Chromosomal inversions are increasingly recognized as important drivers of local adaptation and ecological divergence because they suppress recombination and maintain adaptive allele combinations despite ongoing gene flow. However, the eco-evolutionary conditions favouring the establishment of such indirectly adaptive inversions, as well as the genomic features that distinguish them from other inversions remain incompletely understood. In this study, we investigated these questions in a wild sunflower system comprising two species: Helianthus debilis and Helianthus praecox, which exhibit diverse ecotypes and varying degrees of geographic overlap across Texas and Florida in the USA. To resolve the evolutionary relationships between and within these species, and identify potentially adaptive inversions, we generated haplotype-resolved reference assemblies and integrated comparative and population genomic analyses. We identified three major genetic clusters that only partially corresponded to taxonomic classifications. We further detected 156 inversions across the genome, 11 of which showed signatures consistent with a role in local adaptation. Notably, nine of the 11 putatively adaptive inversions were found in sympatric Texas populations. Together with a similar enrichment of inversions in genome assemblies from sympatric versus allopatric populations, our results suggest that inversions are more likely to evolve in heterogeneous environments with ongoing gene flow than in allopatry. Lastly, locally adaptive inversions were generally larger, contained more genes, and showed greater sequence divergence between haplotypes than other types of inversions. Our findings provide empirical support for the role of gene flow in promoting inversion establishment and identify genomic characteristics associated with indirectly adaptive inversions.
Yue Yu, Eric Gerardo González Segovia, Ji Wang et al.· bioRxiv· 0 citations
Understanding how plants adapt to elevational niches is essential for uncovering mechanisms of natural selection and diversity patterns in mountain systems. Integrating genomic and ecological approaches is therefore important for advancing our knowledge of plant adaptation and informing conservation under climate change. In this study, we investigate 15 populations of an alpine shrub Rhododendron intricatum in the Mt. Gongga region of the eastern Hengduan Mountains, focusing on genomic and phenotypic responses across elevations. Genotype-environment association analyses identified multiple outlier genomic regions associated with elevation, consistent with polygenic responses to environmental gradients, and candidate genes were broadly linked to functions such as signalling, stress responses, metabolism and reproductive regulation. Distinct allele turnover patterns along precipitation seasonality and mean annual temperature further indicate the combined effects of climatic heterogeneity in shaping genomic responses. Concurrently, systematic trends were detected in phenotypic traits along elevation, including increased leaf spectral reflectance, shifts in vegetative dimensions and changes in floral morphology. Predictive models under future climate scenarios reveal increasing genetic offset through time, and projected mismatch becomes uniformly severe across the entire elevational gradient by the end of the century. Together, multiple lines of evidence reveal coordinated genomic and phenotypic responses to shared environmental gradients. Our findings demonstrate generalized ecological strategies in mountain systems and highlight the extreme vulnerability of alpine endemics to ongoing climate change.
Qin Li, Kai-Ning Hu, Ji Wang et al.· Molecular Ecology· 0 citations
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