The Roalson Lab

Phylogenetic patterns and processes of diversification in Carex subgenus Vignea (Cyperaceae).

The evolution of chromosome arrangements and genome organization plays a fundamental role in speciation and the diversification of lineages. Large clades with substantial ecological and chromosomal diversity provide an excellent opportunity to understand the pattern of genomic rearrangements and their consequent effects on lineage diversification and species’ ecology. While numerous studies have focused on modification of genome structure associated with speciation or the influence of polyploidy on diversification , there has been no detailed phylogenetic comparative study of chromosome and genome evolution in a large, densely sampled clade.

Carex is the largest genus in the angiosperm order Cyperales, a clade that has undergone one of the highest rates of diversification among angiosperms. This clade, composed of the sedges (Cyperaceae) and rushes (Juncaceae), is marked by holocentric chromosomes, which lack the localized centromeres typical of most organisms. Holocentric chromosomes are fascinating in that fragments resulting from breakages during meiosis or mitosis have the potential to segregate in Mendelian fashion , and artificial hybrids between different euploid chromosome races (e.g., between plants of 2n = 24 and 2n = 26) produce individuals of the median count between the two in the first (F1) generation. They have the potential to evolve rapidly by fission (breakages without duplication) and fusion rather than by reciprocal translocation or duplication . Although intraspecific chromosomal variants are typically not entirely reproductively isolated from one another, chromosome rearrangements nonetheless appear to play a role in rapid lineage diversification by reducing hybridization between divergent populations that come into secondary contact .

Holocentric chromosomes are limited to some members of the Arthropoda ; nematodes, including Caenorhabditis elegans ; a few algae, and several angiosperm clades, including the Juncaceae and Cyperaceae (the Cyperales lineage), Cuscuta subgenus Cuscuta (Cuscutaceae), Chionographis (Melanthiaceae), and Myristica fragrans (Myristicaceae). This chromosomal feature has been described as “…the only striking, derived chromosomal character for angiosperm macrosystematics”. Yet despite the biological implications of holocentry, the coordinated evolution of genomes and chromosome arrangements in organisms with holocentric chromosomes has never been studied, and the only detailed studies of genome structure in holocentric organisms have been in Caenorhabditis elegans and the wood rush Luzula, and a partial linkage map in Colias butterflies.

In this proposal, we request funds to pursue an intensive systematic study of the evolution of chromosome number and genome size in Carex subgenus Vignea (Cyperaceae), utilizing a combination of newly developed nuclear markers and phylogenetic comparative methods to accomplish four goals:

1. Develop a molecular phylogenetic framework for classification of Carex subgenus Vignea. We will use a multigene nuclear / organellar DNA dataset to test whether hybridization and lineage sorting have been a source of incongruence in previous studies based on nrDNA. This work will form the framework for revising the sectional taxonomy of the subgenus, addressing the question of how current classifications compare with phylogenetic estimates and how effectively traditional morphological characters reflect phylogenetic relationships.
2. Collect plants from under-sampled lineages within the subgenus for cytogenetic work and genome size measurements. Fieldwork funded by this project will focus on collecting from lineages in North America, where the subgenus is most diverse, and China, where the subgenus is poorly understood. Additional material from Japan, South America, and Europe will be collected by collaborators or through ongoing projects and research travel already funded. This work will ensure that we have adequate materials for experimental study.
3. Reconstruct the evolution of chromosome number and genome size in Carex subgenus Vignea. This will be the first study designed to address several basic questions about genome evolution in organisms with holocentric chromosomes. Do shifts in chromosome number correlate with shifts in genome size that support or rule out polyploidy? Moreover, do correlations between chromosome number differences and species divergence in allopatry versus sympatry support a role of chromosome number in sedge diversification? These questions are key to understanding the role of chromosome evolution in species diversification and form an important context to ongoing research on the conservation implications of intraspecific gene flow being conducted separately by both PIs.
4. Provide training and outreach in plant systematics. Training in systematics methods—molecular, cytological, statistical, and field work—will be provided to undergraduates at Taylor University, a graduate research assistant at Washington State University, and a postdoctoral researcher at The Morton Arboretum. Outreach activities include incorporation of research results in ongoing field guide projects and teaching endeavors. This outreach and training goal complements the mission and strategic goals of both Washington State University and The Morton Arboretum, both of which feature training and outreach in plant conservation and biology.

Addressing these goals entails gathering several datasets: (1) coding and spacer regions from three rapidly-evolving chloroplast DNA regions; (2) coding and intron regions from putative members of nine nuclear gene families, which we have developed specifically for this project; (3) morphological characters that have been used in defining classification units previously; (4) meiotic chromosome counts; and (5) genome size estimates based on flow-cytometry. These datasets allow us to simultaneously address substantial questions about classification and genome / chromosome evolution within the subgenus and develop molecular tools that will be of use in understanding the genetics and systematics of the remainder of the Cyperaceae.