Molecular Ecology最新文献

Sponge microbial communities play a crucial role in marine ecosystem functioning and serve as a rich source of bioactive compounds. While host identity is recognised as a major determinant of microbiome diversity, the underlying evolutionary mechanisms remain poorly understood. This study aimed to comprehensively assess phylosymbiosis patterns within the sponge family Petrosiidae. In total 21 sponge species, collected across a broad geographic scale, were examined to investigate how host phylogeny influences microbiome composition. Using 28S rRNA, 18S rRNA and COI gene barcoding to identify host sponges, combined with 16S rRNA gene amplicon sequencing to characterise prokaryotic communities, we provide evidence of phylosymbiosis through multiple analytical approaches, including distance-based metrics and topological congruence. Our results show that host phylogeny and identity play a significant role in structuring sponge microbiomes, even at finer taxonomic resolutions. However, we observed notable incongruencies, where closely related sponge species exhibit divergent microbial communities that appear to be associated with depth or geographical location. This study represents the first large-scale investigation of phylosymbiosis in sponges at the family level, providing valuable insights into the evolutionary and ecological drivers shaping sponge microbiomes, particularly in the sponge family Petrosiidae.

Allochronic divergence is a key evolutionary mechanism that can frequently lead to incipient speciation. Although theoretical models suggest that such divergence is notably facilitated by small population size and genetic polymorphisms influencing reproductive timing, though constrained by genetic load, empirical validation remains limited. We investigated these predictions by re-analysing a case of allochronic differentiation between two sympatric populations of pine processionary moth (Thaumetopoea pityocampa) in Portugal, using whole genome resequencing (IndSeq and PoolSeq) of those two populations and eight allopatric ones. We inferred the demographic history of those populations, assessed their genetic load and searched for genomic regions associated with life cycle differences. Our analyses revealed a recent split between the sympatric allochronic populations, accompanied by a strong reduction in gene flow, bottlenecks, inbreeding and accumulation of deleterious variants. Genome scans identified several loci associated with life cycle variation, including genes putatively involved in circadian rhythm regulation, predominantly located on the Z chromosome. We discuss how these empirical genomic findings support theoretical expectations that assortative mating driven by differences in reproductive timing, underpinned by polymorphisms in circadian genes, along with genetic drift and purge of genetic load at high-impact sites, can promote the onset and persistence of allochronic divergence.

Conservation genomics has increasingly transitioned from a promising concept to a science that integrates a range of advanced analytical approaches, providing new insights into inbreeding, genetic load, demographic history and adaptive divergence in species of conservation concern. Yet, questions remain about how effectively these advances translate into practical conservation action. This Special Issue, Conservation Genomics—Making a Difference, brings together 37 papers that collectively assess how genomic data are contributing to conservation science and management. The contributions encompass empirical studies, reviews, and perspectives that together demonstrate how genomic tools are now used to identify management units, quantify inbreeding, analyse inbreeding depression, reveal adaptive variation, forecast genomic vulnerability under climate change, and guide genetic rescue and assisted migration. Several papers show direct integration of genomics into conservation planning, including fisheries management, guiding restoration of endangered or habitat-forming species, and monitoring of genetic indicators under the Convention on Biological Diversity. Others highlight emerging questions in conservation, such as the significance of structural variation, and the genomic basis of invasiveness. However, persistent challenges remain, notably in bridging the gap between research and policy, uneven global distribution of genomic resources, and translating complex analyses into practical management advice. Nevertheless, the advances presented in the 37 papers show that conservation genomics is moving beyond its early theoretical and technical focus towards real-world applications. The field is maturing and is increasingly fulfilling its promise to make a real difference for populations, species, and ecosystems.

Tropical Asia's complex, dynamic geological and climatic history, coupled with its diverse topography, provides a fascinating setting to study evolutionary processes driving high biodiversity. This phylogenomic research reconstructs the evolutionary history of the strictly arboreal and forest-dependent Oriental Giant Squirrels (Ratufa) to gain insights into the interplay between paleo-forest distribution and regional diversification. By analysing genomic data (complete mitochondrial genomes and approximately 4000 nuclear ultraconserved elements) from historic museum specimens and conducting divergence time estimation and niche modelling, we uncover how global paleoclimate cooling, the uplift of the Himalayas and Tibetan Plateau, and habitat fragmentation led to allopatric speciation in refugia during the mid-Miocene, Miocene–Pliocene boundary, and late Pliocene, in synchrony with other evergreen forest-dependent species. Our findings underscore the potential role of grassland expansion during climatic oscillations and the North Sunda and Mekong paleorivers in isolating populations and promoting vicariance and speciation in this region. This research suggests a species-level diversity underestimation within R. bicolor and R. affinis, supporting the recognition of R. gigantea as a distinct species, along with several candidate species that warrant integrative taxonomic revision. Additionally, this study highlights the rapid and independent evolution of dwarfism in three Ratufa lineages and discusses challenges in museum genomics. Ultimately, this study serves as a valuable reference on the historical biogeography of tropical Asia, providing important insights for the conservation of these threatened taxa and the evolutionary processes that generate and maintain biodiversity in this hyperdiverse region.

