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Background Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted. Results Here we used microsatellite and SNP data generated from Gunnison sage-grouse ( Centrocercus minimus ) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity ( H O , H E , F IS , A R ) and differentiation ( F ST , G ST , D Jost ). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for H E , F IS , A R , and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data. Conclusion We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.

Freshwater ecosystems are being heavily exploited and degraded by human activities all over the world, including in North America, where fishes and fisheries are strongly affected. Despite centuries of taxonomic inquiry, problems inherent to species identification continue to hamper the conservation of North American freshwater fishes. Indeed, nearly 10% of species diversity is thought to remain undescribed. To provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application, we generated a standard reference library of mtDNA sequences (DNA barcodes) derived from expert-identified museum specimens for 752 North American freshwater fish species. This study demonstrates that 90% of known species can be delineated using barcodes. Moreover, it reveals numerous genetic discontinuities indicative of independently evolving lineages within described species, which points to the presence of morphologically cryptic diversity. From the 752 species analyzed, our survey flagged 138 named species that represent as many as 347 candidate species, which suggests a 28% increase in species diversity. In contrast, several species of parasitic and nonparasitic lampreys lack such discontinuity and may represent alternative life history strategies within single species. Therefore, it appears that the current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, although artificially creating diversity in others. In addition to providing an easily accessible digital identification system, this study identifies 151 fish species for which taxonomic revision is required.

Defining appropriate conservation units is crucial to the protection and management of biodiversity. These delineations deliver further benefit when they include assessments of population vulnerability to extinction from pressures such as climate change. However, delineations and vulnerability assessments are particularly difficult within highly diverse species, such as the salmonid fish Arctic charr (Salvelinus alpinus), that show extensive phenotypic and genetic variation within and across locations, variable and complex life histories and broad geographic distributions. As yet, the nature and scope of Arctic charr diversity has not been characterised at the scale needed to delineate key conservation units in Scotland. To identify evolutionarily significant and vulnerable populations to prioritise for conservation, we conducted a genomic study of Arctic charr populations across Britain and Ireland with a focus on Scottish populations (N = 64 populations; 24,878 SNPs; 410 individuals). We found that most lake populations represented distinct genetic clusters, with limited gene flow between them and resulting in substantial genetic differentiation. Higher level groupings of genetic similarity across catchments likely reflect historic anadromy and migration, with populations primarily grouping east or west of the central watershed divide in Scotland. Analysing genetic offset, also known as genomic vulnerability, we identified strong inverse correlations between genetic vulnerability and latitude and distance to the sea, suggesting that more southern and more inland populations are more vulnerable to the effects of climate change. Additionally, patterns of vulnerability across several additional metrics identified other populations that may be at higher risk of loss. We further used our genetic data, along with phenotypic and geographic information, to identify populations of greatest evolutionary significance. This highlighted that the most important ones to protect are those in locations with multiple ecotypes, a key facet of functional Arctic charr biodiversity, and populations that are the only ones in their Hydrometric Area.

Background The jaguar ( Panthera onca ) is a keystone species within diverse ecosystems ranging from dense rainforests to open grasslands across Central and South America. However, its populations are declining rapidly due to anthropogenic actions, such as deforestation and poaching. Here we investigate the effects of this decline on genetic diversity and genetic health. Utilizing both modern and historical museum samples, we infer population structure and immunome variability in 25 jaguars to identify unique genetic diversity that can inform targeted conservation efforts. Results Our genome-wide analyses identifies three distinct geographic populations: Central America, South American lowlands, and South American highlands. Modern samples that exhibit lower levels of heterozygosity also show higher levels of inbreeding. The South American lowland population shows the lowest levels of inbreeding, while the highland population exhibits the lowest overall immunome-wide variability. However, the innate (Natural Killer Cell Complex, Toll-Like Receptor) and adaptive (Major Histocompatibility Complex Class II) immune genes, which are crucial for adaptive responses and disease resilience, show high diversity in terms of heterozygosity and haplotype diversity in individuals of all three populations. Conclusions South American highland and Central American jaguars face significant threats from habitat loss and fragmentation. The observed genome- and immunome-wide diversity in historical and modern jaguars reflect their recent demographic decline and challenges of local adaptation. We recommend re-evaluating evolutionarily significant units to prioritize conservation strategies, ensuring the preservation of unique genetic and adaptive diversity crucial for the species’ resilience and long-term survival.

