, our results suggest that biogeographic patterns can retain signals from Pleistocene 'palaeo-islands' and that present-day islands can be thought of as hosting bottlenecks or transient refugia rather than discrete genetic units. Thus, the signatures of gene flow associated with palaeo-islands may be stronger than the isolating effects of contemporary islands in terrestrial species distributed on continental shelf islands.

Phylogenomic Analysis of Wide-Ranging Least Shrews Refines Conservation Priorities and Supports a Paradigm for Evolution of Biota Spanning Eastern North America and Mesoamerica

Anthropogenic global change is impacting the evolutionary potential of biodiversity in ways that have been difficult to predict. Distinct evolutionary units within species may respond differently to the same environmental trends, reflecting unique geography, ecology, adaptation, or drift. Least shrews (Cryptotis parvus group) have a widespread distribution across North America, yet systematic relationships and ongoing evolutionary processes remain unresolved. Westernmost peripheral populations have been prioritized for conservation, but little is known of their evolutionary histories or population trajectories. The broad range of this group of species is coincident with many other temperate taxa, presenting a hypothesis that diversification of least shrews follows a repeated process through the Pleistocene, leading to regionally diagnosable conservation units. We use genomic data and niche modeling to delimit species and conservation units of least shrews. Our results show that least shrews warrant recognition as multiple distinct species, along with geographically discrete infraspecific lineages of C. parvus (sensu stricto). Western peripheral populations are evolutionarily distinct based on nuclear, but not mitochondrial data, possibly reflecting mitochondrial capture during the last glacial phase. This population represents a relict conservation unit, consistent with both an "adaptive unit" and "management unit" based on non-neutral and neutral divergence, respectively. Hindcast niche modeling supports growing evidence for a shared process of diversification among co-distributed biota, and forecast modeling suggests continued future loss of suitable environmental niche in peripheral regions. Given mito-nuclear discordance among samples of parapatric lineages, future environmental perturbation may continue to impact the genomic integrity of important conservation units, making ecological and genomic monitoring a critical need.

Genomes of critically endangered saola are shaped by population structure and purging

The saola is one of the most elusive large mammals, standing at the brink of extinction. We constructed a reference genome and resequenced 26 saola individuals, confirming the saola as a basal member of the Bovini. Despite its small geographic range, we found that the saola is partitioned into two populations with high genetic differentiation (FST = 0.49). We estimate that these populations diverged and started declining 5,000-20,000 years ago, possibly due to climate changes and exacerbated by increasing human activities. The saola has long tracts without genomic diversity; however, most of these tracts are not shared by the two populations. Saolas carry a high genetic load, yet their gradual decline resulted in the purging of the most deleterious genetic variation. Finally, we find that combining the two populations, e.g., in an eventual captive breeding program, would mitigate the genetic load and increase the odds of species survival.

Complete mitogenomes reveal high diversity and recent population dynamics in Antarctic krill

BACKGROUND

The Antarctic krill (Euphausia superba) is a keystone species in the Southern Ocean ecosystem, influencing food web dynamics and ecosystem functionality. Despite its ecological importance, further exploration is essential to understand their population dynamics.

RESULTS

In this study, we present the complete mitogenome of the Antarctic krill. The assembly is 18,926 bp, including a notably large 3,952 bp control region (CR). The CR features a satellite repeat spanning 2,289 bp, showcasing the effectiveness of long-read sequencing in resolving complex genomic regions. Additionally, we identified 900 nuclear-mitochondrial segments (NUMTs) totaling 2.79 Mb, shedding light on the dynamic integration of mitochondrial DNA (mtDNA) into the nuclear genomes. By establishing a dataset comprising 80 krill mitogenomes, we unveil substantial mitochondrial diversity, particularly within the ND4 gene. While our analysis reveals no significant differentiation among four geographically distinct groups, we identify at least four maternal genetic clusters. Haplotype network analysis and demographic reconstructions suggest a recent population expansion, likely driven by favorable environmental conditions during the late Pleistocene. Furthermore, our investigation into selection pressures on mitochondrial genes reveals evidence of purifying selection across all 13 protein-coding genes, underscoring the pivotal role of mtDNA conservation in maintaining mitochondrial function under extreme environments.

CONCLUSIONS

This study provides a repository of Antarctic krill mitogenomes and insights into the population genetics and evolutionary history of this ecologically important species from a mitogenomic perspective, with implications for krill conservation and management in the Southern Ocean.

Satellite-observed mountain greening predicts genomic erosion in a grassland medicinal herb over half a century

Mountains are biodiversity hotspots contributing essential benefits to human societies, but global environmental change is rapidly altering their habitats. During the past five decades, increasing temperatures and land-use change in montane and subalpine elevations facilitated the productivity and expansion of competitive vegetation, termed as "greening," with adverse effects on open grassland habitats. Although vegetation greening is well-documented through satellite observations, its impact on the populations and genomic integrity of affected species remains underexplored. Here, we address this challenge by integrating 40 years of remote sensing data with museum genomics and fieldwork to assess the impact of mountain greening on the genomic diversity of grassland plants in the southern Balkan peninsula. We sequenced the genomes of historical and modern populations of Ironwort, a plant of significant medicinal value, and demonstrate widespread genomic erosion across its populations. Our results show that, on average, 6% (0%-20%) of Ironwort's genome is affected by inbreeding accumulation over the past half century, indicating various degrees of population declines. Importantly, we show that genomic erosion is highly predictable by the normalized difference vegetation index (NDVI) rates of change. Our models suggest that faster increases in vegetation density are associated with higher population declines in this grassland species, revealing the negative impacts of increasing productivity in mountain ecosystems. By linking two independent and disparate monitoring indicators, we demonstrate the ability of remote sensing to predict the consequences of environmental change on temporal genomic change in mountain grassland species, with far-reaching implications for protecting natural resources in these fragile ecosystems.

De novo whole-genome assembly of the critically endangered southern muriqui (Brachyteles arachnoides)

The southern muriqui (Brachyteles arachnoides) is one of the 2 species of muriquis (genus Brachyteles), the largest body-sized nonhuman primate from the Neotropics. Deforestation and illegal hunting have led to a continuing decline in the muriqui population, leading to their current classification as critically endangered. The lack of a reference genome for the genus Brachyteles prevents scientists from taking full advantage of genomic tools to improve their conservation status. This study reports the first whole-genome assemblies of the genus Brachyteles, using DNA from 2 zoo-housed southern muriqui females. We performed sequencing with Oxford Nanopore Technologies' PromethION 2 Solo using a native DNA library preparation to preserve DNA modifications. We used Flye to assemble genomes for each individual. The best final assembly was 2.6 Gb, in 319 contigs, with an N50 of 58.8 Mb and an L50 of 17. BUSCO completeness score for this assembly was 99.5%. The assembly of the second individual had similar quality, with a length of 2.6 Gb, 759 contigs, an N50 of 47.9 Mb, an L50 of 18, and a BUSCO completeness score of 99.04%. Both assemblies had <1% duplicates, missing, or fragments. Gene model mapper detected 24,353 protein-coding genes, and repetitive elements accounted for 46% of the genome. We also reported the mitogenome, which had 16,562 bp over 37 genes, and global methylation of CpG sites, which revealed a mean of 80% methylation. Our study provides a high-quality reference genome assembly for the southern muriqui, expanding the tools that can be used to aid in their conservation efforts.

