Molecular Ecology最新文献

Chromosomal rearrangements, such as inversions, have received considerable attention in the speciation literature due to their hampering effects on recombination. Less is known about how other rearrangements, such as chromosome fissions and fusions, can affect the evolution of reproductive isolation. Here, we use crosses between populations of the wood white butterfly (Leptidea sinapis) with different karyotypes to identify genomic regions associated with hybrid inviability. We map hybrid inviability candidate loci by contrasting allele frequencies between F₂ hybrids that survived until the adult stage with individuals of the same cohort that succumbed to hybrid incompatibilities. Hybrid inviability candidate regions have high genetic differentiation between parental populations, reduced recombination rates, and are enriched near chromosome fusions. By analysing sequencing coverage, we exclude aneuploidies as a direct link between hybrid inviability and chromosome fusions. Instead, our results point to an indirect relationship between hybrid inviability and chromosome fusions, possibly related to reduced recombination in fused chromosomes. Thus, we map postzygotic isolation to chromosomal rearrangements, providing crucial empirical evidence for the idea that chromosome number differences between taxa can contribute to speciation.

Humulus lupulus L., commonly known as hop, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hop has undergone intense artificial selection, with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavour and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study explores the global population structure and domestication history of 98 hop cultivars. We assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Our study revealed that worldwide hop cultivars cluster into four subpopulations: Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modelling the evolutionary history of domesticated hop reveals divergence of the common ancestors of modern US cultivars around 2800 years before present (ybp), and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition under common-garden settings in the United States.

Genome annotation, alignment and phylogenetics are at the centre of most studies in evolutionary genomics. These techniques function best when rooted in prior work. Genes are mined from new genomes using evidence from old gene models. These genomes are aligned to well-worn references to create matrices for tree reconstruction. Trees are often populated with well-characterised genomes to add context to the newly sequenced. Genome inference traces a line back to model organisms, yoking the analysis of new genomes to layers of previous knowledge. Here, we present an alternative approach that uses unannotated and unaligned sequence to understand the information diversity of sequence ensembles. Any set of genomes can comprise our sequence ensemble. In a pandemic context, a sequence ensemble might be clinically isolated strains from one day. In a systematic context, a sequence ensemble could be the pangenome available for a clade. The normal bioinformatics playbook would have us align. But we instead compress. A sequence ensemble that compresses easily contains lower information diversity. For pandemics, we can use curves of information diversity to trace genomic novelty and monitor selective sweeps in new strains. For systematics, we can calculate compressibility quickly across all known bacterial taxa, levelling the criteria for species across clades. If we tolerate data loss, we can go one step further and capture structural evolution as we compress. Our approach sacrifices a lot. We skip many of the products of modern bioinformatics like variation anchored to known genes or genome alignment to prescribed references or pangenome graphs. But we gain speed, breadth and the ability to rapidly respond to novelty.

Phylogenetic reconstruction is indispensable for inferring evolutionary trajectories of novel traits and historical biogeography of extant species. However, resolving phylogenetic relationships remains particularly challenging during episodes of rapid radiation, as exemplified by Rhinolophus-the second-largest genus of Chiroptera. This Old World bat lineage underwent rapid diversification, resulting in persistent ambiguities in its species-level phylogeny. To date, limited taxonomic sampling and insufficient molecular markers have precluded robust identification of the ancestral clade within Rhinolophus. Here, we address this knowledge gap using genome-wide nuclear datasets with comprehensive taxon sampling. Phylogenetic reconstructions integrating concatenation and coalescent-based approaches robustly recovered two strongly supported sister clades within Rhinolophus-the Afro-Palaearctic clade and the Asian clade-and resolved R. hipposideros as the ancestral lineage of the Afro-Palaearctic clade. This topology received further validation from PhyloNet analyses accounting for gene flow. Notably, mitochondrial phylogenomics exhibited significant topological discordance with nuclear DNA, suggesting widespread mito-nuclear discordance attributable to historical introgression. Genome-scale introgression analyses revealed pervasive cross-lineage nuclear gene flow, occurring not only among sister taxa but also between distantly related lineages. Crucially, highly introgressed genes (RANBP2 and SERINC3) functionally associated with antiviral defence mechanisms were previously shown to be under positive selection in bats. This pattern supports the occurrence of adaptive introgression facilitating viral resistance across the genus. Overall, our findings demonstrate the power of genome-scale data in resolving deep evolutionary relationships within rapidly radiating groups and underscore the importance of hybridization and introgression as key mechanisms in mammal diversification.