Aim As climate change presents a major threat to biodiversity in the next decades, it is critical to assess its impact on species habitat suitability to inform biodiversity conservation. Species distribution models (SDMs) are a widely used tool to assess climate change impacts on species’ geographical distributions. As the name of these models suggests, the species level is the most commonly used taxonomic unit in SDMs. However, recently it has been demonstrated that SDMs considering taxonomic resolution below (or above) the species level can make more reliable predictions of biodiversity change when different populations exhibit local adaptation. Here, we tested this idea using the Japanese crayfish (Cambaroides japonicus), a threatened species encompassing two geographically structured and phylogenetically distinct genetic lineages. Location Northern Japan. Methods We first estimated niche differentiation between the two lineages of C. japonicus using n‐dimensional hypervolumes and then made climate change predictions of habitat suitability using SDMs constructed at two phylogenetic levels: species and intraspecific lineage. Results Our results showed only intermediate niche overlap, demonstrating measurable niche differences between the two lineages. The species‐level SDM made future predictions that predicted much broader and severe impacts of climate change. However, the lineage‐level SDMs led to reduced climate change impacts overall and also suggested that the eastern lineage may be more resilient to climate change than the western one. Main conclusions The two lineages of C. japonicus occupy different niche spaces. Compared with lineage‐level models, species‐level models can overestimate climate change impacts. These results not only have important implications for designing future conservation strategies for this threatened species, but also highlight the need for incorporating genetic information into SDMs to obtain realistic predictions of biodiversity change.

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3–14% increase in AUC; 1–23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species’ capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly “adaptive management” approach to support conservation genetic management of species facing global change.

Aim We examine the phylogeographic genetic structure of the endangered pig‐nosed turtle Carettochelys insculpta, the last remaining member of a once globally widespread family, now restricted to northern Australia and southern New Guinea, a region with a complex geological and eustatic history. We examine their historical biogeography, demographic history and genetic status of threatened populations. Location Northern Australia, Southern New Guinea. Methods We reconstruct phylogenetic relationships and patterns of genetic diversity using a genome‐wide dataset of 15,081 single nucleotide polymorphisms and two mitochondrial loci from samples spanning the full species' range. Results The Australian, Papua New Guinea and Indonesian Papua turtles are recovered as three distinct lineages; the Australian lineage diverged from the New Guinea lineages ca 660 Kya, while the Papua New Guinea and Indonesian Papua Province lineages diverged ca 564 Kya. Although the fossil record shows that C. insculpta has been a long‐standing representative of the Australia and New Guinea fauna (since at least the Miocene), extant lineages diverged later in the Middle Pleistocene. Both the Australian and Papua New Guinea lineages were likely shaped by bottlenecks, isolation and genetic drift, which in the Australian lineage greatly reduced effective population sizes to 48–88. Main Conclusions The contemporary genetic structure of C. insculpta is most consistent with a vicariance model whereby a large interchanging population occupying northern Australia and New Guinea came to be fragmented and diverged into Australian, Papua New Guinea and Indonesian Papua lineages. Subsequent dispersal via paleodrainages of the submerged continental shelf under the influence of Pleistocene sea‐level change is thought to have been impeded by the isolation of the Akimeugah and Arafura Basins. All populations of the Australian lineage show low genetic diversity without contemporary gene flow, suggesting they are vulnerable to inbreeding and reduced fitness, requiring the consideration of genetic rescue.