Evaluation of non-invasive hair snares for North American beavers (Castor canadensis): placement, efficiency, and beaver's behavioral response

Although the commercial demand for North American beaver (Castor canadensis) hair shaped much of the socio-ecological landscape of North America, use of beaver hair in wildlife research has focused on the Eurasian beaver (Castor fiber) and collection methods have largely involved handling animals alive or sampling dead animals. In 2022 and 2023, we tested the utility of barbed-wire hair snares to non-invasively collect hair from beavers around ponds in Northern Minnesota. At 56 different beaver ponds, we deployed 64 hair snares with remote cameras. From these data, we determined the efficiency of hair snares to collect samples, from what side of the body samples are collected, the weight and dirtiness of samples collected, the potential for bycatch, and if snares impede beavers' ability to travel on land. We collected beaver hair samples from 94% of snares deployed, with snares sampling beaver legs and back most often. Forty-two percent of samples collected had no dirt on them, and the most productive snare collected on average 3.4 mg of clean hair per day. Muskrats were the second most sampled animal, but only made up on average 16% of total samples recorded on video per snare. Snares inhibited beaver travel in 0.1% of videos (n = 5,627 videos of beavers recorded, n = 6 videos where beaver travel was inhibited). We did not find any predictive variable that influenced the collection of beaver hair (e.g., location of snare at pond, presence of wire brushes on snare, number of times beavers touched snares, or location on the beaver's body that was sampled). Our study provides in depth evidence of passive hair snare methods used to collect North American beaver hair, and serves as a guide to non-invasive hair snaring for multiple objectives such as hormone, genetic, and stable-isotope sample collection.

Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala

Koalas are arboreal herbivorous marsupials, endemic to Australia. During the late 1800s and early 1900s, the number of koalas declined dramatically due to hunting for their furs. In addition, anthropogenic activities have further decimated their available habitat, and decreased population numbers. Here, we utilize 37 historic and 25 modern genomes sampled from across their historic and present geographic range, to gain insights into how their population structure and genetic diversity have changed across time; assess the genetic consequences of the period of intense hunting, and the current genetic status of this iconic Australian species. Our analyses reveal how genome-wide heterozygosity has decreased through time and unveil previously uncharacterized mitochondrial haplotypes and nuclear genotypes in the historic dataset, which are absent from today's koala populations.

Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA

Mitonuclear discordance between species is readily documented in marine fishes. Such discordance may either be the result of past natural phenomena or the result of recent introgression from previously seperated species after shifts in their spatial distributions. Using ancient DNA spanning five millennia, we here investigate the long-term presence of Pacific bluefin tuna (Thunnus orientalis) and albacore (Thunnus alalunga) -like mitochondrial (MT) genomes in Atlantic bluefin tuna (Thunnus thynnus), a species with extensive exploitation history and observed shifts in abundance and age structure. Comparing ancient (n = 130) and modern (n = 78) Atlantic bluefin MT genomes from most of its range, we detect no significant spatial or temporal population structure, which implies ongoing gene flow between populations and large effective population sizes over millennia. Moreover, we identify discordant MT haplotypes in ancient specimens up to 5000 years old and find that the frequency of these haplotypes has remained similar through time. We therefore conclude that MT discordance in the Atlantic bluefin tuna is not driven by recent introgression. Our observations provide oldest example of directly observed MT discordance in the marine environment, highlighting the utility of ancient DNA to obtain insights in the long-term persistence of such phenomena.

Conservation genomics of a threatened subtropical Rhododendron species highlights the distinct conservation actions required in marginal and admixed populations

With the impact of climate change and anthropogenic activities, the underlying threats facing populations with different evolutionary histories and distributions, and the associated conservation strategies necessary to ensure their survival, may vary within a species. This is particularly true for marginal populations and/or those showing admixture. Here, we re-sequence genomes of 102 individuals from 21 locations for Rhododendron vialii, a threatened species distributed in the subtropical forests of southwestern China that has suffered from habitat fragmentation due to deforestation. Population structure results revealed that R. vialii can be divided into five genetic lineages using neutral single-nucleotide polymorphisms (SNPs), whereas selected SNPs divide the species into six lineages. This is due to the Guigu (GG) population, which is identified as admixed using neutral SNPs, but is assigned to a distinct genetic cluster using non-neutral loci. R. vialii has experienced multiple genetic bottlenecks, and different demographic histories have been suggested among populations. Ecological niche modeling combined with genomic offset analysis suggests that the marginal population (Northeast, NE) harboring the highest genetic diversity is likely to have the highest risk of maladaptation in the future. The marginal population therefore needs urgent ex situ conservation in areas where the influence of future climate change is predicted to be well buffered. Alternatively, the GG population may have the potential for local adaptation, and will need in situ conservation. The Puer population, which carries the heaviest genetic load, needs genetic rescue. Our findings highlight how population genomics, genomic offset analysis, and ecological niche modeling can be integrated to inform targeted conservation.

Genetic diversity, population genetic structure and demographic history of the Ribbontail stingray Taeniura lymma (Fabricius, 1775) (elasmobranchii: myliobatiformes: dasyatidae) along the Tanzanian coastline

The Ribbontail stingray Taeniura lymma is an economically important fish and attractive species for the aquarium trade industry. Overfishing, habitat degradation, and pollution, however, pose a threat to this species. This study used partial mitochondrial cytochrome oxidase subunit I (COI) sequences (603 base pairs long) from 96 samples of T. lymma collected at five fish-landing sites (Deep Sea-Tanga, Malindi-Unguja, Kaole-Bagamoyo, Kivukoni-Dar es Salaam, and Bandarini-Mtwara) located along the coast of Tanzania to determine the species' genetic diversity, population genetic structure, and demographic history. The findings revealed an average nucleotide diversity of 0.24 ± 0.16% and a haplotype diversity of 0.75 ± 0.04. Nucleotide and haplotype diversities were relatively low at Kaole-Bagamoyo compared to the other studied localities. An Analysis of Molecular Variance (AMOVA) indicated limited but statistically significant genetic differences among populations (Overall FST = 0.09, p < 0.01). Pairwise AMOVA revealed genetic difference between the Deep Sea-Tanga population and all other populations studied with exception of Malindi-Unguja. Analyses of mismatch distribution, demographic history, and a haplotype network support a scenario of historical population expansion in the studied species. Immediate effort is required to protect population exhibiting low genetic diversity in this commercially important ray.

