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Molecular Phylogenetics and Evolution 53 (2009) 881–890

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Molecular Phylogenetics and Evolution
journal homepage: www.elsevier.com/locate/ympev

The utility of nuclear conserved ortholog set II (COSII) genomic regions for species-level phylogenetic inference in Lycium (Solanaceae)
Rachel A. Levin *, Andrew Whelan, Jill S. Miller
Department ofBiology, McGuire Life Sciences Building, Amherst College, Amherst, MA 01002, USA

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The identification of genomic regions with sufficient variation to elucidate fine-scale relationships among closely related species is a major goal of phylogenetic systematics. However, the accumulation of such multi-locus data sets brings its own challenges, given that genetrees do not necessarily represent the true species tree. Using genomic tools developed for Solanum (Solanaceae), we have evaluated the utility of nuclear conserved ortholog set II (COSII) regions for phylogenetic inference in tribe Lycieae (Solanaceae). Five COSII regions, with intronic contents ranging from 68% to 91%, were sequenced in 10 species. Their phylogenetic utility was assessed andcompared with data from more commonly used nuclear (GBSSI, nrITS) and cpDNA spacer data. We compared the effectiveness of a traditional total evidence concatenation approach versus the recently developed Bayesian estimation of species trees (BEST) method to infer species trees given multiple independent gene trees. All of the sampled COSII regions had high numbers of parsimony-informative (PI)characters, and two of the COSII regions had more PI characters than the GBSSI, ITS, and cpDNA spacer data sets combined. COSII markers are a promising new tool for phylogenetic inference in Solanaceae, and should be explored in related groups. Both the concatenation and BEST approaches yielded similar topologies; however, when multiple individuals with polyphyletic alleles were included, BEST wasclearly the more robust approach for inferring species trees in the presence of gene tree incongruence. Ó 2009 Elsevier Inc. All rights reserved.

Article history: Received 9 December 2008 Revised 24 June 2009 Accepted 13 August 2009 Available online 19 August 2009 Keywords: Bayesian estimation of species trees (BEST) Concatenation COSII Fine-scale relationships GBSSI Gene trees HybridizationIncongruence ITS Lycium Multi-locus Phylogeny Species trees Solanaceae

1. Introduction Although DNA sequence data have allowed for major advances in plant systematics, there remains a considerable challenge to identify regions with sufficient variation to differentiate closely related species. Recently there has been much progress in the identification of rapidly evolving cpDNA regions (Shaw et al.,2005, 2007), with many of these regions advocated for use in DNA barcoding (Kress and Erickson, 2007; Lahaye et al., 2008). In addition, considerable efforts have been made in the identification of low copy nuclear regions that are useful for phylogenetic inference (reviewed by Sang, 2002; Small et al., 2004; see also Cronn et al., 2002; Howarth and Baum, 2002; Wu et al., 2006; Chapman et al., 2007;Álvarez et al., 2008; Li et al., 2008; Steele et al., 2008; Yuan and Olmstead, 2008). Despite recent advances in the development of phylogenetic markers for plant systematics, it has become clear that no single gene region is the answer; rather, studies have emphasized the importance of the combined use of large numbers
* Corresponding author. Fax: +1 413 542 7955. E-mail address: rlevin@amherst.edu(R.A. Levin). 1055-7903/$ - see front matter Ó 2009 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2009.08.016

of orthologous sequences for robust phylogenetic inference (Cronn et al., 2002; Sang, 2002; Rokas et al., 2003; Small et al., 2004). Although sequence data from multiple loci may result in robust topologies, each locus has its own genetic history, which may result in...