Human disturbance can have profound effects on biodiversity, including increasing hybridization between reproductively isolated species. One approach for understanding how human activity affects hybridization dynamics is to evaluate correlations between disturbance (e.g., urbanisation, temperature change) and hybridization. Because variation in hybridization can also arise from historical factors unrelated to recent human disturbance, it is essential to account for population structure to avoid spurious correlations. Here, we combine environmental and high-coverage whole-genome resequencing data to investigate how human disturbance and population structure affect hybridization dynamics between a pair of pine sawflies adapted to different pines, Neodiprion lecontei and Neodiprion pinetum. We find that N. lecontei and N. pinetum exhibit strikingly different patterns of population structure, which we hypothesise stem from differences in host use. We also find that recent admixture is both asymmetric and geographically variable. Linear regression analyses reveal that admixture proportion is predicted by indirect human disturbance (i.e., climate change) and not direct human disturbance (e.g., urbanisation) in both N. lecontei and N. pinetum. Lastly, in N. pinetum, we find evidence of a spurious association between admixture and direct human disturbance that disappears when regression models account for population structure via inclusion of genetic principal component scores as covariates. Together, our data suggest that indirect human disturbance and population structure both contribute to geographic variation in admixture between N. lecontei and N. pinetum. Our study also highlights the importance of adequately controlling for population structure when attempting to identify environmental predictors (human disturbance-related or not) of hybridization.

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.

Population genomics can reveal trends and drivers of biodiversity loss, but it is still unclear how best to use measures of genome variation to understand population vulnerability in insects. Here we study genome variation in three species of Anthophora bees that show contrasting population trends in northern Europe. Two species, Anthophora plagiata and Anthophora retusa , have experienced declines and recoveries of different magnitudes in the last 50 years, whereas a third species, Anthophora quadrimaculata , has relative population stability. We generate highly contiguous genome assemblies and use them to study genome variation in 136 samples of these species collected throughout Sweden. We find exceedingly low genetic variation in A. plagiata , which has experienced a severe recent bottleneck, but high genetic variation in A. retusa , despite a similar recent population trajectory. Fragmented populations of the threatened species A. plagiata appear isolated from each other, but in A. retusa, there is a lack of deep population structure among geographically separated subpopulations. We infer population size in the distant past using MSMC2 and recent past using GONE. These methods are remarkably concordant and indicate ancient fluctuations in population size dating back to the Pleistocene, with moderate expansions in the past century in all three species. These results are comparable to some other studies of endangered insects, which have experienced population declines that predate the modern era. We detect long blocks of identity-by-state in A. plagiata , indicative of severe recent inbreeding. Translocations between isolated populations of this species could have a positive effect on their resilience.