Species Delimitation Using Genomic Data: Options and Limitations

The most effective approaches for species discovery and species validation with genomic data remain underexplored. This study evaluates the merits and limitations of phylogenetic approaches based on the multispecies coalescent model and population genetic approaches for species discovery, i.e., species delimitation in the absence of prior knowledge, using genomic datasets from four well-known radiations. Furthermore, it demonstrates how geographic data can be integrated with the genomic data for species validation, i.e., for testing primary species hypotheses. The multispecies coalescent model-based approaches tr2 and soda resulted in high over-splitting of species, low percentages of species delimited according to the current classification, and low percentages of individuals assigned to the same species as in the current classification across all four species complexes studied. Conversely, the species numbers were slightly underestimated based on the structure results. Although the proportion of species delimited according to the current classification and the proportion of individuals assigned to the same species as in the current classification in the classifications based on the structure results is approximately twice that of the classifications proposed by the multispecies coalescent model-based approaches, it remains unsatisfactory. A slight over-splitting of species into population groups can be corrected by species validation with isolation-by-distance tests if a sufficient number of populations have been sampled for each species. Sampling design is an essential step in any taxonomic study, as it has a significant impact on the delimitation of the species and the possibility of their validation.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

Toward a Global Science of Conservation Genomics: Coldspots in Genomic Resources Highlight a Need for Equitable Collaborations and Capacity Building

Advances in genomic sequencing have magnified our understanding of ecological and evolutionary mechanisms relevant to biodiversity conservation. As a result, the field of conservation genomics has grown rapidly. Genomic data can be effective in guiding conservation decisions by revealing fine-scale patterns of genetic diversity and adaptation. Adaptive potential, sometimes referred to as evolutionary potential, is particularly informative for conservation due to its inverse relationship with extinction risk. Yet, global coldspots in genomic resources impede progress toward conservation goals. We undertook a systematic literature review to characterise the global distribution of genomic resources for amphibians and reptiles relative to species richness, IUCN status, and predicted global change. We classify the scope of available genomic resources by their potential applicability to global change. Finally, we examine global patterns of collaborations in genomic studies. Our findings underscore current priorities for expanding genomic resources, especially those aimed at predicting adaptive potential to future environmental change. Our results also highlight the need for improved global collaborations in genomic research, resource sharing, and capacity building in the Global South.

Genomic Landscape of Divergence in Ballan Wrasse (Labrus bergylta)

The architecture underpinning genomic divergence is still a largely uncharted territory and likely case-dependent. Here, we investigated genome-wide variation in Ballan wrasse, a northeastern Atlantic fish species that displays two sympatric colour morphs, spotty and plain, that have been suggested to represent subspecies. We produced a chromosome-level reference genome and thereafter investigated genomic divergence among 152 individuals including both morphs, from two localities in Spain and Norway each and one in France. Differences between morphs dominated in Spain in accordance with sympatric divergence, whereas in Norway allopatric differentiation was prominent and repeated genomic signals of local divergence were found. Chromosomes had large low-recombining areas shared across all populations. Within the Spanish morphs, these areas contained large islands of divergence, totalling ~11% of the genome, and showed high morph specificity and strong selection. The same regions showed frequent admixture in the French morphs and no differentiation in Norway. In contrast, divergent regions observed between sampling localities in Norway were shorter and found throughout the genome. High inbreeding and lower diversity were observed in the Norwegian samples, consistent with the proposed recolonisation bottleneck and subsequent drift. Several genomic regions were significantly associated with morphs and contained tens of genes of diverse functions, suggesting that colouration is unlikely to be the sole driver of divergence. Our results do not support the hypothesis of shared larger genomic features underlying intraspecific colour divergence. Instead, we observe gradual accumulation of differences into low-recombining regions, likely when additional factors like assortative mating and/or lack of gene flow favour their development.

Genome-wide SNPs reveal novel genetic relationships among Atlantic cod (Gadus morhua) from the south coast of Newfoundland, Canada (subdivision 3Ps), Northern cod stock complex, and Gulf of St Lawrence

The south coast of Newfoundland, Canada (Northwest Atlantic Fisheries Organization (NAFO) Subdivision 3Ps) is known to be a mixing zone for Atlantic cod (Gadus morhua). Tagging and genetic studies have shown cod from the Northern and Southern Gulf of St. Lawrence (NAFO Divisions 3Pn, 4RST), Southern Grand Banks (3NO), and the Northern cod stock complex (2J3KL) frequent the waters of 3Ps at various times throughout the year, but the extent of genetic mixing is unknown. However, 3Ps has not been the central focus of previous large-scale genomic analyses of population structure, a knowledge gap that we address using single nucleotide polymorphisms. Using 38,111 neutral markers from reduced representation next-generation sequencing data, we determined the provenance of 3Ps cod relative to the Northern stock complex, Gulf of St. Lawrence, Bay of Fundy, and Gulf of Maine. We present evidence for genetic similarity between 3Ps and the Northern stock complex, particularly NAFO Division 3L. Additionally, genetic clustering analyses suggest 3Ps to be a mixed stock, containing individuals from the Northern stock complex and Gulf of St. Lawrence. Genetic clustering also suggests that there are two subtle subclusters of Northern stock complex and 3Ps cod, indicating there may be subtle population structure within the Northern stock complex and surrounding zones. This new information on population structure gives insight into connectivity and may be useful in future management for rebuilding cod populations.

Contrasting Genomic Diversity and Inbreeding Levels Among Two Closely Related Falcon Species With Overlapping Geographic Distributions

Genomic resources are valuable to examine historical demographic patterns and their effects to better inform management and conservation of threatened species. We evaluated population trends and genome-wide variation in the near-threatened Orange-breasted Falcon (Falco deiroleucus) and its more common sister species, the Bat Falcon (F. rufigularis), to explore how the two species differ in genomic diversity as influenced by their contrasting long-term demographic histories. We generated and aligned whole genome resequencing data for 12 Orange-breasted Falcons and 9 Bat Falcons to an annotated Gyrfalcon (F. rusticolus) reference genome that retained approximately 22.4 million biallelic autosomal SNPs (chromosomes 1-22). Our analyses indicated much lower genomic diversity in Orange-breasted Falcons compared to Bat Falcons. All sampled Orange-breasted Falcons were significantly more inbred than the sampled Bat Falcons, with values similar to those observed in island-mainland species comparisons. The distribution of runs of homozygosity showed variation suggesting long-term low population size and the possibility of bottlenecks in Orange-breasted Falcons contrasting with consistently larger populations in Bat Falcons. Analysis of genetic load suggests that Orange-breasted Falcons are less likely to experience inbreeding depression than Bat Falcons due to reduced inbreeding load but are at elevated risk from fixation of deleterious gene variants and perhaps a reduced adaptive potential. These genomic analyses highlight differences in the historical demography of two closely related species that have influenced their current genomic diversity and should result in differing strategies for their continued conservation.

Genomic Vulnerability of a Sentinel Mammal Under Climate Change

Climate change poses a significant threat to biodiversity, particularly in alpine ecosystems where species have already undergone elevational range shifts. Genomics can be used to estimate the adaptive potential of species, as well as the shift in adaptive genomic composition necessary for populations to adjust to climate change (e.g., genomic offset). Here, we investigated patterns of climate-mediated adaptive genetic variation and predicted the degree of genomic offset under multiple climate change scenarios for a sentinel alpine mammal, the American pika (Ochotona princeps). We collected genome-wide data (29,709 SNPs) from 363 individuals spanning the entire range in western North America and employed genotype-environment association analyses to identify 924 robust outlier SNPs, several of which were linked to genes previously associated with high elevation and hypoxia responses in various pika species (Ochotonidae). Adaptive genomic variation was most strongly influenced by mean warmest month temperature, followed by precipitation of the coldest quarter. Spatial patterns of genomic offset were heterogeneous, significantly predicted by levels of adaptive genetic variation, elevation and latitude. Sites within the Northern Rocky Mountains exhibited the highest genomic offset under projected climate change despite possessing high levels of adaptive genetic variation. As such, while our study provides an example of how genomic data can be used to explore the potential consequences of climate change, it further highlights the need for careful consideration of genomic offset values within their proper ecological context.

