jabbrv-ltwa-all.ldf jabbrv-ltwa-en.ldf Adaptation to different environments in geographically separated populations is key for allopatric speciation. Most research has focused on the effects of geographical isolation and abiotic factors, but disjunct populations frequently co-occur with different pools species, favouring divergent adaptation and speciation. We show the importance of plant neighbourhood, compared to geographic and environmental factors, in the allopatric speciation across the Iberian Peninsula of two closely related plants, Carex elata and Carex reuteriana. Using regularized generalized linear models, we identified the key variables explaining distribution patterns. We also examined the relationships between inter-population genetic distances, using genomic data (genotyping-by-sequencing), and biotic, abiotic and geographic factors to understand the drivers of lineage splitting. Plant neighbourhood emerged as a stronger predictor of allopatric distributions than abiotic or geographic factors. Additionally, inter-population genetic distances were significantly associated with all the factors studied, albeit with varying degrees of influence. Notably, plant neighbourhood had the largest effect in C. elata, which showed the greatest population differentiation. These findings suggest that the biotic and microenvironmental factors influencing divergent plant neighbourhoods have significantly contributed to the differentiation of these taxa, providing new insights into the evolutionary processes shaping the origin and distribution of species.

Geographic isolation and chromosome evolution are two of the major drivers of diversification in eukaryotes in general, and specifically, in plants. On one hand, range shifts induced by Pleistocene glacial oscillations deeply shaped the evolutionary trajectories of species in the Northern Hemisphere. On the other hand, karyotype variability within species or species complexes may have adaptive potential as different karyotypes may represent different recombination rates and linkage groups that may be associated with locally adapted genes or supergenes. Organisms with holocentric chromosomes are ideal to study the link between local adaptation and chromosome evolution, due to their high cytogenetic variability, especially when it seems to be related to environmental variation. Here, we integrate the study of the phylogeography, chromosomal evolution and ecological requirements of a plant species complex distributed in the Western Euro-Mediterranean region (Carex gr. laevigata, Cyperaceae). We aim to clarify the relative influence of these factors on population differentiation and ultimately on speciation. We obtained a well-resolved RADseq phylogeny that sheds light on the phylogeographic patterns of molecular and chromosome number variation, which are compatible with south-to-north postglacial migration. In addition, landscape genomics analyses identified candidate loci for local adaptation, and also strong significant associations between the karyotype and the environment. We conclude that karyotype distribution in C. gr. laevigata has been constrained by both range shift dynamics and local adaptation. Our study demonstrates that chromosome evolution may be responsible, at least partially, for microevolutionary patterns of population differentiation and adaptation in Carex.

Holocentric organisms, unlike typical monocentric organisms, have kinetochore activity distributed along almost the whole length of the chromosome. Because of this, chromosomal rearrangements through fission and fusion are more likely to become fixed in holocentric species, which may account for their extraordinary rates of chromosome evolution. Genome synteny has been reported to be conserved in animals with holocentric chromosomes despite high rates of chromosome rearrangements. Comparing genomes of Carex species and a genome of a distantly related Cyperaceae we have characterised conserved vs. rearranged genome regions across pairs of species that range in time since divergence between 2 and 50 million years. We have compared a C. scoparia genome with a linkage map of the same species to study rearrangements at a population level and suppression of recombination patterns. We found a surprisingly conserved genome synteny even between very distantly related species and extraordinarily high rates of chromosome evolution in genus Carex. Comparing the distribution of repetitive DNA and gene density between conserved and rearranged genomic regions, we found repetitive DNA to be related to holocentromeres and as well as rearranged regions of the genome. This evidence of extremely conserved synteny in sedges and the massive events of chromosome fission and fusion found across the evolution of genus Carex suggests the presence of common genomic hotspots of chromosome evolution related to repetitive DNA.