Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene?

Manuel Pimentel,Elvira Sahuquillo,Marcial Escudero,Pilar Catalán,Miguel Ángel Minaya

doi:10.7717/peerj.3815

Abstract

The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.

Highlights

A combination of phylogenetic inference and cytological and taxonomic diversity information is commonly used to investigate the tempo and mode of diversification and the impact of chromosome changes in diversity (e.g., Escudero et al, 2012)
Our aims were to: (i) analyze the diversification dynamics of the Pooideae, including the timing of divergence and the diversification rates of its main lineages; (ii) investigate the patterns of evolution of chromosomal changes operating in the core pooids, and (iii) assess the possible correlation between times of divergence, diversification rates and patterns of chromosome evolution of the main Pooideae lineages with major climatic and biome changes that occurred on Earth throughout the Cenozoic
Bayesian phylogenetic trees from the different cpDNA data sets were congruent in topology, trees based on coding regions recovered higher posterior probability values

Summary

Introduction

A combination of phylogenetic inference and cytological and taxonomic diversity information is commonly used to investigate the tempo and mode of diversification and the impact of chromosome changes in diversity (e.g., Escudero et al, 2012). This date predates that of the bursting diversification of grasses that took place in the Oligocene-Miocene resulting in the adaptation of the Pooideae to open habitats (Bouchenak-Khelladi et al, 2010), and could explain the current extraordinarily small diversity of these two monotypic tribes, adapted to opposite ecological conditions (moist habitats Nardeae, aridic saline-soil habitats Lygeae) Another shift (an increase in the rate) was detected for the Meliceae + Stipeae In BAMM analysis—with speciation rates allowed to change within regimes-, we found a shift in diversification rates in the clade of tribe Brachyelytreae but this was not detected in MEDUSA analyses

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