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

Kelp forests are declining in many parts of the northeast Pacific.1,2,3,4 In small populations, genetic drift can reduce adaptive variation and increase fixation of recessive deleterious alleles,5,6,7 but natural selection may purge harmful variants.8,9,10 To understand evolutionary dynamics and inform restoration strategies, we investigated genetic structure and the outcomes of genetic drift and purging by sequencing the genomes of 429 bull kelp (Nereocystis luetkeana) and 211 giant kelp (Macrocystis sp.) from the coastlines of British Columbia and Washington. We identified 6 to 7 geographically and genetically distinct clusters in each species. Low effective population size was associated with low genetic diversity and high inbreeding coefficients (including increased selfing rates), with extreme variation in these genetic health indices among bull kelp populations but more moderate variation in giant kelp. We found no evidence that natural selection is purging putative recessive deleterious alleles in either species. Instead, genetic drift has fixed many such alleles in small populations of bull kelp, leading us to predict (1) reduced within-population inbreeding depression in small populations, which may be associated with an observed shift toward increased selfing rate, and (2) hybrid vigor in crosses between small populations. Our genomic findings imply several strategies for optimal sourcing and crossing of populations for restoration and aquaculture, but these require experimental validation. Overall, our work reveals strong genetic structure and suggests that conservation strategies should consider the multiple health risks faced by small populations whose evolutionary dynamics are dominated by genetic drift.

Genome-Assisted Gene-Flow Rescued Genetic Diversity Without Hindering Growth Performance in an Inbred Coho Salmon (Oncorhynchus kisutch) Population Selected for High Growth Phenotype

Selective breeding is a powerful tool for improving aquaculture production. A well-managed breeding program is essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, genetic diversity in broodstock must be restored by introducing individuals from external populations. However, this can reduce the accumulated genetic gains from selective breeding. However, the selective introduction of individuals with superior phenotypes will allow the restoration of genetic diversity without sacrificing these gains. In this study, we demonstrated this possibility using a selectively bred (SB) and a randomly bred (RB) population of coho salmon (Oncorhynchus kisutch). Forty males with superior growth were selected from the RB population using genomic selection and crossed with 127 randomly collected females from the SB population, producing a newly bred (NB) population. Genetic diversity, assessed from population statistics such as effective number of alleles, allele richness, and observed heterozygosity of 11 microsatellite markers, was higher in NB than in SB and RB. Additionally, fork length and body weight were compared among the three populations after 12 months of growth post-fertilization in common tanks. The least-squares means of fork length and body weight were similar between NB (164.9 mm and 57.9 g) and SB (161.1 mm and 53.7 g), while both were significantly greater than RB (150.4 mm and 43.0 g). Our results highlight the effectiveness of genome-assisted gene flow in restoring the genetic diversity of a population without compromising accumulated genetic gain in growth.

Kinship clustering within an ecologically diverse killer whale metapopulation

Metapopulation dynamics can be shaped by foraging ecology, and thus be sensitive to shifts in prey availability. Genotyping 204 North Atlantic killer whales at 1346 loci, we investigated whether spatio-temporal population structuring is linked to prey type and distribution. Using population-based methods (reflecting evolutionary means), we report a widespread metapopulation connected across ecological groups based upon nuclear genome SNPs, yet spatial structuring based upon mitogenome haplotypes. These contrasting patterns of markers with maternal and biparental inheritance are consistent with matrilineal site fidelity and philopatry, and male-mediated gene flow among demes. Connectivity between fish-eating and 'mixed-diet' (eating both fish and mammal prey) killer whales, marks a deviation within a species renowned for its marked structure associated with ecology. However, relatedness estimates suggest distinct spatial clusters, and heterogeneity in recent gene flow between them. The contrasting patterns between inference of structure and inference of relatedness suggest that gene flow has been partially restricted over the past two to three generations (50-70 years). This coincides with the collapse of North Atlantic herring stocks in the late 1960s and the subsequent cessation of their seasonal connectivity. Statistically significant association between diet types and assignment of Icelandic killer whales to relatedness-based clusters indicated limited gene flow was maintained through Icelandic 'mixed-diet' whales when herring-mediated connectivity was diminished. Thus, conservation of dietary variation within this metapopulation is critical to ensure genetic health. Our study highlights the role of resource dynamics and foraging ecology in shaping population structure and emphasises the need for transnational management of this widespread migratory species and its prey.

Atlantic mackerel population structure does not support genetically distinct spawning components

Background

The Atlantic mackerel, Scomber scombrus (Linnaeus, 1758) is a commercially valuable migratory pelagic fish inhabiting the northern Atlantic Ocean and the Mediterranean Sea. Given its highly migratory behaviour for feeding and spawning, several studies have been conducted to assess differentiation among spawning components to better define management units, as well as to investigate possible adaptations to comprehend and predict recent range expansion northwards.

Methods

Here, the genome of S. scombrus was sequenced and annotated, as an increasing number of population genetic studies have proven the relevance of reference genomes to investigate genomic markers/regions potentially linked to differences at finer scale. Such reference genome was used to map Restriction-site-associated sequencing (RAD-seq) reads for SNP discovery and genotyping in more than 500 samples distributed along the species range. The resulting genotyping tables have been used to perform connectivity and adaptation analyses.

Results

The assembly of the reference genome for S. scombrus resulted in a genome of 741 Mb. Our population genetic results show that the Atlantic mackerel consist of three previously known genetically isolated units (Northwest Atlantic, Northeast Atlantic, Mediterranean), and provide no evidence for genetically distinct spawning components within the Northwest or Northeast Atlantic.

Conclusions

Therefore, our findings resolved previous uncertainties by confirming the absence of genetically isolated spawning components in each side of the northern Atlantic, thus rejecting homing behaviour and the need to redefine management boundaries in this species. In addition, no further genetic signs of ongoing adaptation were detected in this species.

The first complete mitochondrial genome of Sumatran striped rabbit Nesolagus netscheri (Schlegel, 1880), and its phylogenetic relationship with other Leporidae

Nesolagus netscheri, a Sumatran striped rabbit, is one of the rarest rabbits in the Leporidae family, and its genetic information is still limited. This study provides the first mitochondrial genome and molecular systematic characterization of the Sumatran striped rabbit, Nesolagus netscheri, Indonesia's rarest rabbit. It consists of a circular double-stranded DNA of 16,709 bp. It showed that the mitochondrial genome structure of N. netscheri is similar to that of N. timminsi. The mitochondrial genome of N. netscheri contained 22 transfer RNA (tRNA) genes, and all tRNA except for trnS1 showed a characteristic cloverleaf secondary structure. Evidence was found that the atp8 gene of N. netscheri is under positive selection pressure. The phylogenetic analysis shows Leporidae was monophyletic, with Nesolagus at the basal. The study indicates a split between N. netscheri and N. timminsi in the Late Pleistocene around 0.43 million years ago. This research is a fundamental reference for the conservation of the rarest lagomorph species and provides important information for future evolutionary studies in the Leporidae family.

