SAJB-00967; No of Pages 9 South African Journal of Botany xxx (2013) xxx–xxx Contents lists available at ScienceDirect South African Journal of Botany journal homepage: www.elsevier.com/locate/sajb Towards a new classification of Leguminosae: Naming clades using non-Linnaean phylogenetic nomenclature Martin F. Wojciechowski ⁎ School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA article info abstract Available online xxxx The past three decades of research have greatly advanced our understanding of phylogenetic relationships in the family Leguminosae. It has become clear in recent years that our classification system is in need of signif- Edited by B-E Van Wyk icant updating if it is to reflect our current understanding of the phylogeny of the family and facilitate effec- tive communication of that knowledge. The goal of this paper is to suggest a set of guidelines for formally Keywords: defining and naming clades, which draws on many of the recommendations embodied in the draft Interna- Phylogenetic nomenclature tional Code of Phylogenetic Nomenclature or “PhyloCode”. I provide specific examples of phylogenetic no- Papilionoids Clade definitions menclature applied to several well recognized and well-supported, informally named papilionoid clades to serve as a model for standardizing legume clade names by the legume community in the future. For the most part the clades named here are below subfamily and above tribal ranks in the Linnaean system. It is my contention that a new Linnaean classification, designed to reflect phylogeny, and a clade-based system of phylogenetic nomenclature are mutually complementary approaches to achieving a new classification of the legume family. © 2013 SAAB. Published by Elsevier B.V. All rights reserved. 1. Introduction legume phylogeny and classification in a more collaborative manner (LPWG, 2013a). As eloquently described by Doyle (in this issue) and LPWG (in this Towards a new classification system for legumes” was the theme issue), the modern era of legume systematics had its origins in the of the Sixth International Legume Conference (ILC6) held at the Uni- landmark series Advances in Legume Systematics, with the publication versity of Johannesburg, in South Africa, January 2013. While signifi- of the first volume edited by Roger M. Polhill and Peter H. Raven cant challenges remain to achieve a comprehensive revision of the in 1981. The intervening 30 years have been especially productive current Linnaean classification (Polhill and Raven, 1981; Polhill, ones for many areas of legume biology, and systematics, in particular, 1994; Lewis et al., 2005; LPWG, 2013a, in this issue), the desire on has made tremendous advances. We are now in a new era of legume the part of the delegates to ILC6 for a new phylogenetically-based systematics, symbolized by the publication of the Legumes of the classification was clearly evident. However, as always the case with World (Lewis et al., 2005), which summarizes the biogeography, phy- contentious or difficult issues, the “devil is in the details”. What was logenetic relationships, and the taxonomy of the family in light of two also clear from discussions at the meeting was that whatever the decades of investigation that have seen a revolution in the kinds and shape of a new Linnaean classification, it will not name and accom- amounts of data coupled with an important conceptual shift in our modate all well-supported clades that merit inclusion, not least be- approaches to inferring evolutionary relationships (e.g., their Fig. 1), cause insufficient ranks exist to accommodate them all, but also and the publication of the first paper authored by the Legume Phylog- because of the requirement under the Linnaean system to name all eny Working Group or “LPWG”, an international coalition of re- taxa at equivalent rank. Nevertheless, clades exist in nature, and searchers working together to tackle the important challenges in knowledge of their relationships and overall place in the phylogeny of the family can be important for accurate communication about le- gumes. It is my contention, and one that is shared with others, that any new Linnaean classification of legumes, even one that names only monophyletic groups, and an approach that formally defines clades and their overall relationship outside of the traditional Linnae- an framework are not mutually exclusive endeavors, but rather, com- ⁎ Tel.: +1 1 480 727 7767. plementary, and should be utilized together to develop a new legume E-mail address: [email protected]. classification. 