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Papers by Kelly Steele

with contributions from Stephen Boatwright,10 Gillian Brown,11 Domingos Cardoso,12 Michael Crisp,... more with contributions from Stephen Boatwright,10 Gillian Brown,11 Domingos Cardoso,12 Michael Crisp,13 Ashley Egan,14 Renée H. Fortunato,15 Julie Hawkins,16 Tadashi Kajita,17 Bente Klitgaard,7 Erik Koenen,5 Matt Lavin18, Melissa Luckow,3 Brigitte Marazzi,8 Michelle M. McMahon,19 Joseph T. Miller,20 Daniel J. Murphy,21 Hiroyoshi Ohashi,22 Luciano P. de Queiroz,12 Lourdes Rico,7 Tiina Särkinen,23 Brian Schrire,7 Marcelo F. Simon,24 Elvia R. Souza,12 Kelly Steele,25 Benjamin M. Torke,26 Jan J. Wieringa27 and Ben-Erik van Wyk28

BMC genomics, Mar 27, 2017

Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on... more Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while ex...

Taxon, 2017

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogen... more A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny The Legume Phylogeny Working Group (LPWG) Recommended citation: LPWG (2017) This paper is a product of the Legume Phylogeny Working Group, who discussed, debated and agreed on the classification of the Leguminosae presented here, and are listed in alphabetical order. The text, keys and descriptions were written and compiled by a subset of authors indicated by §. Newly generated matK sequences were provided by a subset of authors indicated by *. All listed authors commented on and approved the final manuscript.

American journal of botany, 2015

Cacti are conspicuous elements of the arid and semiarid succulent biome in the New World (Hern á ... more Cacti are conspicuous elements of the arid and semiarid succulent biome in the New World (Hern á ndez-Hern á ndez et al., 2014). Recent studies have elucidated many details of the timing and tempo of their diversifi cation (Arakaki et al., 2011 ; Hern á ndez-Hern á ndez et al., 2011 , 2014), their role in ecological interactions of arid ecosystems (Fleming et al., 2001 ; Bustamante et al., 2010), and diversifi cation of associated species, such as cactophilic insects (Pfeiler and Markow, 2011). Molecular phylogenetic work has narrowed their position within the angiosperm clade Caryophyllales to a diverse subclade, Portulacineae (Nyff eler and Eggli, 2010), which also includes the remnants of the former Portulacaceae and the Madagascan succulent radiation Didiereaceae (Nyff eler, 2007 ; Arakaki et al., 2011). Multigene taxon-rich molecular phylogenies within cacti have established the monophyly of and many detailed relationship within two diverse subclades, Cactoideae and Opuntioideae, embedded within a paraphyletic assemblage of the tropical genus

Genome size in flowering plants has been correlated with various aspects of life history, rarity ... more Genome size in flowering plants has been correlated with various aspects of life history, rarity and geographic distribution. To consider these hypotheses in the genus Medicago we obtained genome size estimates for 49 species (over half of the species in the genus) representing all major lineages using standard methods of flow cytometry performed on a FACSCalibur flow cytometer. Glycine max ‘Polanka’ with an estimated genome size of 2.5 pg was used as the primary standard, and Medicago truncatula Jemalong, with an estimated genome size of 1.15 pg, was used for species with a genome size close to that of Glycine. Genome size ranged from just under 1.0 to 3.8 pg among diploid species with an average genome size of 1.79 (s.d. = 0.66). Five polyploid species were sampled, interestingly all have smaller genome sizes than that of the largest two diploid species, M. carstiensis (3.8 pg) and M. suffruticosa (3.5 pg). Genome sizes were mapped onto a phylogeny based on DNA sequence data from ...

Taxon, 2013

Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need ... more Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non-Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL-trnF and psbA-trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized. Numerous phylogenetic studies of Acacia Mill. s.l. over the last 10 years have shown that Acacia is not monophyletic and it is now widely agreed that Acacia s.l. needs to be divided into at least five genera corresponding to the former Acacia subgenus Phyllodineae (DC.

Systematic Botany, 1994

... Gene matK Kelly P. Steele Department of Biology, Appalachian State University, Boone, North C... more ... Gene matK Kelly P. Steele Department of Biology, Appalachian State University, Boone, North Carolina ... Gilia capitata Sims Gilia diegensis (Munz) AD Grant &amp; V. Grant Gilia leptantha Parish ... Sequences were manually aligned; the few length mutations did not hin-der alignment. ...

