Introduction

Chromosome evolution is one of the most important drivers of biodiversity (Stebbins, 1950; Butlin, 2005; Ayala & Coluzzi, 2005; Hoffmann & Rieseberg, 2008). Chromosomal rearrangements are often associated with speciation (Rieseberg, 2001), as they have the potential to reduce gene flow between diverging populations (Grant, 1963). In angiosperms, karyotypic diversity is significantly associated with both clade species richness and diversification rates, which suggests chromosomal rearrangements promote or reinforce the speciation process (Carta & Escudero, 2023). Much research into chromosome evolution in plants has focused on the physiological and ecological implications of polyploidy (e.g. Otto & Whitton, 2000; Otto, 2007), while the evolutionary consequences of dysploidy have received comparatively much less attention (Escudero et al., 2014).
Speciation mediated by chromosome evolution has been explained by two models. First, the hybrid-dysfunction model of chromosomal speciation presumes reduced fitness of hybrids between chromosome races. This model is undermined by the fact that strong selection against structural heterozygotes (underdominance) would make new cytotypes extremely difficult to succeed, meaning that underdominant mutations are not likely to cause speciation (Coyne & Orr, 2004). The alternative model, the suppressed recombination model of chromosomal speciation is better supported theoretically as it does not involve underdominance. In this case, chromosomal rearrangements promote divergence between populations by preventing recombination in clusters of locally coadapted gene complexes (supergenes; Schwander et al., 2014; Black & Shuker, 2019). These rearrangements may facilitate species divergence even in the presence of ongoing gene flow between chromosomatically differentiated populations (Navarro & Barton, 2003; Ortiz-Barrientos et al., 2002; Noor et al., 2001; Lowry & Willis, 2010).
In holocentric chromosomes, centromeric regions are distributed along the entire length of the chromosome, which may therefore attach to microtubules during mitosis and meiosis (Márquez-Corro et al., 2019a). In contrast, monocentric chromosomes have microtubule attachments localized exclusively in a single centromeric region. Holocentric chromosome organization has been described for ca. 20 lineages in three of the six kingdoms in the domain Eukarya (the Eukaryotes): plants (angiosperms and green algae); animals (at least six species-rich arthropod clades, plus velvet worms and nematodes); and Rhizaria (Escudero et al., 2016; Márquez-Corro et al., 2018). As a consequence, approximately, ca. 20% of all Eukaryotes have holocentric chromosomes (Márquez-Corro et al., 2018). The evolutionary implications of holocentricity are potentially profound but largely misunderstood. Because of these special features of holocentric chromosomes, they have been suggested as ideal systems to test the proposed models of chromosomal speciation (Lucek et al., 2022).
Chromosome fragments from fissions that would be lost in monocentric chromosomes may be inherited and become fixed in organisms with holocentric chromosomes (Márquez-Corro et al., 2019a). Likewise, enlarged chromosomes from fusion events can align and segregate correctly in holocentric chromosomes. Conversely, in organisms with monocentric chromosomes fusions usually result in the formation of dicentric chromosomes that fail to segregate properly (Márquez-Corro et al., 2019a). Consequently, large series of chromosome numbers and high rates of karyotype evolution are found in holocentric lineages (i.e. , butterflies and moths –Lepidoptera– 2n = 10 to 250, sedges –Cyperaceae– 2n = 4 to 226; de Vos et al. 2020; Márquez-Corro et al., 2019b, 2021). In Lepidoptera, phylogenetic comparative evidence suggests that chromosome fission and fusion drive cladogenesis (de Vos et al. 2020; Augustijnen et al., 2023). In the sedge genus Carex (Cyperaceae), chromosome rearrangements contribute to genetic diversity within species (Hipp et al., 2010; Escudero et al., 2013a) and the karyotype diversity is positively associated with the time of coalescence of the species (Escudero et al., 2010). Finally, chromosome number changes from fission and fusion are related to linkage groups and, in holocentrics, they also determine recombination rates as the number of chiasmata during meiosis is directly proportional to chromosome number (Nokkala et al., 2004). As a consequence, linkage groups and recombination rates (chromosome numbers) have been positively associated with adaptive speciation towards different environmental conditions in holocentric sedges (Escudero et al., 2012, 2013b; Spalink et al., 2018; Márquez-Corro et al., 2021). Some of the patterns of chromosome number association with environmental conditions are rather weak at the macroevolutionary level (Escudero et al., 2012; Spalink et al., 2018; Márquez-Corro et al., 2021), probably based on the fact that chromosome evolution is much faster than speciation rates in sedges (Márquez-Corro et al., 2021).
We hypothesize that holocentric chromosomes may be playing an important role in species’ ability to adapt and colonize new environments. Therefore, having a direct impact on niche expansion for some of the most widespread species of the study group. Karyotype rearrangements may leave a traceable signature in the different individuals’ genomes, probably linked to specific loci in the linkage groups. Landscape genomics constitutes a currently developing approach that may help to identify specific genetic markers, including chromosome number variation, associated with environmental variables and therefore involved in local adaptation processes (Rellstab et al., 2015; Hoban et al, 2016; Ahrens et al., 2018). To our knowledge, no study using landscape genomics has addressed this topic in organisms with holocentric chromosomes.
The goals of this study are: (i) to infer patterns of holocentric chromosome evolution at phylogeography scale in a lineage of four closely related and recently diversified Carex species, (ii) to identify genomic signatures of adaptive evolution and investigate the associations between chromosome numbers and local environmental conditions, (iii) to elucidate the role of cytogenetic evolution on the diversification of the group and specifically the model of chromosomal speciation.