Telomere-to-telomere genome and resequencing of 254 individuals reveal evolution, genomic footprints in Asian icefish, Protosalanx chinensis

The Asian icefish, Protosalanx chinensis, has undergone extensive colonization in various waters across China for decades due to its ecological and physiological significance as well as its economic importance in the fishery resource. Here, we decoded a telomere-to-telomere (T2T) genome for P. chinensis combining PacBio HiFi long reads and ultra-long ONT (nanopore) reads and Hi-C data. The telomere was identified in both ends of the contig/chromosome. The expanded gene associated with circadian entrainment suggests that P. chinensis may exhibit a high sensitivity to photoperiod. The contracted genes' immune-related families and DNA repair associated with positive selection in P. chinensis suggested the selection pressure during adaptive evolution. The population genetic analysis reported the genetic diversity and genomic footprints in 254 individuals from 8 different locations. The natural seawater samples can be the highest diversity and different from other freshwater and introduced populations. The divergent regions' associated genes were found to be related to the osmotic pressure system, suggesting adaptations to alkalinity and salinity. Thus, the T2T genome and genetic variation can be valuable resources for genomic footprints in P. chinensis, shedding light on its evolution, comparative genomics, and the genetic differences between natural and introduced populations.

A Genomic-Based Workflow for eDNA Assay Development for a Critically Endangered Turtle, Myuchelys georgesi

Environmental DNA (eDNA) analysis has become a popular conservation tool for detecting rare and elusive species. eDNA assays typically target mitochondrial DNA (mtDNA) due to its high copy number per cell and its ability to persist in the environment longer than nuclear DNA. Consequently, the development of eDNA assays has relied on mitochondrial reference sequences available in online databases, or in cases where such data are unavailable, de novo DNA extraction and sequencing of mtDNA. In this study, we designed eDNA primers for the critically endangered Bellinger River turtle (Myuchelys georgesi) using a bioinformatically assembled mitochondrial genome (mitogenome) derived from a reference genome. We confirmed the accuracy of this assembled mitogenome by comparing it to a Sanger-sequenced mitogenome of the same species, and no base pair mismatches were detected. Using the bioinformatically extracted mitogenome, we designed two 20 bp primers that target a 152-base-pair-long fragment of the cytochrome oxidase 1 (CO1) gene and a 186-base-pair-long fragment of the cytochrome B (CytB) gene. Both primers were successfully validated in silico, in vitro, and in situ.

De Novo Genome Assembly for an Endangered Lemur Using Portable Nanopore Sequencing in Rural Madagascar

As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next-generation sequencing technologies and the resulting reduction in associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first published reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archived E. rufifrons specimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.157 gigabase, 2980-contig nuclear assembly with an N50 of 101.6 Mb and a 17,108 bp mitogenome. The nuclear assembly had 30× average coverage and was comparable in completeness to other primate reference genomes, with a 96.1% BUSCO completeness score for primate-specific genes. As the first published reference genome for E. rufifrons and the only annotated genome available for the speciose Eulemur genus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

South African indigenous chickens' genetic diversity, and the adoption of ecological niche modelling and landscape genomics as strategic conservation techniques

Selection pressures found in the prevailing production environments have shaped the genetic structure of indigenous chickens we see today. Indigenous chickens, raised in villages, provide essential genetic resources and income for poverty alleviation by providing affordable protein. However, they are threatened by predators, emerging diseases, and market demand for ideal breeds and fast production which causes loss of their valuable traits. The lack of knowledge about genetic diversity and genetic mechanisms underlying adaptive variants may compromise the goal of conserving indigenous chicken breeds. The main insights of the study are that indigenous chickens are highly diversified, and environmental factors play a key role in enabling chicken adaptation and distribution. Genomic and spatial technologies have made it possible to explore the genetic structure and fully comprehend the mechanism underlying the local adaptation of indigenous chickens. These technologies can aid in creating programs that enhance productivity and promote climate-resilient breeds. This review explores the impact of natural selection on indigenous chicken, genetic diversity, population size, and the advancement of technologies in understanding local adaptation drivers. In conclusion, this review highlights the importance of studying the habitats and how this will guide in conserving local breeds in their intended production environment.

How can biodiversity strategy and action plans incorporate genetic diversity and align with global commitments?

National, subnational, and supranational entities are creating biodiversity strategy and action plans (BSAPs) to develop concrete commitments and actions to curb biodiversity loss, meet international obligations, and achieve a society in harmony with nature. In light of policymakers' increasing recognition of genetic diversity in species and ecosystem adaptation and resilience, this article provides an overview of how BSAPs can incorporate species' genetic diversity. We focus on three areas: setting targets; committing to actions, policies, and programs; and monitoring and reporting. Drawing from 21 recent BSAPs, we provide examples of policies, knowledge, projects, capacity building, and more. We aim to enable and inspire specific and ambitious BSAPs and have put forward 10 key suggestions mapped to the policy cycle. Together, scientists and policymakers can translate high level commitments, such as the Convention on Biological Diversity's Kunming-Montreal Global Biodiversity Framework, into concrete nationally relevant targets, actions and policies, and monitoring and reporting mechanisms.

Family Matters: Linking Population Growth, Kin Interactions, and African Elephant Social Groups

AbstractIn many species, individuals are embedded in a network of kin with whom they interact. Interactions between kin can affect survival and fertility rates and thus the life history of individuals. These interactions indirectly affect both the network of kin and the dynamics of the population. In this way, a nonlinear feedback between the kin network and individual vital rates emerges. We describe a framework for integrating these kin interactions into a matrix model by linking the individual kin network to a matrix model. We demonstrate the use of this framework for African elephant populations under varying poaching pressure. For this example, we incorporate effects of the maternal presence and matriarchal age on juvenile survival and effects of the presence of a sister on young female fecundity. We find that the feedback resulting from the interactions between family members shifts and reduces the expected kin network. The reduction in family size and structure severely reduces the positive effects of family interactions, leading to an additional decrease in population growth rate on top of the direct decrease due to the additional mortality. Our analysis provides a framework that can be applied to a wide range of social species.

Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes

Examination of the host-associated microbiome in wildlife can provide critical insights into the eco-evolutionary factors driving species diversification and response to disease. This is particularly relevant for isolated populations lacking genomic variation, a phenomenon that is increasingly common as human activities create habitat 'islands' for wildlife. Here, we characterised the gut and otic microbial communities of one such species: Channel Island foxes (Urocyon littoralis). The gut microbiome provided evidence of phylosymbiosis by reflecting the host phylogeny, geographic proximity, history of island colonisation and contemporary ecological differences, whereas the otic microbiome primarily reflected geography and disease. Santa Catalina Island foxes are uniquely predisposed to ceruminous gland tumours following infection with Otodectes cynotis ear mites, while San Clemente and San Nicolas Island foxes exhibit ear mite infections without evidence of tumours. Comparative analyses of otic microbiomes revealed that mite-infected Santa Catalina and San Clemente Island foxes exhibited reduced bacterial diversity, skewed abundance towards the opportunistic pathogen Staphylococcus pseudintermedius and disrupted microbial community networks. However, Santa Catalina Island foxes uniquely harboured Fusobacterium and Prevotella bacteria as potential keystone taxa. These bacteria have previously been associated with colorectal cancer and may predispose Santa Catalina Island foxes to an elevated cancer risk. In contrast, mite-infected San Nicolas Island foxes maintained high bacterial diversity and robust microbial community networks, suggesting that they harbour more resilient microbiomes. Considered together, our results highlight the diverse eco-evolutionary factors influencing commensal microbial communities and their hosts and underscore how the microbiome can contribute to disease outcomes.

Cryptic divergence in and evolutionary dynamics of endangered hybrid Picea brachytyla sensu stricto in the Qinghai-Tibet Plateau

BACKGROUND

The visual similarities observed across various plant groups often conceal underlying genetic distinctions. This occurrence, known as cryptic diversity, underscores the key importance of identifying and understanding cryptic intraspecific evolutionary lineages in evolutionary ecology and conservation biology.

