Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae).

Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain.
New Phytologist (Impact Factor: 6.55). 04/2012; 195(1):237-47. DOI: 10.1111/j.1469-8137.2012.04137.x
Source: PubMed

ABSTRACT • Changes in chromosome number as a result of fission and fusion in holocentrics have direct and immediate effects on the recombination rate. We investigate the support for the classic hypothesis that environmental stability selects for increased recombination rates. • We employed a phylogenetic and cytogenetic data set from one of the most diverse angiosperm genera in the world, which has the largest nonpolyploid chromosome radiation (Carex, Cyperaceae; 2n = 12-124; 2100 spp.). We evaluated alternative Ornstein-Uhlenbeck models of chromosome number adaptation to the environment in an information-theoretic framework. • We found moderate support for a positive influence of lateral inflorescence unit size on chromosome number, which may be selected in a stable environment in which resources for reproductive investment are larger. We found weak support for a positive influence on chromosome number of water-saturated soils and among-month temperature constancy, which would be expected to be negatively select for pioneering species. Chromosome number showed a strong phylogenetic signal. • We argue that our finding of small but significant effects of life history and ecology is compatible with our original hypothesis regarding selection of optima in recombination rates: low recombination rate is optimal when inmediate fitness is required. By contrast, high recombination rate is optimal when stable environments allow for evolutionary innovation.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Determining phylogenetic relationships among very closely related species has remained a challenge for evolutionary biologists due to interlocus phylogenetic discordance and the difficulty of obtaining variable markers. Here, we used a Genotyping-by-Sequencing (GBS) approach to sample a reduced representation genomic data set and infer the phylogeny of seven closely related species in the genus Carex (Cyperaceae). Past attempts to reconstruct phylogenetic relationships among these species produced conflicting and poorly-supported results. We inferred a robust phylogeny based on >3,000 GBS loci and >1,300 SNPs (with a minimum sequence depth within individuals of 10) using maximum likelihood and Bayesian inference. We also tested for historical introgression using the D-statistic test. We compared these analyses with partitioned RAD analysis, which is designed to identify suboptimal trees reflecting secondary phylogenetic signal that may be obscured by the dominant signal in the data. Phylogenetic analyses yielded fully resolved trees with high support. We found two main clades, one grouping Carex scoparia populations and C. waponahkikensis, and a second clade grouping C. longii, C. vexans, C. suberecta and C. albolutescens. We detected marginal significant signals of introgression between C. scoparia and C. suberecta or C. albolutescens, and we rejected a hybrid origin hypothesis for C. waponahkikensis. Our results demonstrate the power of NGS data sets for resolving some of the most difficult phylogenetic challenges where traditional phylogenetic markers have failed.
    Molecular Phylogenetics and Evolution 07/2014; 79. DOI:10.1016/j.ympev.2014.06.026 · 4.02 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Premise of the study: In organisms with holocentric chromosomes like Carex species, chromosome number evolution has been hypothesized to be a result of fission, fusion and/or translocation events. Negative, positive or the absence of correlations have been found between chromosome number and genome size in Carex. Methods: Using the inferred diploid chromosome number and 80 genome size measurements from 26 individuals and 20 populations of Carex gr. laevigata, we have tested the null hypothesis of chromosome number evolution by duplication and deletion of whole chromosomes. Results: Our results show a significant positive correlation between genome size and chromosome number, but the slope of such correlation supports the hypothesis of proliferation and removal of repetitive DNA fragments to explain genome size variation rather than duplication and deletion of whole chromosomes. Conclusions: Our results refine the theory of the holokinetic drive: this mechanism is proposed to facilitate repetitive DNA removal (or any segmental deletion) when smaller homologous chromosomes are preferentially inherited or repetitive DNA proliferation (or any segmental duplication) when larger homologs are preferred. This study sheds light on how karyotype evolution plays an important role in the diversification of the species of the genus Carex.
    American Journal of Botany 01/2015; 122(2). DOI:10.3732/ajb.1400433 · 2.46 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: With approximately 2000 species, tribe Cariceae (Cyperaceae) comprises a morphologically distinctive cosmopolitan clade, with holocentric chromosomes (N = 6 to 56), complex biogeographical patterns, and habitat diversity ranging from rainforests to deserts. Such a remarkable combination of characteristics should make Cariceae an ideal model for studying the evolution of biodiversity, although they also obscure their relationships in Cyperaceae, complicating attempts to identify the contributing factors to diversity of Cariceae. Recent molecular studies place Cariceae in a strongly supported clade consisting of tribes Dulichieae, Scirpeae s.s, and the enigmatic monotypic genus Khaosokia, although relationships in this clade are unresolved. Using the plastid genes matK and ndhF and a greatly improved taxonomic sampling covering 16 of 17 genera and 55% of the species outside Cariceae, our analyses firmly position Dulichieae and Khaosokia (79% and 85% bootstrap support) as successive sisters to a clade consisting of five major lineages (Calliscirpus, Trichophorum + Oreobolopsis + Cypringlea, Cariceae, Scirpus + Eriophorum, and Amphiscirpus + Phylloscirpus + Zameioscirpus), the first four of which receive good to strong support (> 80% bootstrap support). Cariceae are sister to the Trichophorum clade, although topological tests cannot exclude either Calliscirpus or a Scirpus clade + Zameioscirpus clade as sister to the tribe. Trichophorum appears to be paraphyletic and Eriophorum is firmly nested in Scirpus. There appears to be a trend in the increase of chromosome numbers in Scirpus and Eriophorum and a trend in the reduction and proliferation of the inflorescence throughout the major Cariceae-Dulichieae-Scirpeae clades. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, ●●, ●●–●●.
    Botanical Journal of the Linnean Society 09/2014; 176(1). DOI:10.1111/boj.12193 · 2.70 Impact Factor


Available from
May 30, 2014

Similar Publications