Molecular Ecology最新文献

The effective population size (N_e) is a fundamental parameter in population genetics. Despite its central importance, there are relatively few estimates of N_e available and there have been limited attempts to compare values across eukaryotes. Here, we estimate long-term effective population sizes for 120 species, broadly distributed across the eukaryotic tree of life, using nucleotide diversity and direct mutation rate estimates. We find that N_e varies by nearly 4 orders of magnitude and that it shows strong phylogenetic structure across broad taxonomic scales but not within individual lineages. Phylogenetically controlled regressions reveal that Nₑ correlates with key life history traits, including generation time and propagule size, and that nucleotide diversity serves as a useful proxy for Nₑ. Finally, we show that small Nₑ is generally associated with a reduction in the efficacy of natural selection, as indicated by an elevated ratio of non-synonymous to synonymous diversity (π_N/π_S), but not with an increase in genome size after accounting for phylogenetic non-independence. These results provide a broad comparative perspective on the factors driving variation in Nₑ and its evolutionary consequences across eukaryotes.

Understanding gene flow between ploidy levels in polyploid complexes is essential for species delimitation and conservation. This study explores evolutionary dynamics in the polyploid complex Thymus sect. Mastichina (Lamiaceae), comprising three taxa: T. mastichina subsp. mastichina, T. mastichina subsp. donyanae, and the endangered T. albicans. Using Hyb-Seq data, phylogenomics (nuclear orthologs), and population genomics (SNPs), we confirm the section consists of two sister groups with distinct ploidy levels: a diploid and a tetraploid one. The tetraploid group shows low genetic differentiation among its populations, probably indicating rapid expansion across diverse environments. In contrast, the diploid group exhibits more complex genetic structuring, potentially shaped by geomorphology, interploidy introgression, and incipient isolation. Four diploid subgroups (Algarve, Cádiz, Doñana, and Hercynian) are identified, with reticulate evolution. The dense reticulation observed is compatible with incomplete lineage sorting in diploid lineages due to recent and rapid divergence events. Phylogeographic analyses suggest isolation-by-distance, with two major riverbeds maybe playing a role in shaping genetic differentiation, while interploidy gene flow detected could have facilitated ancient and/or ongoing admixture between diploid and tetraploid lineages, despite geographic isolation. These findings highlight cryptic genetic diversity and emphasise the need for an integrative taxonomy that includes multiple lines of evidence: morphological, cytological, genomic, and ecological. Conservation efforts should prioritise protecting the four diploid subgroups, aided by flow cytometry, since they may harbour critical adaptive potential to both specific habitat types and/or environmental conditions. This work contributes to advancing our knowledge of evolution in polyploid complexes by combining genomic approaches and highlighting cryptic diversity in Thymus species. Future research should investigate morphometric and chemical data, hybridisation events, divergence times, diversification dynamics, and relationships with other Thymus species to further understand polyploid evolution and its impact on biodiversity.

Many species have become threatened during the Anthropocene, requiring conservation strategies based on biological evidence. Wood-inhabiting fungi face multiple threats due to a complex interplay of a short lifespan, removal of dead wood as a resource and climate change. Furthermore, rare fruiting events might restrict dispersal via spores, leading to a significant population genetic structure. Yet, little is known about the genetic structure of both rare and common wood-inhabiting fungal species across Europe. Here, we investigate the rare polypore fungus Antrodiella citrinella, which co-occurs with the common wood-decay fungus Fomitopsis pinicola. We analysed a total of 149 individuals of both species across 13 countries, sequenced their genomes and analysed single-nucleotide polymorphisms. Based on a broad set of analyses, we found a very weak population structure in A. citrinella, suggesting historically wide dispersal and effective gene flow across Europe. In contrast, we found support for two moderately differentiated populations following a southwest-northeast separation in F. pinicola, possibly due to dispersal limitation through its relatively larger spores, a more intense forest use history in southern Europe and a post-glacial history of co-immigration with the main host tree species, Norway spruce. While the weak to moderate genetic structure of wood-inhabiting fungi suggests historically sufficient habitat connectivity, conservation measures should consider strategies providing deadwood as an important habitat to restore and maintain connectivity throughout Europe.