RESULTS

In this study, we conducted transcriptome analysis of 81 individuals from 18 natural populations of a northern lineage of Picea brachytyla sensu stricto that is endemic to the Qinghai-Tibet Plateau. Our analysis revealed the presence of two distinct local lineages, emerging approximately 444.8 thousand years ago (kya), within this endangered species. The divergence event aligns well with the geographic and climatic oscillations that occurred across the distributional range during the Mid-Pleistocene epoch. Additionally, we identified numerous environmentally correlated gene variants, as well as many other genes showing signals of positive selection across the genome. These factors likely contributed to the persistence and adaptation of the two distinct local lineages.

CONCLUSIONS

Our findings shed light on the highly dynamic evolutionary processes underlying the remarkably similar phenotypes of the two lineages of this endangered species. Importantly, these results enhance our understanding of the evolutionary past for this and for other endangered species with similar histories, and also provide guidance for the development of conservation plans.

Both Structural Variant and Single Nucleotide Polymorphism Load Impact Lifetime Fitness in a Threatened Bird Species

The field of conservation genomics is becoming increasingly interested in whether, and how, structural variant (SV) genotype information can be leveraged in the management of threatened species. The functional consequences of SVs are more complex than for single nucleotide polymorphisms (SNPs), as SVs typically impact a larger proportion of the genome due to their size and thus may be more likely to contribute to load. While the impacts of SV-specific genetic load may be less consequential for large populations, the interplay between weakened selection and stochastic processes means that smaller populations, such as those of the threatened Aotearoa hihi/New Zealand stitchbird (Notiomystis cincta), may harbour a high SV load. Hihi were once confined to a single remnant population, but have been reestablished into six sanctuaries and reserves, often via secondary bottlenecks, resulting in low genetic diversity, low adaptive potential, and inbreeding depression. In this study, we use whole genome resequencing of 30 individuals from the Tiritiri Matangi population to identify the nature and distribution of both SNPs and SVs within this small avian population. We find that SNP and SV individual mutation load is only moderately correlated, likely because SVs arise in regions of high recombination and that are less evolutionarily conserved. Finally, we leverage a long-term monitoring dataset of pedigree and fitness data to assess the impact of SNP and SV mutation loads on individual fitness, and find that SNP and SV realised load had similar negative correlations with lifetime fitness. However, of the masked load metrics, only SVs had a positive significant correlation with lifetime fitness, indicating that masking of deleterious alleles may be more important for SVs than for SNPs. The results of this study indicate that only examining SNPs neglects important aspects of intra-specific variation and that studying SVs has direct implications for linking genetic diversity and genomic health to inform management decisions.

Advancements in noninvasive koala monitoring through combining Chlamydia detection with a targeted koala genotyping assay

Wildlife diseases are major players in local and global extinctions. Effective disease surveillance, management and conservation strategies require accurate estimates of pathogen prevalence. Yet pathogen detection in wild animals remains challenging. Current gold standards often require samples collected through veterinary examination, but this method is costly, intensive, invasive, and requires specialised staff and equipment. Collection of non-invasive samples, such as scats, is an effective monitoring tool which can be deployed at large scale, as scats contain DNA of both host and pathogens. The koala (Phascolarctos cinereus) is listed as 'endangered' under the EPBC Act 1999, with chlamydial disease representing a major threat. Here, we present a new approach that combines restriction-enzyme associated sequencing and targeted-sequence-capture genotyping, namely DArTcap, to detect Chlamydia pecorum in koala scats. We found this method has similar accuracy to current gold standards (qPCR of swab samples), with a sensitivity of 91.7% and a specificity of 100%. This method can be incorporated into existing koala genetic studies using marker panels, where population attributes can be estimated alongside C. pecorum presence, using the same scat samples, with the option to add further markers of interest. Such a one-stop-shop panel would considerably reduce processing times and cost.

Reduced Representation and Whole-Genome Sequencing Approaches Highlight Beluga Whale Populations Associated to Eastern Canada Summer Aggregations

Effective conservation strategies inherently depend on preserving populations, which in turn requires accurate tools for their detection. Beluga whales (Delphinapterus leucas) inhabit the circumpolar Arctic and form discrete summer aggregations. Previous genetic studies using mitochondrial and microsatellite loci have delineated distinct populations associated to summer aggregations but the extent of dispersal and interbreeding among these populations remains largely unknown. Such information is essential for the conservation of populations in Canada as some are endangered and harvested for subsistence by Inuit communities. Here, we used reduced representation and whole-genome sequencing approaches to characterize population structure of beluga whales in eastern Canada and examine admixture between populations. A total of 905 beluga whales sampled between 1989 and 2021 were genotyped. Six main genomic clusters, with potential subclusters, were identified using multiple proxies for population structure. Most of the six main genomic clusters were consistent with previously identified populations, except in southeast Hudson Bay where two clusters were identified. Beluga summer aggregations may consequently be comprised of more than one distinct population. A low number of dispersers were identified between summer aggregations and limited interbreeding was detected between the six genomic clusters. Our work highlights the value of genomic approaches to improve our understanding of population structure and reproductive behavior in beluga whales, offering insights applicable to other cetacean species of conservation concern. An expansion of the geographical scope and increase in number of genotyped individuals will, however, be needed to improve the characterization of the finer scale structure and of the extent of admixture between populations.

Levels and Spatial Patterns of Effective Population Sizes in the Southern Damselfly (Coenagrion mercuriale): On the Need to Carefully Interpret Single-Point and Temporal Estimations to Set Conservation Guidelines

The effective population size (N e) is a key parameter in conservation and evolutionary biology, reflecting the strength of genetic drift and inbreeding. Although demographic estimations of N e are logistically and time-consuming, genetic methods have become more widely used due to increasing data availability. Nonetheless, accurately estimating N e remains challenging, with few studies comparing N e estimates across molecular markers types and estimators such as single-sample methods based on linkage disequilibrium or sibship analyses versus methods based on temporal variance in allele frequencies. This study aims at bridging this gap by analysing single-sample and temporally spaced populations in the southern damselfly (Coenagrion mercuriale), a bioindicator Odonata species of conservation concern found in southwestern Europe's freshwater stream networks. A total of 77 local populations were sampled from a semi-urbanised area located in eastern France near Strasbourg city, yielding 2842 individuals that were genotyped with microsatellites and 958 of which were also genotyped for 2092 SNPs. Spatial genetic structure was stable over time, suggesting porosity between alternate-year cohorts. When accounting for spatial genetic structure, single-sample and temporal estimations of N e were consistent for each set of molecular markers. Biologically meaningful results were obtained when the effect of migration was minimising by considering metapopulation N e estimates based on the level of genetic differentiation and population boundaries. In terms of applied conservation and management, most depicted metapopulations displayed large N e, indicating no immediate need for conservation measures to mitigate anthropogenic pressures, provided that a continuous suitable freshwater network is maintained. However, urbanisation negatively impacted N e levels in populations close to Strasbourg city. Because N e is used to inform conservation decisions, caution is crucial in interpreting N e estimates, especially in continuously distributed populations undergoing migration. Altogether, our study highlights the challenge of obtaining robust N e estimates and the necessity of careful interpretation to set relevant conservation guidelines.

