Evolutionary Applications最新文献

Applying environmental DNA (eDNA) metabarcoding to samples from waterholes and their surroundings offers a promising approach for monitoring terrestrial vertebrates in semi-arid and arid ecosystems, such as the southern African savannas. However, minimal guidance exists on key sampling design parameters for terrestrial ecosystems, which can significantly influence species detection. This study investigated the effects of sampled substrate, sampling season, and metabarcoding primer pair on species richness and taxonomic group detection in terrestrial vertebrates, with a focus on mammals, using eDNA samples from waterholes in Botsalano Game Reserve, South Africa. A total of 725 eDNA samples were collected from 94 sampling events across wet and dry seasons, detecting 95 species (45 birds, 42 mammals, 4 amphibians, 3 reptiles, and 1 fish). Sediment samples provided more reliable detection of abundant taxa, whereas water samples had higher detection frequencies of rare taxa. A mixed sampling approach yielded the highest species richness. Sampling during the wet season yielded higher species richness overall, while more mammal species were detected from dry season sampling. Overlap in species detection between the two metabarcoding primers tested was low (47%). We formulate recommendations for future eDNA metabarcoding study designs in similar systems, including remote sampling logistics and discuss potential sources of false positives in eDNA metabarcoding, including (1) secondary eDNA input, (2) incomplete genetic reference databases, and (3) the low genetic resolution of metabarcoding markers.

Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.

Effective population size (N_e) is a key concept in biology and conservation. Stripped to its bare essentials, it reflects how much genetic drift a population experiences, expressed as a number of individuals of an ideal theoretical population. Superficially, N_e seems like a fairly simple concept, but the more layers of the onion you peel, the more you feel like crying. Really understanding N_e in all its facets is daunting, as there are various temporal, spatial, biological, and mathematical ways in which N_e can be defined and approached, many of which are erroneously interchanged and often not distinguished. If that is not enough, understanding the intricacies and the assumptions of the many ways in which N_e can be calculated is required to make sense of the concept. This is why a special issue on this topic, especially in relation to biodiversity monitoring, is timely. We assembled 19 original papers, perspectives, and reviews on effective population size estimation in relation to conservation to help practitioners in conservation research and practical management see the forest for the trees with regards to N_e.

Ultraconserved elements (UCEs) have emerged as a powerful tool for resolving deep evolutionary relationships due to their low DNA quality requirements and broad taxonomic applicability. While their utility for intraspecific and shallow-divergence studies is growing, only a few studies have explored their performance in marine taxa, some of them with metapopulations spanning thousands of kilometers. Here, we employed the UCE approach to investigate the population genomics of Gigantidas platifrons—a deep-sea mussel with a long larval dispersal period that exhibits a panmictic genetic structure across its extensive distribution range in the chemosynthetic ecosystems of the Western Pacific. With its published whole genome and prior restriction site-associated DNA sequencing using IIB restriction enzymes (2b-RAD seq) study, this species is an excellent candidate for evaluating the effectiveness of UCEs. We conducted UCE target capture sequencing on 123 individuals collected from two hydrocarbon seeps and four hydrothermal vents, yielding 1960 UCEs. To assess the impact of different reference choices, we identified 11,870 single-nucleotide polymorphisms (SNPs) by mapping against the published genome and 8936 SNPs by mapping to the representative 1960 UCEs. Both datasets were similar, with over 80% of the SNPs located in intronic and intergenic regions. Analyses based on both datasets consistently implied a clear genetic divergence between the South China Sea (SCS) and Okinawa Trough-Sagami Bay (OT-SB) populations, with predominant gene flow from OT to SB, consistent with previously published 2b-RAD seq findings. Additionally, UCE-based SNPs identified a dynamic decline in population size for individuals in the three regions and revealed selective adaptation signals to their environments. Overall, our study serves as a proof-of-concept demonstrating that UCEs provide a comparable resolution to RAD-Seq in detecting shallow-level genetic divergence and delineating conservation units in a high-dispersal marine species, even when lacking a sequenced genome.

Herbicides are a valuable tool in agricultural ecosystems to manage nuisance species. Due to the reliance on herbicides for weed control, herbicide resistance is a growing concern. Herbicides are also used extensively in aquatic and natural systems, but the genetics and evolutionary dynamics of resistance are not as frequently incorporated into management plans in these systems. In Eurasian watermilfoil, a widespread and heavily managed invasive aquatic weed in the United States, clonal lineages have been characterized as resistant to fluridone, a commonly used phytoene desaturase (PDS)-inhibitor herbicide. In order to locate genomic loci associated with herbicide resistance, we created an F2 mapping population segregating for fluridone resistance. Using this population, we examined the pds gene for amino acid alterations in resistant individuals and performed bulk segregant analysis between the highly resistant and susceptible F2 individuals. Additionally, we compared pds gene expression between resistant and susceptible strains in control and treated environments using RT-qPCR. We found no evidence of amino acid alterations to the pds gene in fluridone resistant individuals or increased pds expression in the resistant strain, either in the presence or absence of fluridone. Our QTL mapping identified a putative QTL on chromosome seven, while the gene encoding fluridone's target molecule, phytoene desaturase (PDS) is located on chromosomes 10–12. Our results indicate that fluridone resistance in the Eurasian watermilfoil strain isolated from Lake Lansing, MI, is due to at least one non-target site mechanism. Characterizing mechanisms of herbicide resistance within invasive plants enables effective and thoughtful herbicide usage, as well as the development of diagnostic biomarkers for resistance in unknown populations.