Systematic Biology, 2013

Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult ... more Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the Medicago truncatula reference genome to confidently identify 87 596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago species, to investigate the number of sites needed to provide robust phylogenetic estimates and to identify specific genomic regions supporting topologies in conflict with the genome-wide phylogeny. Our full genomic data set resolves relationships within the genus that were previously intractable. Subsampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5000 sites, no random sample of the data supports a topology identical to that of the genome-wide phylogeny. Phylogenetic relationships estimated from 500-site sliding windows revealed genome regions supporting several alternative species relationships among recently diverged taxa, consistent with the expected effects of deep coalescence or introgression in the recent history of Medicago. [Medicago; phylogenomics; whole-genome resequencing.]

This study was designed to produce a comprehensive flora of Usery Mountain Regional Park and Pass... more This study was designed to produce a comprehensive flora of Usery Mountain Regional Park and Pass Mountain of the Tonto National Forest. A total of 168 vascular plant species representing 46 families and 127 genera were collected or documented at this study area. Sixteen species were not native to the flora of Arizona and represent 9.5% of the flora. Nevertheless, the study area does not appear to be significantly damaged or degraded in spite of its historical and current land use. The location and types of invasive species recorded in this study will assist with implementing preventative measures to prevent further spreading of certain species. The complete list of all vascular species recorded in this study ACKNOWLEDGMENTS I want to acknowledge my Graduate Supervisory Committee for their support and expertise; committee chair Dr. Kelly P. Steele for sharing her vast knowledge and love of plants with me in the classroom and out in the field, committee member Dr. William H. Miller for his expertise and guidance in GIS and statistical analysis, and committee member Dr. Eddie J. Alford with his background of the Sonoran Desert and Tonto National Forest area and experience with saguaro research. I appreciate Dr. Douglas Green, Chair of the Department of Applied Sciences and Mathematics, for supporting my efforts as both a student and an employee during this research project. Dr. Les Landrum, ASU Herbarium Curator, was instrumental in both the selection of my study area and training I received on the process of creating voucher specimens. Robert Wilson, State Resources Soil Scientist for NRCS, provided information and resources for my research project.

South African Journal of Botany 89: 3–9, Nov 1, 2013

Legume systematists have been making great progress in understanding evolutionary relationships w... more Legume systematists have been making great progress in understanding evolutionary relationships within the Leguminosae (Fabaceae), the third largest family of flowering plants. As the phylogenetic picture has become clearer, so too has the need for a revised classification of the family. The organization of the family into three subfamilies and 42 tribes is outdated and evolutionarily misleading. The three traditionally recognized subfamilies, Caesalpinioideae,Mimosoideae, and Papilionoideae, do not adequately represent relationshipswithin the family. The occasion of the Sixth International LegumeConference in Johannesburg, South Africa in January 2013, with its theme “Towards a new classification system for legumes,” provided the impetus to move forward with developing a new classification. A draft classification, based on current phylogenetic results and a set of principles and guidelines, was prepared in advance of the conference as the basis for discussion. The principles, guide...

American Journal of Botany, 1997

Phylogenetic relationships were examined within the ''higher'' Hamamelididae using 21 species rep... more Phylogenetic relationships were examined within the ''higher'' Hamamelididae using 21 species representing eight families and related outgroups. Chloroplast DNA sequences encoding the matK gene (ϳ1 kilobase) provided 258 informative nucleotide sites. Phylogenetic analysis of this variation produced one most parsimonious tree supporting three monophyletic groups. In this tree, Nothofagus was basal to a well supported clade of remaining ''higher'' hamamelids, in which Fagaceae, including Fagus, were sister to a clade of core ''higher'' hamamelids that share wind-pollination, bicarpellate flowers, granular pollen walls, and reduced pollen apertures. Within the core ''higher'' hamamelids three subclades were resolved, Myricaceae, (Casuarina-(Ticodendron-(Betulaceae))), and (Rhoiptelea-Juglandaceae). Each subclade was well supported but relationships among them were not. The basal position of Nothofagus within the matK tree is consistent with the fossil record of ''higher'' hamamelids in which Nothofagus pollen appears earlier than microfossils with affinities to other modern ''higher'' hamamelids. This placement supports the exclusion of Nothofagus from Fagaceae and suggests two hypotheses for the origin of the cupule. The cupule may be ancestral within ''higher'' hamamelids and subsequently lost in core members of the clade or there may have been two independent origins. It is suggested that the three clades (1) Nothofagaceae, (2) Fagaceae, and (3) Juglandaceae, Rhoiptelea, Myricaceae, Casuarina, Ticodendron, and Betulaceae be considered at the ordinal level and that traditional orders, such as Fagales sensu Cronquist (Fagaceae, Nothofagaceae, and Betulaceae) be abandoned. Comparative analyses of matK sequences with previously published rbcL sequences demonstrate that for the taxa considered here matK sequences produced trees with greater phylogenetic resolution and a higher consistency index.

American Journal of Botany, 2010

includes the widely cultivated major forage crop and weedy species M. sativa L. (alfalfa, lucerne... more includes the widely cultivated major forage crop and weedy species M. sativa L. (alfalfa, lucerne) and the legume model species M. truncatula Gaertn. (Cannon et al., 2006). Taxonomically, Medicago along with Melilotus Mill. (sweetclovers) and Trigonella L. were included in the tribe Trigonellinae, fi rst recognized by Schultz (1901) , but as circumscribed this tribe was not accepted by most taxonomists. Instead, most authors recognized the tribe Trifolieae, which included these three genera and Trifolium L. (e.g., Rechinger, 1984). Some authors have also included Ononis L. and Parochetus Buch.-Ham. ex D. Don (e.g., Heyn, 1981). More recently, Trigonellinae were recognized as a subtribe of Trifolieae by Small (1987b) , who noted that the species in this group share morphological character states including leaves that are digitately trifoliate with stipules adnate to the stem, but not encircling it entirely. Delimitation of the three genera in the subtribe has been problematic, particularly between Medicago and Trigonella. Nevertheless, using several fl oral features associated with the explosive pollination syndrome, Small et al. (1987) transferred 23 species of Trigonella (the so-called " medicagoid Trigonella ") to the genus Medicago , which currently comprises sections Buceras and Lunatae. The three genera of Trigonellinae can be further distinguished using biochemical characteristics, specifi cally the type of phytoalexins produced after fungal infection. While species of Medicago accumulate vesitol and sativan, these substances are absent from Trigonella and Melilotus (Ingham and Harborne, 1976). Furthermore, species of Medicago contain hemolytic saponins, which are not found in Trigonella or Melilotus (Jurzysta et al., 1988). Medicago and Trigonella , as delimited by Small and Jomphe (1989b) , have always been strongly supported as sister genera based upon analyses of both the nuclear ribosomal internal transcribed spacer region (nrDNA

Taxon, Feb 1, 1988

In a recent paper Bremer et al.(1987) presented a cladistic analysis of green plants using a vari... more In a recent paper Bremer et al.(1987) presented a cladistic analysis of green plants using a variety of morphological, biochemical, and cytological features. They considered, but chose not to include, 5S rRNA sequence information in their data set. Prior to that decision they performed a parsimony analysis of 5S rRNA sequences presented by Hori et al.(1985); they illustrated one of the 57 most parsimonious trees from that analysis. A variety of" novel groupings" are present in that tree. Based on the likelihood that those groups do not reflect ...

Mol. Biol. Evol, Mar 1, 1991

In the past decade there has been considerable interest in the use of nucleotide sequence data fo... more In the past decade there has been considerable interest in the use of nucleotide sequence data for the reconstruction of evolutionary history. Such data are now available from a wide variety of organisms, making phylogenetic analyses of distantly related organisms possible (eg, see Hori and Osawa 1986, 1987; Pace et al. 1986; Field et al. 1988; Lake 1988; Gogarten et al. 1989a, 1989b). Many sophisticated methods are available for the analysis of sequence data, including parsimony methods (Eck and Dayhoff 1966; Fitch 197 1, 1977; ...

Advances in legume systematics, …, 2003

Tribes Trifolieae and Vicieae along with Cicereae and Galega (Galegeae) form a monophyletic group... more Tribes Trifolieae and Vicieae along with Cicereae and Galega (Galegeae) form a monophyletic group that has been designated informally as the "vicioid clade". There is good support from analyses of various molecular data for the clade itself, but relationships of genera within the clade are not fully understood nor has monophyly of the tribes and genera been fully tested. Sequences of the plastid gene matK from 84 members of the vicioid clade were analysed using maximum parsimony. Results presented here provide strong support for a monophyletic Vicieae that includes Vicia, Lathyrus, Pisum and Lens. Vicia is paraphyletic with regard to other genera of Vicieae, but there is support for monophyletic groups of species of Vicia. Pisum is sister to a monophyletic Lathyrus, and Lens is sister to a small group of species of Vicia. A monophyletic Trifolium is sister to the Vicieae, and together they form a moderately supported monophyletic group. Similarly, a monophyletic Ononis is sister to genera of tribe Trifolieae including Medicago, Trigonella and Melilotus. Medicago is monophyletic and includes previously transferred species from Trigonella. Medicago and Trigonella are sister taxa, but Melilotus is nested within Trigonella. Morphological and biochemical features are considered as they support particular groups within the vicioid clade.