Genomic Evidence for the Purging of Deleterious Genetic Variation in the Endangered North Atlantic Right Whale

The reduced genetic diversity and frequent inbreeding associated with small population size may underpin the accumulation and expression of deleterious mutations (mutation load) in some declining populations. However, demographic perturbations and inbreeding coupled with purifying selection can also purge declining populations of deleterious mutations, leading to intriguing recoveries. To better understand the links between deleterious genetic variation and population status, we assess patterns of genetic diversity, inbreeding, and mutation load across the genomes of three species of Balaenidae whale with different demographic histories and recoveries following the end of commercial whaling in the 1980s. Unlike bowhead (BH) and Southern right whales (SRW), which show signs of recent recovery, reproductive rates of the endangered North Atlantic right whale (NARW) remain lower than expected. We show that the NARW is currently marked by low genetic diversity, historical inbreeding, and a high mutation load. Still, we reveal evidence that genetic purging has reduced the frequency of highly deleterious alleles in NARW, which could increase chances of future population recovery. We also identify a suite of mutations putatively linked to congenital defects that occur at high frequencies in nulliparous NARW females but are rare in NARW with high reproductive success. These same mutations are nearly absent in BH and SRW in this study, suggesting that the purging of key variants may shape the probability of population recovery. As anthropogenic disturbances continue to reduce the sizes of many populations in nature, resolving the links between population dynamics and mutation load could become increasingly important.

Seascape Genomics of the Smooth Hammerhead Shark Sphyrna zygaena Reveals Regional Adaptive Clinal Variation

Globally, hammerhead sharks have experienced severe declines owing to continued overexploitation and anthropogenic change. The smooth hammerhead shark Sphyrna zygaena remains understudied compared to other members of the family Sphyrnidae. Despite its vulnerable status, a comprehensive understanding of its genetic landscape remains lacking in many regions worldwide. The present study aimed to conduct a fine-scale genomic assessment of Sphyrna zygaena within the highly dynamic marine environment of South Africa's coastline, using thousands of single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (3RAD). A combination of differentiation-based outlier detection methods and genotype-environment association (GEA) analysis was employed in Sphyrna zygaena. Subsequent assessments of putatively adaptive loci revealed a distinctive south to east genetic cline. Among these, notable correlations between adaptive variation and sea-surface dissolved oxygen and salinity were evident. Conversely, analysis of 111,243 neutral SNP markers revealed a lack of regional population differentiation, a finding that remained consistent across various analytical approaches. These results provide evidence for the presence of differential selection pressures within a limited spatial range, despite high gene flow implied by the selectively neutral dataset. This study offers notable insights regarding the potential impacts of genomic variation in response to fluctuating environmental conditions in the circumglobally distributed Sphyrna zygaena.

Genomic signatures of inbreeding and mutation load in tree ferns

Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome-wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole-genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long-term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species.

Sonification of Genomic Data to Represent Genetic Load in Zoo Populations

Maintaining a diverse gene pool is important in the captive management of zoo populations, especially in endangered species such as the pink pigeon (Nesoenas mayeri). However, due to the limited number of breeding individuals and relaxed natural selection, the loss of variation and accumulation of harmful variants is inevitable. Inbreeding results in a loss of fitness (i.e., inbreeding depression), principally because related parents are more likely to transmit a copy of the same recessive deleterious genetic variant to their offspring. Genomics-informed captive breeding can manage harmful variants by artificial selection, reducing the genetic load by avoiding the inheritance of two copies of the same harmful variant. To explain this concept in an interactive way to zoo visitors, we developed a sonification game to represent the fitness impacts of harmful variants by detuning notes in a familiar musical melody (i.e., Beethoven's Für Elise). Conceptually, zoo visitors play a game aiming to create the most optimal pink pigeon offspring in terms of inbreeding depression. They select virtual crosses between pink pigeon individuals and listen for the detuning of the melody, which represents the realised load of the resultant offspring. Here we present the sonification algorithm and the results of an online survey to see whether participants could identify the most and least optimal offspring from three potential pink pigeon offspring. Of our 98 respondents, 85 (86.7%) correctly identified the least optimal offspring, 73 (74.5%) correctly identified the most optimal, and 62 (63.3%) identified both the most and least optimal offspring using only the sonification.

Evolutionary drivers of reproductive fitness in two endangered forest trees

Population genetics theory predicts a relationship between fitness, genetic diversity (H0) and effective population size (Ne), which is often tested through heterozygosity-fitness correlations (HFCs). We tested whether population and individual fertility and heterozygosity are correlated in two endangered Mexican spruces (Picea martinezii and Picea mexicana) by combining genomic, demographic and reproductive data (seed development and germination traits). For both species, there was a positive correlation between population size and seed development traits, but not germination rate. Individual genome-wide heterozygosity and seed traits were only correlated in P. martinezii (general-effects HFC), and none of the candidate single nucleotide polymorphisms (SNPs) associated with individual fertility showed heterozygote advantage in any species (no local-effects HFC). We observed a single and recent (c. 30 thousand years ago (ka)) population decline for P. martinezii; the collapse of P. mexicana occurred in two phases separated by a long period of stability (c. 800 ka). Recruitment always contributed more to total population census than adult trees in P. mexicana, while this was only the case in the largest populations of P. martinezii. Equating fitness to either H0 or Ne, as traditionally proposed in conservation biology, might not always be adequate, as species-specific evolutionary factors can decouple the expected correlation between these parameters.

Inter and intra-island genetic structure and differentiation of the endemic Bolle's Laurel Pigeon (Columba bollii) in the Canary archipelago

Islands provide excellent settings for studying the evolutionary history of species, since their geographic isolation and relatively small size limit gene flow between populations, and promote divergence and speciation. The endemic Bolle's Laurel Pigeon Columba bollii is an arboreal frugivorous bird species distributed on laurel forests in four islands of the Canary archipelago. To elucidate the population genetics, we genotyped ten microsatellite loci using DNA obtained from non-invasive samples collected across practically all laurel forest remnants, and subsequently grouped into eight sampling sites. Analyses including F-statistics, Bayesian clustering approaches, isolation by distance tests and population graph topologies, were used to infer the genetic diversity and the population differentiation within and among insular populations. Additionally, we evaluated the effect of null alleles on data analysis. Low genetic diversity was found in all populations of Bolle's Laurel Pigeon, with no significant differences in diversity among them. However, significant genetic differentiation was detected among all populations, with pigeons from La Palma and El Hierro exhibiting the closest affinity. Bayesian clustering supported population separation between islands, and also detected fine-scale structure within the Tenerife and La Gomera populations. Our results suggest that, despite columbids have a high movement ability, they can show signature of genetic divergence among populations, particularly on oceanic islands. Geological history of the islands and distribution range of habitats could have close influence on the evolutionary trajectories of these birds. This approach can provide practical tools to implement appropriate conservation measures for range-restricted species and their habitat.