Movement patterns of marine fish are often difficult to accurately define given seasonal variation, ontogenetic shifts, and changing environmental conditions. However, outlining movement is crucial for understanding population dynamics, as well as for conservation and management efforts. Here, we evaluate seasonal adult movement and juvenile spatial distribution of Pacific cod (Gadus macrocephalus), a highly mobile and commercially important species, by developing and applying a genotyping-in-thousands by sequencing (GT-seq) panel. This panel identifies four genetically distinct stocks within Alaska waters with high confidence in assignment (97% average accuracy across stocks). The application of this panel to adult, summer-caught Pacific cod identified limited seasonal movement within and between populations, with the exception of those in the Northern Bering Sea (NBS). Two stocks occupied this region during the summer, non-spawning season, and mixed at variable proportions in a west-to-east gradient potentially tied to the directionality of sea-ice retreat in the NBS. Juvenile results indicated that although a predominant westward advection of larvae was prevalent in the Gulf of Alaska (GOA), two major deviations from this overall trend were apparent: (i) an eastward advection of a western GOA stock into the eastern GOA that varied interannually and (ii) a consistently high proportion of eastern GOA individuals in a western GOA narrow strait. These two deviating patterns suggest that mesoscale oceanographic processes play an important role in transport dynamics in the GOA that may be contrary to patterns expected based on the prevailing current. Taken together, our study provides novel insights into the movement dynamics of Pacific cod that can be leveraged by managers to help guide decision-making for the species. Additionally, this inexpensive genetic panel can continue to be applied to further explore important questions about the ecology of Pacific cod in Alaska waters.

Populations can be granted conservation status because they harbour a set of unique traits, evolutionary histories, or ecological roles. Such populations are often isolated and specialised and, as such, can be particularly vulnerable to environmental disturbances. Even if distinct populations survive and adapt to severe disturbances, they could show changes in the very traits that made them distinct in the first place. Here, we leverage a natural ‘experiment’ involving an unarmoured population of threespine stickleback (Gasterosteus aculeatus) in Rouge Lake (Haida Gwaii, BC)—a population listed as Special Concern under the Canadian Species at Risk Act. In 2015, Rouge Lake nearly dried up during a severe drought event; yet the stickleback population appeared to have fully recovered its abundance in subsequent years. Using phenotypic measurements, we assessed the extent to which evolution in this population was impacted by the drought. We document important shifts in several phenotypic traits, with the largest occurring in precisely the trait that made the population distinct and prompted its original conservation designation. Specifically, fish with no lateral plates (i.e., ‘unarmoured’) made up 51% of the population before the drought but only 13% after the drought. This shift held (13%–16% unarmoured) over the 4 years of our post-drought monitoring. Field observations support a strong demographic bottleneck, which we suggest might have been coupled with a shift in the selective regime. These findings underscore how populations of conservation concern are not only at risk of extinction; they are also at risk of losing the characteristics that make them unique. These dynamics highlight the need for policies to consider a population's evolutionary potential and develop more flexible approaches than simply considering single-timepoint assessments of diversity.

Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (Gelochelidon nilotica) has declined from 500 breeding pairs in the 1940s to 52 in 2025, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data among the declining population, two thriving populations and the ancestors of the declining population. We find comparable nucleotide diversity, but lower observed heterozygosity in the Central European population compared to the Mediterranean populations. The contemporary samples show some population structure as well, although admixture analyses and low genetic differentiation (F_ST) still suggest potential population connectivity. Museum specimens from the historic population reveal an increased level of genetic diversity compared to the contemporary population, with effective population size estimates suggesting two past population declines. While inbreeding coefficients (F_ROH) in the current Central European population are significantly higher than in the historic population, they are similar to those in the Mediterranean populations. These results suggest that population structure may be emerging, and that although inbreeding is not yet at worrisome levels in the last Central European population of gull-billed terns, it may be on the rise. If this endangered population remains small and isolation manifests, the effects of inbreeding depression may become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.

Apocynum venetum L., a saline-alkali-tolerant plant valued for its high-quality bast fiber in textile manufacturing and medicinal compounds in traditional medicine, serves as a key economic species in saline-alkali regions with additional phytoremediation applications. However, its natural populations are becoming increasingly threatened by rapid environmental change and anthropogenic activities. To inform conservation and sustainable utilization, we generated a chromosome-level genome assembly of A. venetum (234.73 Mb; contig N50 = 19.11 Mb, scaffold N50 = 20.46 Mb) using PacBio HiFi, Illumina and Hi-C technologies, and performed whole-genome resequencing of 109 individuals spanning China's saline-alkali regions. Population genetic analyses revealed that the Xinjiang population exhibited the highest level of genetic diversity and strong genetic differentiation from the other populations. Demographic analyses indicated that most populations underwent significant population declines during the late Last Glacial Maximum, followed by recovery in western and northern populations, whereas the eastern coastal populations maintained consistently low effective population sizes. Genome-environment association analyses identified candidate adaptive loci, including a flavonol 4′-sulfotransferase (4′-ST) gene, potentially linked to saline-alkali tolerance and flavonoid biosynthesis. Our findings provide critical insights into the evolutionary history and adaptive mechanisms of A. venetum, offering genomic tools for conservation prioritization and the development of stress-resilient cultivars through marker-assisted breeding.

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.