Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and implications for morphological evolution Galina V. Degtjareva a,⇑ , Carmen M. Valiejo-Roman b , Tahir H. Samigullin b , Miguel Guara-Requena c , Dmitry D. Sokoloff d a Botanical Garden, Biological Faculty, Moscow State University, Moscow 119991, Russia b A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119991, Russia c Departament de Botànica, Facultat de Ciències Biològiques, Universitat de València, Avda. Dr. Moliner, 50, E-46100 Burjassot, València, Spain d Department of Higher Plants, Biological Faculty, Moscow State University, Moscow 119991, Russia article info Article history: Received 3 August 2010 Revised 14 November 2011 Accepted 15 November 2011 Available online 27 November 2011 Keywords: Molecular phylogeny Topological incongruence ITS Plastid DNA Morphology Anthyllis abstract Phylogenetic relationships in the genus Anthyllis (Leguminosae: Papilionoideae: Loteae) were investi- gated using data from the nuclear ribosomal internal transcribed spacer regions (ITS) and three plastid regions (psbA–trnH intergenic spacer, petB–petD region and rps16 intron). Bayesian and maximum parsi- mony (MP) analysis of a concatenated plastid dataset recovered well-resolved trees that are topologically similar, with many clades supported by unique indels. MP and Bayesian analyses of the ITS sequence data recovered trees that have several well-supported topological differences, both among analyses, and to trees inferred from the plastid data. The most substantial of these concerns A. vulneraria and A. lemanni- ana, whose placement in the parsimony analysis of the ITS data appears to be due to a strong long-branch effect. Analysis of the secondary structure of the ITS1 spacer showed a strong bias towards transitions in A. vulneraria and A. lemanniana, many of which were also characteristic of certain outgroup taxa. This may contribute to the conflicting placement of this clade in the MP tree for the ITS data. Additional conflicts between the plastid and ITS trees were more taxonomically focused. These differences may reflect the occurrence of reticulate evolution between closely related species, including a possible hybrid origin for A. hystrix. The patterns of incongruence between the plastid and the ITS data seem to correlate with taxon ranks. All of our phylogenetic analyses supported the monophyly of Anthyllis (incl. Hymenocarpos). Although they are often taxonomically associated with Anthyllis, the genera Dorycnopsis and Tripodion are shown here to be more closely related to other genera of Loteae. We infer up to six major clades in Anthyl- lis that are morphologically well-characterized, and which could be recognized as sections. Four of these agree with various morphology-based classifications, while the other two are novel. We reconstruct the evolution of several morphological characteristics found only in Anthyllis or tribe Loteae. Some of these characters support major clades, while others show evidence of homoplasy within Anthyllis. Ó 2011 Elsevier Inc. All rights reserved. 1. Introduction Anthyllis is a medium-sized genus of legumes (tribe Loteae of subfamily Papilionoideae, Leguminosae) whose taxonomy is highly disputed. Comprehensive studies that consider both plastid and nuclear makers are lacking for the genus. Our aim in the present paper is to fill this gap and to explore the evolution of several key morphological characters. This is the first phylogenetic study of Anthyllis that covers all currently recognized species, and the first to include evidence from plastid markers. In this paper we compare tree topologies inferred from maximum parsimony (MP) and model-based (Bayesian) analyses. We highlight the presence of a long branch effect in MP analysis of nuclear ribosomal ITS data and the absence of such an effect in the plastid dataset. 1.1. Outline of the tribe Loteae As currently circumscribed (Polhill, 1994; Allan et al., 2003; Sokoloff, 2003a; Sokoloff and Lock, 2005), the papilionoid tribe Lo- teae contains ca. 265 species that are mostly herbs to dwarf shrubs, with major centers of diversity in the Mediterranean region, Cali- fornia and Macaronesia. Traditionally, these plants have been seg- regated into two tribes, Loteae s.str. (with non-lomentaceous fruits) and Coronilleae (lomentaceous fruits). Both morphological and molecular data show clearly that the taxa with lomentaceous 1055-7903/$ - see front matter Ó 2011 Elsevier Inc. All rights reserved. doi:10.1016/j.ympev.2011.11.010 ⇑ Corresponding author. Fax: +7 495 939 3181. E-mail address: degavi@genebee.msu.su (G.V. Degtjareva). Molecular Phylogenetics and Evolution 62 (2012) 693–707 Contents lists available at SciVerse ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev