Molecular Ecology最新文献

River barriers have long played a central role in diversification models of tropical regions, including the exceptionally biodiverse island Madagascar. Although their role is best understood by integrating additional factors such as elevation and the ecological niche of a species, empirical studies integrating these variables remain rare. We used restriction site-associated DNA sequencing to assess the combined effect of rivers, topography, climate and forest cover on the distributions and diversity of four Microcebus and two Avahi species (Primates, Lemuriformes) in northeastern Madagascar. We inferred population structure, gene flow and genetic diversity, and assessed the association of these ecogeographic variables and genetic differentiation using isolation-by-resistance models. Our results show that significant differences in genetic diversity and connectivity among species can be explained by species-specific responses to landscape features and phylogeographic histories. Specifically, rivers present general barriers to gene flow, but dispersal between inter-river systems is possible via high-elevation headwater regions. While this led to high connectivity and genetic diversity in M. lehilahytsara and A. laniger, gene flow among M. jonahi populations is limited by low climatic niche suitability at higher elevations. Moreover, the more restricted distributions of M. macarthurii, M. simmonsi and A. mooreorum likely resulted from refugial dynamics and sea level fluctuations leading to allopatric divergence and microendemism. Together, the findings illustrate how ecological differences among species and temporal landscape dynamics mediate the role of rivers as dispersal barriers. They also highlight the importance of prioritising river headwaters and topographically complex regions, which were shown to promote connectivity, in conservation efforts.

We studied the drivers of population-genetic structuring and genetic diversity in specialist parasites based on whole-genome resequencing data from 82 Echinophthirius horridus seal louse individuals sampled from 12 ecologically and behaviourally different phocine seal species, subspecies and populations across the Holarctic. We found that the main genetic disjunctions in E. horridus lice occur across seal host species and subspecies, with a further level of population subdivision emerging among host individuals within some populations. Endemic and relict landlocked seal (sub)species host the genetically most distinct louse populations, while lice associated with sympatric marine seals show signatures of occasional gene flow across hosts. Within the latter, the most extreme case is seen in the near-panmictic lice associated with northern European grey and harbour seals, which aggregate in shared rookeries and colonies. Although the louse and seal phylogenies were overall statistically significantly congruent, evidence for similar host shifts in the past is reflected in several conflicts in the phylogenetic trees of the lice and their hosts. Population-level mean heterozygosity and theta in seal lice varied considerably, and both measures of genetic variation were statistically significantly related to host population size. Taken together, our results support a non-adaptive model of parasite diversification, in which geographic and behavioural isolation among hosts drives parasite genetic differentiation, and genetic erosion in bottlenecked hosts cascades up to their specialist parasites. Our results provide new insights into processes that generate parasite diversity and trigger parallel losses of genetic diversity in endangered host–parasite systems.

Fairyflies (Hymenoptera: Chalcidoidea: Mymaridae) are a diverse but taxonomically understudied group of parasitoid wasps that attack the eggs of other insects. Being among the very smallest of all insects, they are often ignored in biodiversity surveys despite being one of the most abundant microhymenoptera in many habitats. The traditional approach of morphological species delimitation can be challenging due to their minute size and meticulous slide-mounting technique. Ways to accelerate their discovery are needed. We conducted the first large-scale study of Mymaridae in temperate forests, combining DNA megabarcoding and the large-scale integrative taxonomy (LIT) workflow to describe their diversity. We obtained COI barcodes from 2098 specimens and used ASAP and RESL for species delimitation. Between 42 and 114 molecular clusters were delimited. Reducing morphological validation to only 9% of the sample enabled accurate delimitation while limiting time and effort. We confirmed the presence of 55 species, including many potentially new to science. The LIT workflow was effective for Mymaridae, although cryptic diversity remains unresolved in some large clusters, especially in the genera Alaptus and Anagrus, where high haplotype diversity and morphological ambiguity suggest additional hidden species. DNA reference databases proved unreliable, with less than 1% correct species matches, highlighting the taxonomic gap for this group. Nonetheless, we contributed 16 new identified reference barcodes to public databases and added new provincial and national species records for Canada. Our results demonstrate the value of combining molecular and morphological data in a standardised workflow and underscore the importance of improving reference databases for effective biodiversity assessments of dark taxa like microhymenoptera.