Lineage Differentiation and Genomic Vulnerability in a Relict Tree From Subtropical Forests

The subtropical forests of East Asia are renowned for their high plant diversity, particularly the abundance of ancient relict species. However, both the evolutionary history of these relict species and their capacity for resilience in the face of impending climatic changes remain unclear. Using whole-genome resequencing data, we investigated the lineage differentiation and demographic history of the relict and endangered tree, Bretschneidera sinensis (Akaniaceae). We employed a combination of population genomic and landscape genomic approaches to evaluate variation in mutation load and genomic offset, aiming to predict how different populations may respond to climate change. Our analysis revealed a profound genomic divergence between the East and West lineages, likely as the result of recurrent bottlenecks due to climatic fluctuations during the glacial period. Furthermore, we identified several genes potentially linked to growth characteristics and hypoxia response that had been subjected to positive selection during the lineage differentiation. Our assessment of genomic vulnerability uncovered a significantly higher mutation load and genomic offset in the edge populations of B. sinensis compared to their core counterparts. This implies that the edge populations are likely to experience the most significant impact from the predicted climate conditions. Overall, our research sheds light on the historical lineage differentiation and contemporary genomic vulnerability of B. sinensis. Broadening our understanding of the speciation history and future resilience of relict and endangered species such as B. sinensis, is crucial in developing effective conservation strategies in anticipation of future climatic changes.

Plant conservation in the age of genome editing: opportunities and challenges

Numerous plant taxa are threatened by habitat destruction or overexploitation. To overcome these threats, new methods are urgently needed for rescuing threatened and endangered plant species. Here, we review the genetic consequences of threats to species populations. We highlight potential advantages of genome editing for mitigating negative effects caused by new pathogens and pests or climate change where other approaches have failed. We propose solutions to protect threatened plants using genome editing technology unless absolutely necessary. We further discuss the challenges associated with genome editing in plant conservation to mitigate the decline of plant diversity.

Assessment of health risk of antibiotics resistance genes from human disturbed habitat to wild animals: Metagenomic insights into availability and functional changes of gut microbiome

Not all antibiotic resistance genes (ARGs) pose an ecological risk to their host animals. A standard should be developed to study which types of ARGs posed an ecological risk to wild animals under human disturbances (HDs). In this study, the golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel species. According to the animals-associated enrichment, mobility, and pathogenicity, the ARGs in habitat of sentinel species were divided into four levels. If the mobile and pathogenic ARGs that could be collinear with the metagenome-assembled genome (MAGs) in the gut of the sentinel species, the ARGs were defined as Rank I ARGs and they were considered to have ecological risk to sentinel species. Functional genes in the MAGs that collinear with the Rank I ARGs were used to predict the health risks of sentinel species. The ecological risk to sentinel species was present in 0.158 % of the ARGs-contigs in the habitat. Cultivation and villages, but not grazing, agriculture and ecotourism, increased the ecological risk of the ARGs to wild animals, The ability of gut microbiome to acquire mobile and pathogenic ARGs increased, as did the collinear functional genes, and the health risks of the wild animals also enhanced by the disturbances of cultivation and villages. Cultivation and villages increased the nutrient content of the soil, and they had a positive effect on the ecological risk of Rank I ARGs by affecting the mobile genetic elements (MGEs), microbiome and the resistant group in the habitat, which was why the cultivation and villages increased the health risks of wild animals. We proposed that cultivation and living should be controlled, while grazing, agriculture and ecotourism could be developed in nature reserves of wild animals, but the nutrients in the wild animals' habitat should be monitored.

Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats to biodiversity and nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems and play a crucial and leading role in combating and mitigating the adverse effects of extreme climate events, despite their own vulnerability to these threats. Therefore, understanding and monitoring how natural forests respond to rapid climate change is a key priority for biodiversity conservation. Recent progress in evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools to address several key issues. These include precise delineation of species and evolutionary units, inference of past evolutionary histories and demographic fluctuations, identification of environmentally adaptive variants, and measurement of genetic load levels. As the urgency to deal with more extreme environmental stresses grows, understanding the genomics of evolutionary history, local adaptation, future responses to climate change, and conservation and restoration of natural forest trees will be critical for research at the nexus of global change, population genomics, and conservation biology. In this review, we explore the application of evolutionary genomics to assess the effects of global climate change using multi-omics approaches and discuss the outlook for breeding of climate-adapted trees.

A Latitudinal Gradient of Reference Genomes

Global inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes, while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state-of-the-art methods. Here, we ask whether a fundamental biogeographic pattern-the latitudinal gradient of species richness in tetrapods-is reflected in the available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last 5 years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes and that reduced representation and whole-genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics.

Quantification of threats to bats at localized spatial scales for conservation and management

In a rapidly changing world, where species conservation needs vary by local habitat, concentrated conservation efforts at small spatial scales can be critical. Bats provide an array of value to the ecosystems they inhabit; many bat species are also of conservation concern. San Diego County, California, contains 22 of the 41 bat species that occur in the United States, 16 of which are on conservation watchlists. Thus, management of bat communities in San Diego County is a pressing need. Because bats exploit vast areas of the landscape and historical sampling strategies have shifted over time, a standardized way of prioritizing areas of the landscape for management would provide an integral asset to bat conservation. We leveraged long-term bat community survey data from sampling areas across San Diego County to prioritize areas with the most management need. We calculated two types of scores: species scores and threat scores. Species scores incorporated richness and conservation status, and threat scores included landscape level threats that bats could encounter. We found that urbanization, the presence of artificial lights, and areas sampled on unconserved land were all significantly associated with decreases in species richness. Further, using species and threat scores, each sampling area was placed into one of four conservation categories, in order from greatest to least conservation need, ranging from highest priority (high species score, high threat score) to lowest (low species score, low threat score). Additionally, we focused on sampling areas in which Townsend's big-eared bat (Corynorhinus townsendii) and/or pallid bat (Antrozous pallidus) occurred. These two species are of exceptional conservation concern in San Diego County and across the western United States. We identified urbanization, the presence of artificial lights, and areas sampled on unconserved land as threats that were all significantly associated with the absence of Townsend's big-eared bat, but not pallid bat. The strategy, methodology, and solutions proposed in our study should assist bat conservation and management efforts wherever bats occur, and can be extended to other species that require conservation attention.

Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism

Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.

Unraveling the Genetic Legacy of Commercial Whaling and Population Dynamics in Arctic Bowhead Whales and Narwhals

Assessing genetic structure and diversity in wildlife is particularly important in the context of climate change. The Arctic is rapidly warming, and endemic species must adapt quickly or face significant threats to persistence. Bowhead whales (Balaena mysticetus) and narwhals (Monodon monoceros) are two long-lived Arctic species with similar habitat requirements and are often seen together in the Canadian Arctic. Although their ranges overlap extensively, bowhead whales experienced significantly greater commercial whaling mortality than narwhals over several centuries. The similar habitat requirements but different harvest histories of these two species provide an opportunity to examine present-day genetic diversity and the demographic and genetic consequences of commercial whaling. We whole-genome resequenced contemporary Canadian Arctic bowhead whales and narwhals to delineate population structure and reconstruct demographic history. We found higher genetic diversity in bowhead whales compared to narwhals. However, bowhead whale effective population size sharply declined contemporaneously with the intense commercial whaling period. Narwhals, in contrast, exhibited recent growth in effective population size, likely reflecting exposure to limited opportunistic commercial harvest. Bowhead whales will likely continue to experience significant genetic drift in the future, leading to the erosion of genetic diversity. In contrast, narwhals do not seem to be at imminent risk of losing their current levels of genetic variation due to their long-term low effective population size and lack of evidence for a recent decline. This work highlights the importance of considering population trajectories in addition to genetic diversity when assessing the genetics of populations for conservation and management purposes.