Evolutionary Applications最新文献

Populations of marine top predators have been sharply declining during the past decades, and one-third of chondrichthyans are currently threatened with extinction. Sustainable management measures and conservation plans of large pelagic sharks require knowledge on population genetic differentiation and demographic connectivity. Here, we present the case of the Mediterranean blue shark (Prionace glauca, L. 1758), commonly found as bycatch in longline fisheries and classified by the IUCN as critically endangered. The management of this species suffers from a scarcity of data about population structure and connectivity within the Mediterranean Sea and between this basin and the adjacent Northeast Atlantic. Here, we assessed the genetic diversity and spatial structure of blue shark from different areas of the Mediterranean Sea and the Northeast Atlantic through genome scan analyses. Pairwise genetic differentiation estimates (F_ST) on 203 specimens genotyped at 14,713 ddRAD-derived SNPs revealed subtle, yet significant, genetic differences within the Mediterranean sampling locations, and between the Mediterranean Sea and the Northeast Atlantic Ocean. Genetic differentiation suggests some degree of demographic independence between the Western and Eastern Mediterranean blue shark populations. Furthermore, results show limited genetic connectivity between the Mediterranean and the Atlantic basins, supporting the hypothesis of two distinct populations of blue shark separated by the Strait of Gibraltar. Although reproductive interactions may be limited, the faint genetic signal of differentiation suggests a recent common history between these units. Therefore, Mediterranean blue sharks may function akin to a metapopulation relying upon local demographic processes and connectivity dynamics, whereby the limited contemporary gene flow replenishment from the Atlantic may interplay with currently poorly regulated commercial catches and large-scale ecosystem changes. Altogether, these results emphasise the need for revising management delineations applied to these critically endangered sharks.

Eld's deer Rucervus eldii (McClelland, 1842) is an ungulate that lives in tropical lowland forests in several countries of Indochina and Hainan Island of China. Its remaining population is small and scattered, and the species is listed as an Endangered species on the IUCN Red List. The debate over the taxonomic status of the Hainan population has persisted for over a century—as an island-endemic subspecies R. e. hainanus, or an insular population of the subspecies R. e. siamensis, would have significant conservation implications. And, given the Hainan population had experienced both population bottleneck and multiple translocations in the past, conservation genomics would be a powerful tool to evaluate the genetic impacts of these events. In this study, we used conservation genomics assessment to study population differentiation and genetic diversity of R. e. siamensis in Cambodia and three Eld's deer subpopulations on Hainan Island. Based on the unique genetic profile and demographic analysis, this study corroborated previous studies using genetic markers that the Hainan Eld's deer warrants the taxonomic status of a distinct subspecies. The Hainan population exhibits a reduction in genetic diversity and an increase in the level of inbreeding when compared to the population of Cambodia. The signs of purifying selection were found against homozygous loss-of-function mutations to decrease the deleterious burden in the Hainan population. However, there was an accumulation of more deleterious missense mutations. Furthermore, significant differences in genetic diversity and level of inbreeding found among the three Hainan subpopulations indicated population isolation and suboptimal translocation strategies, which calls for urgent, coordinated, and science-based genetic management to ensure the long-term viability of the endemic subspecies hainanus. This study provides guidance for the conservation and management of Eld's deer.

The establishment and spread of invasive species are directly related to intersexual interactions as dispersal and reproductive success are related to distribution, effective population size, and population growth. Accordingly, populations established by r-selected species are particularly difficult to suppress or eradicate. One such species, the red swamp crayfish (Procambarus clarkii) is established globally at considerable ecological and financial costs to natural and human communities. Here, we develop a single nucleotide polymorphism (SNP) loci panel for P. clarkii using restriction-associated DNA-sequencing data. We use the SNP panel to successfully genotype 1800 individuals at 930 SNPs in southeastern Michigan, USA. Genotypic data were used to reconstruct pedigrees, which enabled the characterization of P. clarkii's mating system and statistical tests for associations among environmental, demographic, and phenotypic predictors and adult reproductive success estimates. We identified juvenile cohorts using genotype-based pedigrees, body size, and sampling timing, which elucidated the breeding phenology of multiple introduced populations. We report a high prevalence of multiple paternity in each surveyed waterbody, indicating polyandry in this species. We highlight the use of newly developed rapid genomic assessment tools for monitoring population reproductive responses, effective population sizes, and dispersal during ongoing control efforts.

