Nigel P. Barker

Bio: Nigel P. Barker is an academic researcher from University of Pretoria. The author has contributed to research in topics: Endemism & Monophyly. The author has an hindex of 36, co-authored 159 publications receiving 5084 citations. Previous affiliations of Nigel P. Barker include Rhodes University & University of Cape Town.

Phylogeny and subfamilial classification of the grasses (Poaceae)

Abstract: A large collaborative effort has yiel(led a comprehensive study of the phylogeny and a new suhfanilial classification of the grass family (Poaceae/Graminieae). The stu(ly was (con(luc(ted on an integratedl andl representative set of 62 grasses (0.6% of the species and ca. 8% of the genera) plus four outgroup taxa using six molecular sequence (lata sets ({ndhFl, rbcL, rpoC2, phyB, ITS2, and (;BSSI or waxy), chloroplast restriction site (lata, and( morphological idata. A parsimony analysis using 2143 informative characters (the comblined analysis) resulted in a single most parsimonious tree of 8752 steps with an RI of 0.556 and bootstrap support of > 90% for more than half of the internal no(les. Significant relationships that appear consistently in all analyses of all (lata sets and are strongly supported by the combined analysis include the following: Joinvilleaceae are sister to a monophyletic Poaceae; the earliest (liverging lineages of the Poaceae are Anomochlooideae, Pharoideae, and Puelioideae, respectively; and( all remaining grasses form a clade. Multiple monophyletic clades were recovere(, including Bambusoideae s. str., Ehrhartoideae, Pooideae s.l., Aristidoideae, l)anthonioideae, Chloridoideae s. str., Chloridoideae s.l., Panicoideae, Parianeae, Olyreae s. str., Oryzeae, Stipeae, Meliceae, Lygeum + Nardus, and Molinia + Phragmites. 'The PACCAI) Clade is monophyletic, containing Aristidoideae, Danthonioideae, Arundinoideae s. str., Chloridoideae s.l., Centothecoideae, Panicoideae, Eriachne, Micraira, and Gynerium. Based on the phylogeny, a classification of 11 previously published subfamilies (Anomochlooideae, Pharoideae, Puelioideae, Bambusoideae, Ehrhartoideae, Pooideae, Aristidoideae, Arundinoideae, Chloridoideae, Centothecoideae, and Panicoideae) and 1 new subfamily (Danthonioideae) is proposed. Several changes in the circumscription of traditionally recognized subfamilies are included. Previous phylogenetic work and classifications are reviewed in relation to this classification and circumscription, and major characteristics of each subfamily are discussed and described. The matrix, trees, and updated data matrix are available at (http://www.virtualherbarium.org/grass/gpwg/ default.htm).

Contrasted patterns of hyperdiversification in Mediterranean hotspots.

Abstract: Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.

A review of marine phylogeography in southern Africa

Abstract: The southern African marine realm is located at the transition zone between the Atlantic and Indo-Pacific biomes. Its biodiversity is particularly rich and comprises faunal and floral elements from the two major oceanic regions, as well as a large number of endemics. Within this realm, strikingly different biota occur in close geographic proximity to each other, and many of the species with distributions spanning two or more of the region’s marine biogeographic provinces are divided into evolutionary units that can often only be distinguished on the basis of genetic data. In this review, we describe the state of marine phylogeography in southern Africa, that is, the study of evolutionary relationships at the species level, or amongst closely related species, in relation to the region’s marine environment. We focus particularly on coastal phylogeography, where much progress has recently been made in identifying phylogeographic breaks and explaining how they originated and are maintained. We also highlight numerous shortcomings that should be addressed in the near future. These include: the limited data available for commercially important organisms, particularly offshore species; the paucity of oceanographic data for nearshore areas; a dearth of studies based on multilocus data; and the fact that studying the role of diversifying selection in speciation has been limited to physiological approaches to the exclusion of genetics. It is becoming apparent that the southern African marine realm is one of the world’s most interesting environments in which to study the evolutionary processes that shape not only regional, but also global patterns of marine biodiversity.

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

Abstract: The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

Genome sequencing and analysis of the model grass Brachypodium distachyon

Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

Genome sequencing and analysis of themodel grass Brachypodium distachyon

Abstract: Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.