Molecular Phylogenetics and Evolution 84 (2015) 266–283 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Multilocus phylogenetic inference in subfamily Chlorogaloideae and related genera of Agavaceae – Informing questions in taxonomy at multiple ranks a, b b c d Jenny K. Archibald ⇑, Susan R. Kephart , Kathryn E. Theiss , Anna L. Petrosky , Theresa M. Culley a Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA b Department of Biology, Willamette University, Salem, OR 97301, USA c Department of Integrative Biology, University of California, Berkeley, CA 94709, USA d Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA article info abstract Article history: A series of taxonomic questions at the subfamilial, generic, and intrageneric levels have remained within Received 21 July 2014 subfamily Chlorogaloideae s.s. (comprising Camassia, Chlorogalum, Hastingsia, and Schoenolirion) and Revised 8 December 2014 relatives in Agavaceae. We present the first phylogenetic hypotheses focused on Chlorogaloideae that Accepted 16 December 2014 are based on multiple independent loci and include a wide sampling of outgroups across Agavaceae. In Available online 10 January 2015 addition to chloroplast regions ndhF and trnL–trnF, we used nrDNA ITS for phylogenetic inference. Incom- plete concerted evolution of the latter is indicated by intra-individual site polymorphisms for nearly half Keywords: of the individuals. Comparisons of four coding and analysis methods for these characters indicate that the Agavaceae region remains phylogenetically informative. Our results confirm that Chlorogaloideae s.s. is not Chlorogaloideae Chlorogalum monophyletic, due to the close relationship of Schoenolirion with Hesperaloe and Hesperoyucca, as well Hesperaloe as the likely sister relationship between Hesperocallis and core Chlorogaloideae (Camassia, Chlorogalum, Hesperocallis and Hastingsia). Chlorogalum is also not monophyletic, being divided with strong support into vespertine ITS and diurnal clades. This study produced the first phylogenetic hypotheses across Hesperaloe, allowing initial tests of several taxonomic disagreements within this genus. Our results reveal the lack of cohesion of H. funifera, indicating that H. funifera ssp. funifera may be more closely related to H. campanulata than to H. funifera ssp. chiangii (=H. chiangii). With potential gene flow between many members of Hesperaloe and a possible hybrid origin for H. campanulata, the genetic relationships within this genus appear complex. Further population-level investigation of many of the taxa in Chlorogaloideae s.l. would benefit our understanding of the evolution and taxonomy of these groups; Camassia and Hastingsia are the current focus of ongoing study. Published by Elsevier Inc. 1. Introduction in Asparagaceae (APG, 2009; Chase et al., 2009). Some members of this family have received significant attention, such as the Although there are groups of plants whose taxonomic limits classic study system of Yucca – yucca moth mutualisms have been clearly and robustly inferred since the time of Linnaeus (Pellmyr, 2003) and economically-relevant taxa (e.g., FNA, 1993+; (e.g., Asteraceae; Funk et al., 2009), lilies and their relatives are Zizumbo-Villarreal et al., 2013). Within Agavaceae, the less well- certainly not among them. Massive family-level rearrangements studied Chlorogaloideae s.l. (Halpin and Fishbein, 2013) provides of Liliaceae s.l. into potentially over 20 families have resulted from many potential avenues for evolutionary studies. This group efforts to discern their evolutionary relationships (e.g., APG, 2003, comprises a diverse assemblage of species that inhabit deserts to 2009; Cronquist, 1981). One challenging family within this wetlands (FNA, 1993+); the distributions of some species cover complex group of plants is Agavaceae, also known as Agavoideae broad regions of the United States while others are narrowly endemic on serpentine soils (Halpin and Fishbein, 2013). These rosette-forming plants vary greatly in morphology. For example, Corresponding author. ⇑ they range in height from 18 to 400 cm (Hochstätter, 2009; E-mail addresses: [email protected] (J.K. Archibald), skephart@willamette. Sherman, 1969; Starr, 1997) and vary in floral shape among tubular, edu (S.R. Kephart), [email protected] (K.E. Theiss), annapetrosky@berkeley. edu (A.L. Petrosky), [email protected] (T.M. Culley). campanulate, and rotate types (zygomorphic and actinomorphic; http://dx.doi.org/10.1016/j.ympev.2014.12.014 1055-7903/Published by Elsevier Inc. J.K. Archibald et al. / Molecular Phylogenetics and Evolution 84 (2015) 266–283 267 FNA, 1993+; Starr, 1997). As in Agavaceae as a