Assisted migration provides a potential solution to mitigate the increasing risks of forest maladaptation under climate change. Western larch (Larix occidentalis Nutt.) is a deciduous conifer species undergoing assisted migration beyond its natural range in British Columbia into areas that have become suitable based on climatic niche modelling. We established a seedling common garden experiment in raised beds in a warm location outside the natural range for three growing seasons, with 52 natural populations from across the species range and 28 selectively bred families from British Columbia. Intraspecific genetic variation in growth, phenology and cold hardiness was analyzed to test for signals of local adaptation and the effects of selective breeding to better understand the implications for assisted migration and breeding for future climates. We found weak differentiation among populations in all traits, with the proportion of additive genetic variance (Q_ST) ranging from 0.10 to 0.28. Cold hardiness had the weakest population differentiation and exhibited no clines with geographic or climatic variables. Selective breeding for faster growth has maintained genetic variation in bud flush phenology and cold hardiness despite delaying bud set. The weak signals of local adaptation we found in western larch seedlings highlights that assisted gene flow among populations is likely to have limited benefits and risks for mitigating maladaptation with climate change. Our findings suggest that assisted migration outside of the range and selective breeding may be important management strategies for western larch for future climates.

To date, studies of the impacts of climate warming on individuals and populations have mostly focused on mortality and thermal tolerance. In contrast, much less is known about the consequences of sublethal effects, which are more challenging to detect, particularly in wild species with cryptic life histories. This necessitates the development of molecular tools to identify their signatures. In a split-clutch field experiment, we relocated clutches of wild, nesting loggerhead sea turtles (Caretta caretta) to an in situ hatchery. Eggs were then split into two sub-clutches and incubated under shallow or deep conditions, with those in the shallow treatment experiencing significantly higher temperatures in otherwise natural conditions. Although no difference in hatching success was observed between treatments, hatchlings from the shallow, warmer treatment had different length–mass relationships and were weaker at locomotion tests than their siblings incubated in the deep, cooler treatment. To characterise the molecular signatures of these thermal effects, we performed whole genome bisulfite sequencing on blood samples collected upon emergence. We identified 287 differentially methylated sites between hatchlings from different treatments, including on genes with neurodevelopmental, cytoskeletal, and lipid metabolism functions. Taken together, our results show that higher incubation temperatures induce sublethal effects in hatchlings, which are reflected in their DNA methylation status at identified sites. These sites could be used as biomarkers of thermal stress, especially if they are retained across life stages. Overall, this study suggests that global warming reduces hatchling fitness, which has implications for dispersal capacity and ultimately a population's adaptive potential. Conservation efforts for these endangered species and similar climate-threatened taxa will therefore benefit from strategies for monitoring and mitigating exposure to temperatures that induce sublethal effects.

Accurately estimating effective population size (N_e) is essential for understanding evolutionary processes and guiding conservation efforts. This study investigates N_e estimation methods in spatially structured populations using a population of moor frog (Rana arvalis) as a case study. We assessed the behaviour of N_e estimates derived from the linkage disequilibrium (LD) method as we changed the spatial configuration of samples. Moor frog eggs were sampled from 25 breeding patches (i.e., separate vernal ponds, ditches or parts of larger fens) within a single population, revealing an isolation-by-distance pattern and a local spatial genetic structure. Varying buffer sizes around each patch were used to examine the impact of sampling window size on the estimation of effective number of breeders (N_b). Our results indicate a downward bias in LD N_b estimates with increasing buffer size, suggesting an underestimation of N_b. The observed bias is attributed to LD resulting from including genetically divergent individuals (mixture-LD) confounding LD due to drift. This emphasises the significance of considering even subtle spatial genetic patterns. The implications of these findings are discussed, emphasising the need to account for spatial genetic structure to accurately assess population viability and inform conservation efforts. This study contributes to our understanding of the challenges associated with N_e estimation in spatially structured populations and underscores the importance of refining methodologies to address population-specific spatial dynamics for effective conservation planning and management.

Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to “listing” decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.

Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (Clangula hyemalis) and velvet scoter (Melanitta fusca) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found C. hyemalis to show more historical demographic stability, whereas M. fusca was affected particularly by the Last (Weichselian) Glaciation. This likely reflects C. hyemalis breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of M. fusca would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with F_ROH from 0.012 to 0.063 in C. hyemalis and ranging from 0 to 0.047 in M. fusca. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.

Whole-genome duplication (polyploidy) poses many complications but is an important driver for eukaryotic evolution. To experimentally study how many challenges from the cellular (including gene expression) to the life history levels are overcome in polyploid evolution, a system in which polyploidy can be reliably induced and sustained over generations is crucial. Until now, this has not been possible with animals, as polyploidy notoriously causes first-generation lethality. The parasitoid wasp Nasonia vitripennis emerges as a stunningly well-suited model. Polyploidy can be induced in this haplodiploid system through (1) silencing genes in the sex determination cascade and (2) by colchicine injection to induce meiotic segregation failure. Nasonia polyploids produce many generations in a short time, making them a powerful tool for experimental evolution studies. The strong variation observed in Nasonia polyploid phenotypes aids the identification of polyploid mechanisms that are the difference between evolutionary dead ends and successes. Polyploid evolution research benefits from decades of Nasonia research that produced extensive reference—omics data sets, facilitating the advanced studies of polyploid effects on the genome and transcriptome. It is also possible to create both inbred lines (to control for genetic background effects) and outbred lines (to conduct polyploid selection regimes). The option of interspecific crossing further allows to directly contrast autopolyploidy (intraspecific polyploidy) to allopolyploidy (hybrid polyploidy). Nasonia can also be used to investigate the nascent field of using polyploidy in biological control to improve field performance and lower ecological risk. In short, Nasonia polyploids are an exceptional tool for researching various biological paradigms.

The impact of global changes on populations may not be necessarily uniform across a species' range. Here, we aim at comparing the phenotypic and transcriptomic response to warming and an invasive predator cue in populations across different geographic scales in the damselfly Ischnura elegans. We collected adult females in two ponds in southern Poland (central latitude) and two ponds in southern Sweden (high latitude). We raised their larvae in growth chambers and exposed them to combination of temperature and a predator cue released by the crayfish Orconectes limosus. When larvae reached the prefinal larval stage, they were phenotyped for traits related to growth and size and collected for a gene expression analysis. High-latitude populations exhibited greater phenotypic and transcriptomic variation than central-latitude populations. Across latitudes and ponds, temperature generally increased growth rate and the predator cue decreased mass, but the effects of temperature were also pond-specific. Comparison of the transcriptomic profiles revealed a greater overlap in the response to temperature across latitudes and ponds, especially for pathway-related oxidative stress and sugar and lipid metabolism. The transcriptomic response to a predator cue and to the interaction temperature × predator cue was more pond-specific and overlapped only for few genes and pathways related to cuticle, development and signal transduction. We demonstrated that central- and high-latitude populations may partially respond through similar mechanisms to warming and, to a lower extent to a predator cue and to the interaction temperature × predator cue. For the predator cue and the interaction, the large fraction of ponds-specific genes suggests local adaptation. We show that high-latitude populations were generally more plastic at the phenotypic and transcriptomic level and may be more capable to cope with environmental changes than their central-latitude counterparts.