It is demonstrated that herbicide resistance encompasses contrasting genetic routes, with polygenic NTSR evolving largely through selection on standing variation, offering broader insights into the evolutionary dynamics of rapid polygenic adaptation under novel anthropogenic selection.
Hybridization may have multiple impacts on speciation and adaptation. Yet the evidence of adaptive introgression events that have historically occurred between nonradiating or established species is still lacking. The oakleaf butterflies in the genus Kallima include multiple sympatric and incipient species with a known history of diversification and therefore serve as a useful system for addressing historical introgression and adaptation. By integrating population genomics, phylogenomics, CRISPR/Cas9 genome editing and de novo genome assembly, we disentangled the genome-wide pattern of admixture among multiple Kallima species and used the putative introgressed gene pale as an example to reveal its role in scale pigmentation, structure and potentially in sexual dimorphism. We further demonstrated the complex evolutionary history of the Z chromosome largely owing to historical introgression. Our study revealed genome-wide introgression that has historically occurred during butterfly dispersal and differentiation, facilitating the understanding of interspecific relationships and potential local adaptation during gradual evolution.
Shu-Ting Wang, Pei-Wen Yang, Wei-Fan Lv et al.· National Science Review· 0 citations
Demographic processes such as colonization to new environments and gene flow fundamentally shape the genomic landscape, either facilitating or constraining the efficiency of selection by altering the balance between genetic diversity and adaptive responses. Although theoretical predictions suggest that the efficacy of selection is dictated by a species’ demographic history, empirical studies often overlook these constraints, yielding misleading observations. In this study, we present the first functional genome annotation for the wood frog (Lithobates sylvaticus), providing a critical genomic resource for understanding the adaptive capacity of the species. Based on the annotation, we examined the potential for selection to drive genomic and phenotypic divergence among populations distributed across vernal ponds in Northeastern Connecticut, USA. A genotype×environment association analysis revealed that the frequency of an outlier loci (Rab28) spikes in response to one wetland that is notable for having relatively low canopy cover and large area. We also found that selection has driven a strong disparity in embryonic development among populations of wood frog at a rate exceeding that of neutral genetic drift. This genomic signature of selection together with a remarkable phenotypic differentiation suggests that natural selection overcomes the power of genetic drift, even in a landscape characterized by relatively recent colonization and substantial evidence of connectivity among breeding wetlands. These findings improve our understanding of the wood frog’s variation at a microgeographic scale.
Dylan J. Padilla Pérez, Lisa K. Brady, J. Taft et al.· bioRxiv· 0 citations
Chromosomal rearrangements are hypothesized to facilitate speciation by suppressing recombination in locally adapted genomic regions, yet how they shape evolutionary rates during rapid divergence remains poorly understood. Here, we investigate the genomic architecture of two sister Carex (Cyperaceae) species on Réunion Island, which rapidly diverged (∼0.5 Mya) to occupy contrasting tropical-montane and dry-subalpine habitats. Using chromosome-level assemblies and population genomics, we show that genomic divergence is not uniform across the genome but is concentrated within specific large-scale inversions. Crucially, genes within these structural variants exhibit significantly accelerated rates of protein evolution, as evidenced by elevated ω, compared to the collinear genome. This is consistent with recombination suppression and subsequent relaxation of purifying selection driving these patterns, which may complement or even outweigh the signal of positive selection. Functional analysis and environmental associations reveal that these "genomic accelerators" include key adaptive loci: Inversions on chromosomes 14 and 28 are enriched for mechanosensitive ion channels and auxin transport, which is consistent with facilitating the interspecific physiological shift to aridity. Partial redundancy analyses reveal that ongoing intraspecific ecological adaptation is highly polygenic across the collinear genome. Our results demonstrate that genomic architecture actively dictates evolutionary speed, suggesting that certain lineages boosted by structural variants may bypass the typical constraints of purifying selection to rapidly exploit vacant ecological opportunities.
Inés Gómez-Ramos, Rogelio Sánchez-Villegas, A. Mohan et al.· Proceedings of the National...· 0 citations
Defining the genetic basis of local adaptation is a key goal of evolutionary biology and crop improvement. Theory predicts that when selective pressures follow differences in the environment, a cline will be established. Clines can be exploited to uncover adaptive variation by association of alleles with the environment. However, monotonic phenotypic change over a cline is not necessarily mirrored in the behavior of genetic variants and population structure can further complicate analysis. To study genetic and phenotypic variation across the environment, we developed a multi-parent advanced generation inter-cross (MAGIC) population using eight Mexican native maize (Zea mays L. ssp. mays) varieties sourced from distinct agroecological zones. We evaluated the population in a common garden in Mexico and mapped tassel branching and flowering time, two traits that exhibit clinal variation. Variation in tassel branching was dominated by a single QTL with allele effects aligning to a negative elevational cline. By contrast, allele effects associated with 11 identified flowering time QTL were not consistently correlated with any one source environmental factor. Our observations support the prediction that genotype-environment association will be strongest under simple genetic architecture, although, even then, analysis in native populations may be confounded by population structure.