Translocating individuals into existing populations of conspecifics can support threatened species by increasing population size, maintaining genetic diversity and reducing the risk of inbreeding. However, for species whose adaptive potential is compromised due to ongoing threats, like disease, the outcome of such management interventions becomes more complex. The Tasmanian devil (Sarcophilus harrisii) is a prime example, where the emergence of Devil Facial Tumour Disease (DFTD) has led to significant population declines, raising concerns about their long-term survival. It is therefore critical to understand if the introduction of new functional genetic variants through supplementation actions enhances, or potentially hinders, their long-term persistence. We investigated changes in functional gene diversity at both the population- and individual-levels, pre- and post-supplementation, across multiple wild devil sites (four supplemented and four not supplemented). We found that functional diversity increased post-supplementation. Though the magnitude of change was varied among sites, a similar site-specific pattern was also evident in genome-wide diversity. Importantly, we saw no evidence of swamping of local alleles or those putatively associated with DFTD regressions. This is likely due to the source population representing the broad wild genetic diversity and supplementations facilitating gene flow across the current fragmented landscape. Continued and long-term monitoring at multiple wild sites will be necessary to determine whether future generations retain this introduced genetic variation.

The degree or extent of gene reuse during repeated adaptation offers key insights into the genomic constraints on evolution. Although many studies have identified signs of genomic repeatability, a thorough synthesis of methods for detecting gene reuse and estimating its extent is missing. In this review, we first propose a simple framework for studies aimed at identifying gene reuse during repeated adaptation using genomic data. Next, we examine existing approaches to (i) detect gene set overlap, perform significance testing, and perform multivariate dimensionality reduction, (ii) distinguish between gene and allele reuse while emphasising methods for detecting allele reuse, (iii) explore models to identify the mechanisms behind repeated adaptation, and (iv) address issues and potential solutions to differentiate true gene reuse from methodological artifacts. Our review highlights standardised methods developed using genomic data to identify gene reuse. We also note that, although few studies quantify allele reuse, conducting such analyses is essential because it adds a more detailed layer to predicting evolutionary paths. Finally, several strategies can be used to cross-validate signals of gene reuse. These should be applied to confirm true positives, as biological and methodological artifacts can bias predictions. By synthesizing current methods and outlining a robust analytical framework, we provide a roadmap for enhancing the accuracy and reliability of gene reuse detection in adaptive evolution.

Intraspecific genetic diversity (IGD) is a fundamental component of biodiversity, essential for understanding the evolutionary histories and demographic processes of species, and is key to effective conservation planning. However, ecologically important regions such as the Gran Chaco, South America's second-largest forested biome, remain largely underexplored. Encompassing diverse vegetation across climatic and altitudinal gradients, it harbours more than 3400 vascular plant species, 11% of which are endemic. Despite its ecological importance, genetic research in the region is limited and often biased. We reviewed IGD studies on vascular plants in the Gran Chaco from 1985 to 2024, identifying 85 studies covering 74 species. Coverage remains alarmingly low, with only 2.14% of species and 9.95% of the phylogenetic diversity represented. Research is skewed towards perennial (91%) and tree (46%) species, with limited representation of annuals and herbaceous taxa. Most studies relied on nuclear DNA (66%), fewer used chloroplast DNA (27%) and only 7% combined both genomes. Geographically, 33% of the Gran Chaco has no IGD data, and a further 22% includes data from a single species. Genetic sampling is concentrated in more accessible areas with higher road density and proximity to research institutions, particularly at higher altitudes. We found that in the Argentine Chaco ecoregions, 4.4 species have been genetically studied for every 100 species recorded, while in the Bolivia and Paraguay Chaco ecoregions, this proportion drops to 1.1 species for every 100 in each country. Future research on IGD in the Gran Chaco should broaden its taxonomic scope, diversify genomic tools and expand geographic coverage. Addressing these gaps will provide critical insights into the biogeographic history of the Gran Chaco and strengthen conservation strategies in this threatened and understudied biome.