0254-6299/$ – see front matter © 2013 SAAB. Published by Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.sajb.2013.06.017 Please cite this article as: Wojciechowski, M.F., Towards a new classification of Leguminosae: Naming clades using non-Linnaean phylogenetic nomenclature, South African Journal of Botany (2013), http://dx.doi.org/10.1016/j.sajb.2013.06.017 2 M.F. Wojciechowski / South African Journal of Botany xxx (2013) xxx–xxx Thus, it is important to emphasize that the goal of this discussion 2007: Fig. 1). Although these general categories of clades represent paper is not to establish a clade-based classification system for le- convenient ways of partitioning a nested series of clades, they are gumes that is a competitor to a new, more phylogenetically-based not as useful for defining clades as those based on patterns of survival Linnaean system (e.g., LPWG, in this issue). Rather, my goal here is of lineages to the present time, specifically crown clades and total to outline an approach by which clades can be formally defined so clades (de Queiroz, 2007), as discussed below. as to be incorporated into a new, phylogeny-based Linnaean classifi- Phylogenetic nomenclature has certain advantages over the Lin- cation or a rank-free phylogenetic classification depending on the in- naean system. Under the traditional nomenclatural codes, such as terests of the systematics community. First, I will briefly explain the the ICBN, taxa that are not explicitly associated with a rank cannot concept of phylogenetic nomenclature (e.g., de Queiroz and be formally named. Because phylogenetic nomenclature lacks obliga- Gauthier, 1990, 1992, 1994) and a rationale for using such an ap- tory ranks, taxa can be named without reference to a rank, and there proach to naming clades for use in phylogeny-based classifications. I is essentially no limit to the number of nested clades to which names then review the use of informal names applied to groups in legume can be applied. Furthermore, not only can phylogenetic nomenclature systematics, and how they have been defined (or not). Lastly, I pro- be used in the context of either a rank-based or rank-free classifica- pose guidelines for a formalized approach to naming and defining tion, it does not exclude taxa of known Linnaean rank(s) from inclu- clades in legumes that is based on many of the recommendations of sion in a classification (de Queiroz, 2006). the draft International Code of Phylogenetic Nomenclature (ICPN; Nomenclature can be troubled by ambiguity and inconsistency in Cantino and de Queiroz, 2010). In view of the recognition and repeat- the application of names, such that the same name may have been ap- ed occurrence of a number of strongly-supported legume clades in plied to different groups (monophyletic or non-monophyletic) in dif- many studies, I believe now is an appropriate time to provide formal ferent classifications, which leads to confusion (e.g., de Queiroz and phylogenetic definitions for several of these clades. My hope is that Gauthier, 1994). This can result from the application of priority at a this exercise will serve as a useful model for other legume researchers given rank in traditional rank-based systems or application of the to consider for future naming of clades in their groups of interest, and same name to a different group by different authors. The latter situa- in a manner that aims to bring some standardization to clade names tion has been observed in the use of clade names in the legume liter- that will serve the greater community. ature, for example the definition and membership of the “Robinioid” clade (cf. Lavin et al., 2003 and Wojciechowski et al., 2004). Clearly, 2. Concepts of phylogenetic nomenclature these problems can occur in both rank-based and phylogeny-based nomenclature systems, but one of the most important contributions Biological nomenclature, which is concerned with the naming of offered by phylogenetic nomenclature – linking names explicitly to taxa and the application of taxon names (both existing and newly a particular node, branch or apomorphy – is the potential for greater proposed), is governed by international codes (e.g., the International precision in the application of names, which can promote greater Code of Zoological Nomenclature, Ride et al., 1999; the International clarity in communications about phylogeny (Cantino et al., 2007). Code of Nomenclature for Algae, Fungi and Plants, McNeill et al., Phylogenetic nomenclature is currently not governed by any 2012). These codes, based on the Linnaean system (e.g., Linnaeus, existing code. However, the International Code of Phylogenetic No- 1758), typically require the use of categorical ranks for taxa, many menclature (ICPN) or “PhyloCode” (Cantino and de Queiroz, 2010) of which are mandatory, and the designation of a type specimen, is in development, and is intended to regulate it once it is formally and diagnosis, of an organism to define that taxon, essentially defin- established. Unlike other codes, the ICPN establishes a set of princi- ing taxa and thus their names in the context of taxonomic ranks. ples, recommendations, and rules for nomenclature designed to gov- Under the Linnaean system, taxa that are not explicitly associated ern the names of clades rather than those of ranked groups, which with a rank cannot be formally named, and there is also the require- may or may not correspond to clades (Cantino and de Queiroz, ment to name all taxa at equivalent ranks.