Molecular Ecology最新文献

Hybridization and introgression frequently occur even between distantly related species. A central question in speciation research is which genomic regions act as barriers to gene flow and how genome-wide differentiation persists despite hybridization between species. Ecological divergence is well known to promote genomic differentiation, especially during the early stages of speciation. However, the extent to which ecological divergence contributes to genomic divergence and the restriction of gene flow between more strongly isolated species, such as those exhibiting intrinsic hybrid incompatibilities, remains relatively unclear. One promising approach is to compare genomic differentiation and introgression patterns between sympatric sites of ecologically divergent distantly related species and those of ecologically similar species. Here, we identified a new sympatric site of threespine stickleback (Gasterosteus aculeatus) and Japan Sea stickleback (G. nipponicus) in the Okinebe River, Hokkaido, Japan. In this habitat, these two species differ in migratory life histories: G. nipponicus is anadromous (sea-run migratory), whereas G. aculeatus is resident. This contrasts with the other two previously studied sympatric sites, where both species are anadromous. We found that genomic differentiation in the Okinebe pair is maintained at high levels despite limited spatial isolation. Furthermore, the Okinebe pair had more genomic regions with high differentiation and fewer regions of introgression than the other sympatric pairs. These findings suggest that migratory differences may be able to contribute to the restriction of gene flow even between species with strong reproductive isolation. To better understand the role of ecological divergence in speciation, broader comparative studies across multiple sympatric species pairs with varying degrees of ecological differentiation and reproductive isolation are needed.

Conservation management of endangered species increasingly relies on genomic approaches to understand how long-term small population sizes affect the fitness of extant individuals. However, despite the growing investment in genomic resources by conservation programmes, the impact that sequencing methods have on the ability to detect inbreeding-related phenomena has been largely overlooked. Here, we compare the use of whole-genome and reduced-representation sequencing approaches in 148 individuals of the critically endangered parrot, the kākāpō (Strigops habroptilus), to assess inbreeding and its effects on female reproductive success. We explore how sequencing choice influences the identification of long stretches of homozygosity across the genome (runs of homozygosity, ROH), and compare the conservation implications of the results produced by each method. Both whole-genome and reduced-representation sequencing approaches provided comparable estimates of genome-wide inbreeding (F_ROH) and revealed consistent effects on egg hatching success, suggesting that reduced-representation sequencing is capable of detecting inbreeding depression in wild populations under certain conditions. Whole-genome sequencing enabled chromosome-level inbreeding analyses, which revealed no strong evidence of chromosome-specific effects beyond the genome-wide signal. These results suggest that inbreeding depression in kākāpō reflects small effects across many chromosomes rather than strong effects on only a few, and that the primary benefit of whole-genome sequencing lies in improving the precision of genome-wide inbreeding estimates rather than identifying chromosome-specific effects. Our findings highlight the distinct benefits of each sequencing approach in conservation, particularly within the context of resource limitations.

Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. This has paved the way to study the eco-evolutionary dynamics of SVs across the tree of life and within a population genomics framework. In this review, we provide the necessary fundamentals to help researchers generate and analyse population-level SV data. We discuss the unique properties of different SV groups and how these fundamental differences interact with important biological and evolutionary processes using both empirical results and theory. This includes discussion of unresolved issues around SVs, such as technical difficulties in identification, accounting for diversity and evaluating functional effects. We explicitly integrate into this discussion transposable elements, which are an important component of SVs often identified in population-level variant data. Finally, we focus on the practical side of SV analysis, offering a framework for SV identification and data analysis. In particular, we examine the heterogeneous nature of SV properties (type, length, sequence identity) that should be considered when studying them in ecology and evolution. This review aims to provide resources and guidelines to help researchers navigate the complexities of a relatively new field of eco-evolutionary genomics research.

Researchers must navigate several trade-offs when deciding which population sequencing method to use. The decision between reduced representation approaches and whole genome sequencing (WGS) impacts marker density, sequencing depth and costs per sample, which will in turn affect the power to accurately characterise certain genomic features, such as regions of the genome exhibiting signals of selection. To investigate the effect of sequencing method on the detection of putatively adaptive regions, we compared selection scan analyses of a set of restriction site-associated DNA sequencing (RADseq) datasets for the common myna (Acridotheres tristis) with a WGS dataset with fewer individuals. Although selection scan statistics were found to be correlated between datasets, no common outliers were found when using outlier thresholds typically applied in such studies. We compared allele frequencies and genotypes across datasets and found that discordances were due to missing markers, different individuals sampled or erroneous genotyping. Most importantly, two regions with strong signals of selection identified through WGS data were missed in the lower density dataset, and population-specific allelic dropout, which can result from restriction enzyme cut site loss in RADseq, created false signals of selection in these datasets. Our results highlight the advantages of WGS over RADseq when used for selection scan analyses, especially for highly structured populations such as those observed in many invasive or endangered species.