whole, Chlorogaloideae Chlorogaloideae s.s. or expanding the subfamily to encompass core includes many plants utilized by humans, such as those used in Chlorogaloideae, Hesperocallis, and the SHH clade. horticulture (e.g., McGary, 2001; Starr, 1997), for pulp and paper The present study focuses on providing some essential missing applications (Sanchez et al., 2011), and as historically important links in our understanding of phylogenetic relationships in these food sources (Mehalchick et al., 2004; Moerman, 1986). genera. The monophyly of four of the seven genera in Chloroga- Chlorogaloideae s.s. (Speta, 1998) has traditionally included loideae s.l. was supported by the phylogeny of Halpin and four genera with up to 18 species and 29 total infrageneric taxa: Fishbein (2013), with three genera remaining unsupported: Hesp- Camassia (camas), Chlorogalum (soap plants), Hastingsia (rush eraloe (not tested), Hesperoyucca (not tested), and Chlorogalum lilies), and Schoenolirion (rush lilies; Fig. 1 and Table 1). The latter (paraphyletic). At the intrageneric level, only the phylogenetic three genera were first recognized as subtribe Chlorogaleae analysis of Halpin and Fishbein (2013) evaluated Chlorogalum (Watson, 1879). This grouping was maintained for nearly and Schoenolirion, although separate chloroplast phylogenies are 100 years, although Engler (1887) added Hemiphylacus and available for Camassia (Fishbein et al., 2010) and Hastingsia included Hastingsia in Schoenolirion within his Chlorogalinae. A link (Halpin, 2011); each tree provided an initial outline of relation- between Camassia and the original three genera of subtribe ships, but with many unanswered questions. A multilocus Chlorogalinae was supported by the cytological and morphological phylogenetic hypothesis for both genera is being developed as study of Schoenolirion by Sherman (1969), who also suggested that part of a separate integrative taxonomic study (S. Kephart, Hemiphylacus be excluded from the subtribe. Later, Speta (1998) J. Archibald, T. Culley, K. Theiss, unpub.). Hesperocallis is officially proposed Chlorogaloideae as one of five subfamilies in monotypic, but the phylogenetic relationships within Hesperaloe Hyacinthaceae. and Hesperoyucca are not well known. Only one or two species Considerable taxonomic fluidity characterizes Chlorogaloideae, in these two genera had been sampled for broad phylogenetic including at the family level. Some genera have been placed in Lil- studies, limiting assessment of relationships across all iaceae (Baker, 1873; Engler, 1887; Watson, 1879), Anthericaceae Chlorogaloideae s.l. prior to our work. (Schulze, 1982), Hyacinthaceae (Batsch, 1786; Dahlgren et al., No previous phylogenetic analyses have focused on relation- 1985; Speta, 1998), Camassiaceae (Cupov, 1994), Chlorogalaceae ships within Hesperaloe, although the ITS phylogeny of Clary (Hoogland and Reveal, 2005), and Agavaceae. The inclusion of (2001) included three of the 6–9 taxa in the genus and strongly Chlorogaloideae in Agavaceae is well supported by phylogenetic supported its monophyly. Hesperaloe has been consistently placed evidence and by their shared bimodal karyotype, i.e., with chromo- in Agavaceae (see FNA, 1993+), with some species formerly recog- somes of two distinct size classes (Cave, 1970; McKain et al., 2012; nized as members of Yucca or Aloe. The exact number and ranks of Sato, 1935). A potential relationship of Chlorogaloideae with Hesp- taxa within Hesperaloe vary depending on the taxonomic treat- eraloe, Hesperocallis, and Hesperoyucca (Fig. 1 and Table 1) is also ment (Hochstätter, 2009; Hochstätter and Martínez-Ávalos, 2010; supported by recent phylogenetic analyses (Halpin, 2011; Halpin Starr, 1997). and Fishbein, 2013). For simplicity, we will refer to these three Hesperoyucca currently encompasses three species (Clary, genera plus the four genera of Chlorogaloideae s.s. as Chlorogaloi- 2001), with Hesperoyucca whipplei being divided into 0–5 infraspe- deae s.l. (following Halpin and Fishbein, 2013, who summarized cific taxa recognized at the variety or subspecies level (e.g., Haines, key aspects of their taxonomic history). 1941; McKinney and Hickman, 1993). Formerly part of Yucca (e.g., Preliminary phylogenetic insights for some members of Chlorog- Bogler et al., 2006; McKelvey, 1938, 1947), the genus is now recog- aloideae s.l. have been provided by several studies. Based on sam- nized as distinct based on morphological, phenological, pollination, pling 1–3 species per genus, both a Camassia – Chlorogalum clade and phylogenetic criteria (Clary, 2001). Bogler et al. (2006) placed and a Hesperaloe – Hesperoyucca clade were supported as members