The lucinid clam Lucinoma capensis thrives at the oxygen minimum zone margins in the Benguela Upwelling System, where oxygen levels fluctuate dramatically. Understanding its adaptation to such extreme conditions provides key insights into survival strategies under fluctuating oxygen availability. We investigated the transcriptomic and metabolomic responses of L. capensis under normoxia, hypoxia, and recovery, focusing on the gills and digestive gland. Our findings highlight distinct organ-specific responses, with the gills showing strong transcriptional changes to oxygen fluctuations, in contrast to the more stable profile observed in the digestive gland. Under hypoxic conditions, the gills exhibited coordinated downregulation of protein synthesis, transposable element activity, and immune function, suggesting a tightly regulated energy conservation strategy and mechanisms to preserve symbiont stability and genomic integrity. Activation of prokaryotic metabolism in the gills supports the symbionts' role in host energy acquisition and sulfide detoxification during hypoxia. In contrast, the digestive gland showed minimal transcriptional shifts during anoxia, with upregulation of pathways supporting structural maintenance. Upon reoxygenation, the gills displayed an active and asymmetric recovery, characterised by rapid restoration of protein synthesis and gradual normalisation of protein degradation and immune functions. Despite significant transcriptomic changes, the metabolome remained largely stable, reflecting L. capensis's resilience to oxygen fluctuations. However, an overshoot in TCA cycle intermediates and derepression of previously downregulated pathways indicate that reoxygenation involves active metabolic reprogramming, not merely a return to baseline. This study highlights the specialised tissue responses and symbiotic contributions that enable L. capensis to thrive in one of the ocean's most challenging environments.

The marine environment comprises vast regions without physical barriers to movement, making the understanding of population isolation and the evolution of diversity challenging. This is especially the case for highly mobile marine species. Here we investigate populations of the common bottlenose dolphin (Tursiops truncatus) across the Mediterranean Sea and adjacent North Atlantic using high-resolution genomic markers (RADseq) and stable isotope analyses to better understand the evolution of population structure in this system. High-resolution genomic data and broad geographic sampling revealed patterns of structure not previously identified, and integration with stable isotope data suggests that prey choice varies across this region. Unexpected patterns included genetic and isotopic similarity between the North Atlantic and the region around Sicily (but not including the medially located Gulf of Cádiz and surrounding regions). The regional habitat within and beyond the Mediterranean Sea is structured with ocean frontal systems including thermal and halocline transitions, several of which show alignment with genetic transitions within our data. Our data help to distinguish among possible drivers of population differentiation for a marine predator that has the potential for long-distance dispersion.

Past population dynamics during the Pleistocene ice age and the Holocene era have profoundly influenced the genetic structure and diversity of species. Environmental heterogeneity has further shaped local and regional adaptive variation. Here, we ask how historical processes have led to the current genetic diversity of a key North American species across its vast natural range and what genomic signatures indicate regional adaptive divergence and local adaptation. We used sequencing data from 1903 Populus tremuloides Michx. (quaking aspen) trees to assess historical population dynamics and identify genotype –environment associations within and among the species' major genetic lineages. The two northern and western North American aspen lineages exhibited historical population expansion patterns, while the southernmost lineage experienced a historical bottleneck consistent with past glacial oscillations. We found that the earliest split between genetic lineages of P. tremuloides occurred in the southern part of its distribution range. We further identified larger blocks of adaptive SNPs within separate genomic sequence regions on chromosomes 2 and 8 that may exhibit suppressed genetic recombination, contributing to the maintenance of regional and local adaptation in the species. Our study provides key insights into the evolutionary processes affecting adaptive genetic variation and phylogeography at a broad continental and regional scale, with implications for predicting species' responses to future climate change.