Sergio Pérez-Limón, Ana Laura Alonso-Nieves, M. R. Ramírez-Flores et al.· New Phytologist· 0 citations
Climate change is increasing drought and heat stress in European forests, raising concerns about the capacity of long-lived tree species to respond to rapidly changing environmental conditions. While local adaptation has been documented in many forest trees, it remains unclear whether newly established seedlings, which form the forests of the future, are able to persist and adapt to these new climatic conditions. Here, we investigated genomic differences between naturally regenerated seedlings and trees of European beech (Fagus sylvatica) across the three regions of the German Biodiversity Exploratories using low-coverage whole-genome sequencing (∼5x) of 1,032 individuals. Population structure was primarily driven by geographic region, whereas genetic diversity was similar across life stages. Despite this genome-wide similarity, we detected allele frequency shifts between trees and seedlings, concentrated in narrow genomic windows. These shifts were strongest in surviving seedlings, suggesting that environmental filtering during early establishment may contribute to shaping the genetic composition of regenerating populations. The strongest signals were observed within the Swabian Alb, where sampled seedlings were 2-years old and had experienced a longer period of potential filtering prior to sampling. Genotype–environment association analyses identified loci associated with climatic variables, and subsequent GO enrichment analyses of genes linked to these loci revealed significantly more enriched GO terms in seedlings than in trees, suggesting stronger environmental filtering by the current climate in seedlings. In particular, we found associations with maximum air temperature, relative humidity, soil moisture, and precipitation, affecting genes involved in stress responses, growth, metabolism, and developmental processes. Together, our results demonstrate that young cohorts of European beech differ genetically from trees and reveal genomic patterns consistent with life-stage-dependent environmental filtering. These findings suggest that the genetic composition of early life-stages is already altered by current environmental conditions, possibly contributing to adaptation to new climatic conditions.
Marieke Lenga, L. Opgenoorth, K. Heer et al.· bioRxiv· 0 citations
Speciation has classically been viewed as a process requiring complete reproductive isolation between species. However, genomic studies increasingly show that gene flow, the transfer of genetic material between species via hybridization, can promote adaptation and speciation by boosting genetic variation within lineages. For adaptive radiations, where many ecologically diverse species arise rapidly from a common ancestor, gene flow may be an important source of variation for selection to act upon.
The adaptive radiations of cichlid fish found in the East African Great Lakes, which show extraordinary species diversity, are an excellent system for studying the effect of gene flow in the evolution of biodiversity. In each of the major radiations, those of Lake Tanganyika, the Lake Victoria region, and Lake Malawi, gene flow has been shown to be a contributing factor in the generation of species. For the Lake Malawi radiation, which consists of around 800 species that evolved within the last 800 thousand years, only one gene flow event was previously known: the ancestral Malawi lineage hybridized with a riverine species related to Astatotilapia sp. "Ruaha blue," forming a ‘hybrid swarm’ that initialized the radiation. Still, little is known about the true extent, impact and genomic footprint of gene flow in the Malawi radiation.
Using a whole-genome sequencing dataset of 239 Malawi and 76 non-Malawi African cichlid species, we tested for additional gene flow events that affected the Malawi radiation, both before and after the radiation’s onset. Alongside A. sp. "Ruaha blue," we found that three further lineages, related to the Congo South Africa (CSA), Pseudocrenilabrus, and Orthochromis groups, also likely contributed to the Malawi hybrid swarm. We identified and characterized hundreds of long genomic tracts of foreign CSA and Pseudocrenilabrus ancestry which were segregated amongst Malawi species. We found signals of divergent selection among Malawi species, supporting adaptive contributions from CSA- and Pseudocrenilabrus-derived ancestry. We found complex patterns of ancestry sharing between not just the Malawi radiation and neighbouring riverine species, but also with species from the Lake Victoria region, indicating previously unrecognized genetic connectivity among East African cichlids.
Overall, these findings suggest the Malawi radiation formed through repeated intermingling of diverse cichlid lineages and that Malawi genomes are comprised of a complex mosaic of ancestries varying among species and individuals. Our results support the growing recognition that gene flow is an important driver of biodiversity.
S. Gresham· 0 citations
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