Characterising hierarchical population structure is crucial to understanding a species' evolutionary history and informing effective conservation and management strategies. Many terrestrial species in North America have experienced a wide range of evolutionary pressures at multiple scales, ranging from large‐scale range shifts and recolonisations driven by glacial cycles to more localized contemporary habitat degradation and fragmentation. Hence in this region, given the multi‐level evolutionary forces at play, genetic variation and diversity are often hierarchically structured. We analysed genomic diversity and variation in woodland caribou (Rangifer tarandus caribou) across western Canada using genotypes from 33,000 Single Nucleotide Polymorphism (SNP) loci from 759 geo‐referenced individuals spanning 45 pre‐defined subpopulations. We employed genetic clustering methods and measures of genetic differentiation to characterise hierarchical population structure in the region and tested for latitudinal changes in heterozygosity resulting from post‐glacial recolonisation and hybridisation. Our results confirm that woodland caribou genetic diversity and differentiation occur at multiple hierarchical levels, reflecting post‐glacial recolonisation patterns and landscape heterogeneity. Notably, the major genetic clusters identified in our study do not align with current recognised units for the species in this region. We also observe elevated heterozygosity in the mid‐latitudes of the sampled range, indicative of hybridisation following secondary contact during post‐glacial recolonisation. These findings underscore the need to consider and include genetic diversity at all hierarchical levels in conservation planning, as wide‐ranging species often experience diverse and complex evolutionary histories and pressures.

This study explores how climate variables influenced the evolution and diversification of Neurergus newts within the Irano‐Anatolian biodiversity hotspot. We use a dated phylogenetic tree and climatic niche models to analyze their evolutionary history and ecological preferences. Using genetic data from nuclear (KIAA) and mitochondrial (16s and 12s) genes, we estimate divergence times and identify four major Neurergus clades. The initial speciation event occurred approximately 11.3 million years ago, coinciding with the uplift of the Zagros and Anatolian mountains. This geological transformation isolated newt populations, likely triggering the first speciation event. By integrating potential geographic distribution with climate variables, we reconstruct ancestral niche occupancy profiles. This highlights the critical roles of temperature and precipitation in shaping Neurergus habitat preferences and distribution. We observe both phylogenetic niche conservatism and divergence, with niche divergence playing a dominant role in diversification. This research emphasizes the complex interplay of geography, climate, and ecology in speciation and the vulnerability of isolated mountain newt populations to environmental changes. This study investigates the evolutionary history and ecological preferences of Neurergus newts in the Irano‐Anatolian hotspot. Using genetic and climate data, we identify four distinct newt lineages dating back 11.3 million years, coinciding with major geological shifts. The analysis suggests temperature and precipitation as key drivers of newt distribution, with both niche conservatism and divergence observed across the lineages. The findings highlight the complex interplay of geography, climate, and ecology in newt speciation and emphasize the vulnerability of these isolated mountain populations to changing environments.

Genetic data have become an important asset to enhance the delimitation of cetacean species, subspecies, and populations, considering the difficulties in obtaining representative morphological data. The franciscana, Pontoporia blainvillei (Gervais & d’Orbigny 1844 ), is the most threatened small cetacean in the southwestern Atlantic Ocean. Genetic studies have shown a deep genetic divergence between franciscanas from the northern and southern parts of the range; thus, it was proposed that they should be considered two Evolutionarily Significant Units (ESU). Morphological and ecological data also suggest differences across the species range. We used genetic data from samples collected throughout the species distribution (N = 399) to test hypotheses of intraspecific differentiation that could reflect the existence of subspecies within P. blainvillei . We applied the divergence and diagnosability criteria for recognition of cetacean subspecies, based on mitochondrial control region sequences. The net between-group nucleotide divergence ( d A  = 0.0074) and the percent diagnosable (99%) indicate that the franciscana’s North and South ESU meet the criteria to be recognized as subspecies. Morphological and ecological evidence also support the two subspecies claim. Therefore, we propose a trinomial and provide diagnoses for the new subspecies.