Telomeres shorten with advancing age in numerous species, and shorter telomeres are linked to increased mortality risk. While parental age at conception can influence offspring telomere length, the magnitude and direction of this effect differ across studies, species, and parental sexes. To understand how parental age influences offspring telomere length across vertebrates, we conducted a systematic review and meta-analysis to examine the effects of paternal and maternal age at conception on offspring telomere length, incorporating 99 effect sizes from 30 human studies and 49 effect sizes from 12 non-human vertebrate studies. There was a positive overall parental age effect on offspring telomere length within human studies, while no effect was found in non-human vertebrate studies after adjusting for study, estimate, and phylogenetic effects. Considerable heterogeneity was attributed mainly to between-study variance in human studies and to phylogeny in non-human studies. Parental age effect estimates were correlated with the laboratory methods used for measuring telomere length in all studies. In human studies, the interaction between parental and offspring sex affected the parental age effect estimates, and estimates derived from leukocytes were less positive than those from other cells. In non-human vertebrates, parental age effects were less negative when the parents' identity was controlled for in the study. Publication biases suggest overestimation of the parental age effect in human studies. We recommend that future research be conducted on a broader range of taxa, test for within-parent effects, and follow standardised reporting practices to enhance data comparability.

This study investigates the genetic diversity and evolutionary mechanisms driving polymyxin resistance in Klebsiella pneumoniae, a critical priority pathogen. By analysing mgrB, phoPQ and pmrAB genes in susceptible (PM-S) and resistant (PM-R) populations through neutrality tests (Tajima D, Fu & Li's D) we uncovered polygenic adaptation and positive selection as a key driver of resistance. High genetic diversity was observed across all loci, with mgrB insertions dominating PM-R populations. Negative Tajima and Fu & Li's D values and excess rare alleles revealed recent population expansions linked to the reintroduction of polymyxins in the 2010s. Positive selection via selective sweeps was detected in PM-R isolates, exemplified by the rapid spread of haplotype 27, which presents mgrB insertions, the major determinant of LPS modification pathway hyperactivation. The expansion of this haplotype suggests that horizontal gene transfer accelerates resistance dissemination. The elevated genetic diversity observed in the phoPQ and pmrAB systems among isolates harbouring mgrB alterations may reflect reduced adaptive fitness costs, enabling the preservation of genomic variability despite sustained selective pressures. Our results demonstrate that polymyxin resistance arises through polygenic adaptation and positive selection, combining de novo mutations, recombination and selection-driven sweeps. These dynamics threaten to exacerbate resistance in hospital environments, emphasising the need for genomic surveillance and alternative therapies. This study bridges molecular evolution and clinical epidemiology, offering insights into the resilience of K. pneumoniae and the ecological drivers of antimicrobial resistance.

Parthenogenesis, or all-female clonal reproduction, is rare among vertebrates. This is often attributed to the selective disadvantages of assumed reduction of genetic diversity in the absence of sex. However, parthenogenetic vertebrates have highly complex evolutionary histories, with most arising through hybridisation and many being polyploid. Here, we show that geographically widespread triploid parthenogenetic forms of the Australian gekkonid Heteronotia binoei are considerably diverse despite their clonal reproductive mode, with patterns of variation consistent with two previously identified reciprocal hybrid origins and numerous backcrossing events. We also confirm a two-fold increase in genome-wide heterozygosity among parthenogens (10.6%) compared with the sexual progenitors (4.63%). Our SNP-based diversity estimates exceed prior predictions for clonal H. binoei lineages based on karyotype and allozyme data. We also find evidence of repeated and geographically widespread backcrossing in both western and central Australia. This supports the long-standing hypothesis that parthenogens are able to partially recover parental niches by ‘freezing’ genotypic diversity present within the sexual forms. Understanding how asexual clones attain ecological success has implications for managing both invasive species, many of which are clonal, and threatened species, which often face similar challenges associated with reduced genetic diversity. Overall, our findings demonstrate that sex, historical or ongoing, is instrumental in the persistence of asexual lineages, contributing to a broader understanding of the evolutionary dynamics of parthenogenesis.

Short-term responses to temperature stress, such as heat waves and long-term acclimation to temperature changes, including seasonal shifts, are expected to be mediated by distinct molecular pathways. However, in ectotherms, such as reptiles, the effects of exposure duration on molecular responses to temperature change remain unclear. In this study, we investigated temperature-induced molecular changes across distinct timescales in a newly established reptilian model species, the Madagascar ground gecko (Paroedura picta). To determine temperature-responsive phenotypes and assess phenotypic plasticity under long-term temperature changes, we compared thermal traits in individuals acclimated to 25°C and 30°C for more than 30 days. We found significant differences in the critical thermal minimum and maximum as well as sprint speed between the two groups. We then employed RNA sequencing and the assay for transposase-accessible chromatin using sequencing to analyse gene expression, splicing and chromatin states across multiple temperature conditions and durations. Results revealed that abrupt temperature shifts activated known heat stress pathways, whereas prolonged temperature acclimation altered immune function. In the liver, the predicted occupancy of some transcription factors diverged between short- and long-term temperature stimuli. These findings indicate that transient temperature stress responses and long-term temperature acclimation in P. picta involve distinct molecular mechanisms.