Riparian ecosystems are vital interfaces between aquatic and terrestrial environments but are increasingly impacted by anthropogenic pollution. In these systems, merolimnic insects serve as crucial ecological links, occupying aquatic habitats as larvae and terrestrial environments as adults, thus being an essential food source in both. Consequently, pollutant exposure during the aquatic larval stage can have cascading effects across ecosystem boundaries. While the ecological consequences of such exposure are well documented, the evolutionary potential of merolimnic insects to adapt to chronic pollution remains poorly understood. To address this, we previously conducted a selection experiment exposing populations of the non-biting midge Chironomus riparius to the mosquito larvicide Bacillus thuringiensis israelensis (Bti) or heavy metal copper over approximately eight generations, which revealed only limited evidence of consistent phenotypic adaptation. Here we use whole-genome sequencing of these populations to assess their genomic responses to chronic pollutant exposure. Despite similar phenotypic sensitivity in pre-exposed and naïve populations, we detected distinct stressor-specific genomic responses. Copper exposure induced a significant genome-wide reduction in nucleotide diversity and evidence of selection-driven allele frequency changes, while Bti exposure was associated with heterogeneous, replicate-specific shifts, potentially reflecting drift or selection on multiple redundant pathways. Functional enrichment analyses indicated early-stage adaptation: immune- and apoptosis-related pathways were enriched under Bti, while metal detoxification and DNA repair pathways were enriched under copper, highlighting distinct adaptive mechanisms despite weak genome-wide signals of selection. Our findings demonstrate that Evolve and Resequencing approaches enable the detection of early genomic signals of adaptation even when phenotypic change is subtle or absent, offering a powerful framework for studying evolutionary responses to environmental pollution.

Petružela, J., Nürnberger, B., Ribas, A., Koutsovoulos, G., Čížková, D., Fornůsková, A., Aghová, T., Blaxter, M. & Baird, S. J. (2025). Comparative Genomic Analysis of Co-Occurring Hybrid Zones of House Mouse Parasites Pneumocystis murina and Syphacia obvelata Using Genome Polarisation. Molecular Ecology, e70044.

Figure 8: Bayesian phylogenetic trees of Top) Pneumocystis murina; Middle) Syphacia obvelata and Bottom) Mus musculus based on (near) whole mitochondrial sequences. Numbers at the nodes represent posterior probabilities. The scale bars indicate the number of substitutions per site. Trees were midpoint rooted. In the Pneumocystis tree, we included the mitochondrial reference sequence from Genbank (NC020332). For this parasite, a tree including the TANZANIA outgroup is provided in SuppMat 8. The mitochondrial Mus musculus mitogenomes were derived from the host reads of the Pneumocystis dataset.

We apologize for this error.

Chromosomal inversion polymorphisms have been linked to the evolution of phenotypic variation, environmental adaptation, and speciation. The genome of the white-throated sparrow (Zonotrichia albicollis) contains two exceptionally large chromosomal polymorphisms. The rearrangement on the 2nd chromosome (ZAL2/2^m) has been the subject of considerable study and is linked to both plumage morph and alternative reproductive strategies. Using extensive genomic and transcriptomic resources, we molecularly characterised the other polymorphism, which is on the 3rd chromosome (ZAL3/3^a). We estimate that the ZAL3 polymorphism is larger than the ZAL2 polymorphism, capturing nearly 1000 genes. Sequence divergence between ZAL3 and ZAL3^a is approximately half that of ZAL2/2^m, suggesting that ZAL3/3^a evolved in the context of the ZAL2/2^m rearrangement. We found evidence of reduced genetic diversity inside the rearranged region on ZAL3, sequence divergence between ZAL3 and ZAL3^a, and notable gene expression differences and allelic bias between the two haplotypes. We did not, however, find evidence consistent with widespread degeneration of ZAL3. We identified a region inside the rearrangement that shows evidence of balancing selection, consistent with hypotheses that such divergent haplotypes may evolve within non-recombining polymorphisms. Using a newly developed PCR-based genotyping assay for the ZAL3 polymorphism, we genotyped 972 archived samples. We found that ZAL3/3 homozygotes are rare (1.2% of the population), but at the population level the arrangement is in Hardy-Weinberg equilibrium. We report here that rare ZAL3/3 homozygotes are in poorer body condition. Together, our observations of this young inversion polymorphism indicate that reduced genetic diversity, reduced selection efficacy, and the accumulation of adaptive alleles can occur before detectable genetic degeneration.