Submarine groundwater discharge (SGD) supplies large quantities of nutrients and other terrestrial elements to coastal ecosystems, impacting marine biota and ecosystem functioning. Despite the relevance of prokaryotes for marine biogeochemistry, little is known about their responses to groundwater inputs. Here we explored the impact of SGD on the spatiotemporal patterns of prokaryotic communities from the Mar Menor (Murcia, Spain), a highly anthropized hypersaline coastal lagoon that receives large amounts of nutrient-polluted SGD. Using 16S rRNA amplicon sequencing, activity assays, and flow cytometry, we investigated the dynamics of prokaryotic communities across the lagoon and its connected environments (freshwater streams, groundwater, soils, the sea) on two occasions. We found that the lagoon areas most influenced by SGD (i.e., sites closest to the shore) presented on average three-fold higher heterotrophic prokaryotic protein production than the inner lagoon samples, and 2.7-fold higher taxonomic richness. This spatial pattern was likely influenced by solutes supplied by SGD, as higher concentrations of dissolved nitrogen, silicate and SGD tracers (radium [Ra] isotopes) were found in nearshore waters. Increases in these elements also influenced the relative abundance of dominant bacterial groups (e.g., Flavobacteriales, Rhodobacterales). In autumn, increases in lagoon ²²⁴Ra were strongly linked to higher taxonomic richness in microbial assemblages and the influx of allochthonous taxa from the catchment, pointing to seasonally variable transport of coastal groundwater microorganisms via SGD. Our study highlights SGD as an overlooked driver of prokaryotic dynamics in coastal ecosystems, and suggests that changes in this process may significantly impact microbial community structure and functioning.

Hybridization can induce transgressive gene expression, which may often contribute to hybrid vigour or dysfunction. Nevertheless, how different cis- and trans-regulatory variants between parental species influence hybrid expression novelty remains largely unknown. To decipher the detailed genetic architecture underlying this phenomenon, we performed expression quantitative trait locus (eQTL) mapping in a multi-generational Nelumbo population, including parental species (N. nucifera and N. lutea), F₁ hybrids and backcrossed F₂ (BC₁F₂) individuals. Using the Matrix eQTL under an additive linear model with covariates, our analysis identified 147,872 cis-eQTL and 151,632 trans-eQTL SNP-gene associations, which regulated the expression of 2538 cis-eGenes and 4805 trans-eGenes, respectively. Notably, trans-eQTLs exhibit significantly stronger regulatory effects on gene expression variation than cis-eQTLs. Trans-eQTLs, over-represented by transcription factors, such as C2H2, MYB, FAR1, are predominant drivers of transgressive expression in hybrids, which is markedly more prevalent in segregating BC₁F₂ individuals. We further demonstrated that cis- and trans-regulatory variants are linked to transgressive expression of crucial genes in the benzylisoquinoline alkaloid (a key medicinal metabolite of Nelumbo) biosynthetic pathway. These findings collectively highlight the primary influence of trans-regulatory rewiring on generating transgressive expression in hybrid populations. In conclusion, our study provides valuable genetic resources for understanding how regulatory network rewiring contributes to transcriptional variation and transgressive phenotypes in interspecific hybrids between species.

The introduction of populations to novel environments can lead to a loss of genetic diversity and the accumulation of deleterious mutations due to selection and demographic changes. We investigate how the recent introduction of maize to Europe shaped the genetic diversity and differentiation of European traditional maize populations and quantify the impact of its recent range expansion and consecutive breeding on the accumulation of genetic load. We use genome-wide genetic markers of almost 2000 individuals from 38 landraces, 155 elite breeding lines, and a large set of doubled haploid lines derived from two landraces to find extensive population structure within European maize, with landraces being highly differentiated even over short geographic distances. Yet, diversity change does not follow the continuous pattern of range expansions. Landraces maintain high genetic diversity that is distinct between populations and does not decrease along the possible expansion routes. Signals of positive selection in European landraces that overlap with selection in Asian maize suggest convergent selection during maize introductions. At the same time, environmental factors partially explain genetic differences across Europe. Consistent with the maintenance of high diversity, we find no evidence of genetic load accumulating along the maize introduction route in European maize. However, modern breeding likely purged highly deleterious alleles but accumulated genetic load in elite germplasm. Our results reconstruct the history of maize in Europe and show that landraces have maintained high genetic diversity that could reduce genetic load in the European maize breeding pools.