Abstract Detail

Systematics Section/ASPT

Waterway, Marcia [1], Bruhl, Jeremy [2], Gehrke, Berit [3], Hipp, Andrew [4], Hoshino, Takuji [5], Ji, Wenli [6], Jin, Xiao-Feng [7], Luceño, Modesto [8], Masaki, Tomomi [5], Phulphong, Kamolhathai [9], Simpson, David [10], Wilson, Karen [11], Zhang, Shuren [12].

Testing the effect of taxon density and differential DNA sequence sampling on phylogenetic inference using a new 9-gene backbone tree for Carex (Cyperaceae).

Carex (tribe Cariceae, Cyperaceae) is species-rich, widely distributed, and found in a variety of habitats. It forms a monophyletic group of more than 2000 species with the inclusion of segregate genera Cymophyllus, Kobresia, Schoenoxiphium, and Uncinia. We developed a 9-gene by 220 taxon data matrix with less than 8% missing data to explore phylogenetic relationships within this clade and to test the effects of taxon density and of choice and number of DNA regions on phylogenetic inference. Using phylogenetic trees based on two or three genes for more than 650 species, we chose exemplar species to give broad and more or less proportional representation across the Cariceae clade with species drawn from six continents, all segregate genera, and all subgenera of Carex. Six outgroup species representing tribes Scirpeae s. str. and Dulichiae, which are most closely related to tribe Cariceae, completed the data matrix. Both internal and external nuclear ribosomal gene spacers, as well as seven plastid DNA regions, including introns, intergenic spacers, and barcoding genes matK and rbcL were included in the matrix for a total of more than 8000 aligned base pairs. Bayesian, maximum likelihood and parsimony analyses gave similar results. This backbone tree was well resolved with good to excellent support for major clades recovered in previous studies, but better support for relationships among the clades. We use this backbone tree to compare phylogenetic hypotheses generated from the ribosomal spacers only, from plastid DNA only, and from the barcoding genes only, to assess congruence and to demonstrate the effects of increased gene sampling. We use examples of data sets with fewer genes but higher taxon density for particular species groups (Carex sections Hymenochlaenae, Racemosae, and subgenus Vigneastra) to demonstrate the value of using a backbone tree as context for phylogenetic inference in a large diverse group like Carex. Analyzing each species group without the backbone tree can result in misleading sister-group relationships and give impressions of strong support for monophyly of groups that are clearly not monophyletic in a broader sampling of species. These results highlight the importance of a global perspective on phylogenetic inference for large, nearly cosmopolitan genera.

1 - McGill University, Plant Science-Macdonald Campus, 21,111 Lakeshore, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
2 - University Of New England, Botany Department, N.C.W. Beadle Herbarium, Armidale, N/A, 2351, Australia
3 - Johannes Gutenberg Universitat, Institut fur Spezielle Botanik und Botanisher Garten, Mainz, 55099, Germany
4 - The Morton Arboretum, Herbarium, 4100 Illinois Route 53, Lisle, IL, 60532-1293, USA
5 - Okayama University of Science, Biosphere-Geosphere Science, Ridai-cho 1-1, Kita-ku, Okayama-shi, Okayama, 700-0005, Japan
6 - Northwest A & F University, College of Forestry, Yangling, Shaanxi, P.R. China
7 - Hangzhou Normal University, Life and Environmental Science, 16. Xuelin St., Hangzhou, Zhejiang, 310036, P.R. China
8 - Pablo de Olavide University, Molecular Biology and Biochemical Engineering, Carretera de Utrera km 1 sn, Seville, 41013, Spain
9 - Mahasarakham University, Biology, Mueang Maha Sarakham District, Maha Sarakham, 44150, Thailand
10 - Royal Botanic Gardens, Kew, Herbarium, Richmond, Surry, TW9 3AB, UK
11 - Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, N/A, NSW 2000, Australia
12 - Institute of Botany, Chinese Academy of Sciences, State Key Laboratory of Systematic & Evolutionary Biology, Xiangshan, Beijing, 100093, P.R. China

Keywords:
Carex
Cyperaceae
Phylogeny
molecular systematics
taxon density.

Presentation Type: Oral Paper:Papers for Sections
Session: 13
Location: Pines South/Boise Centre
Date: Monday, July 28th, 2014
Time: 2:00 PM
Number: 13003
Abstract ID:745
Candidate for Awards:None