C. Donovan Bailey

rbcL and Legume Phylogeny, with Particular Reference to Phaseoleae, Millettieae, and Allies

Abstract A parsimony analysis was conducted on 319 rbcL sequences, comprising 242 from 194 genera of Leguminosae and 77 from other families. Results support earlier conclusions from rbcL and other molecular data that a monophyletic Leguminosae is part of a Fabales that includes Polygalaceae, Surianaceae, and the anomalous rosid genus Quillaja. Within legumes, results of previous analyses were also supported, such as the paraphyletic nature of Caesalpinioideae and monophyly of Mimosoideae and Papilionoideae. Most new data (74 sequences) were from Papilionoideae, particularly Phaseoleae, Millettieae, and allies. Although the overall topology for Papilionoideae was largely unresolved, several large clades were well-supported. The analysis contained a large sample of Phaseoleae and Millettieae, and not surprisingly showed both tribes to be polyphyletic, though with all taxa except Wisteria and allied Millettieae belonging to a single well supported clade. Within this clade was a strongly supported group that included Phaseoleae subtribes Erythrininae, Glycininae, Phaseolinae, Kennediinae, and Cajaninae, with only the last two being monophyletic. Desmodieae and Psoraleeae were also part of this clade. The monophyletic Phaseoleae subtribes Ophrestiinae and Diocleinae grouped with most Millettieae in a clade that included a group similar to the core Millettieae identified in other studies. All but one of the remaining Millettieae sampled formed an additional clade within the overall millettioid/phaseoloid group. Communicating Editor: Aaron Liston

From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction.

Phylogenetic analyses of DNA sequences have prompted spectacular progress in assembling the Tree of Life. However, progress in constructing phylogenies among closely related species, at least for plants, has been less encouraging. We show that for plants, the rapid accumulation of DNA characters at higher taxonomic levels has not been matched by conventional sequence loci at the species level, leaving a lack of well-resolved gene trees that is hindering investigations of many fundamental questions in plant evolutionary biology. The most popular approach to address this problem has been to use low-copy nuclear genes as a source of DNA sequence data. However, this has had limited success because levels of variation among nuclear intron sequences across groups of closely related species are extremely variable and generally lower than conventionally used loci, and because no universally useful low-copy nuclear DNA sequence loci have been developed. This suggests that solutions will, for the most part, be lineage-specific, prompting a move away from ‘universal’ gene thinking for species-level phylogenetics. The benefits and limitations of alternative approaches to locate more variable nuclear loci are discussed and the potential of anonymous non-genic nuclear loci is highlighted. Given the virtually unlimited number of loci that can be generated using these new approaches, it is clear that effective screening will be critical for efficient selection of the most informative loci. Strategies for screening are outlined.

A new subfamily classification of the leguminosae based on a taxonomically comprehensive phylogeny

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircumscribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or cladebased classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: insights into polyploid origins and nrDNA polymorphism

Previous analyses of species relationships and polyploid origins in the mimosoid legume genus Leucaena have used chloroplast DNA (cpDNA) restriction site data and morphology. Here we present an analysis of a new DNA sequence data set for the nuclear ribosomal DNA (nrDNA) 5.8S subunit and flanking ITS 1 and ITS 2 spacers, a simultaneous analysis of the morphology, ITS and cpDNA data sets for the diploid species, and a detailed comparison of the cpDNA and ITS gene trees, which include multiple accessions of all five tetraploid species. Significant new insights into species relationships and polyploid origins, including that of the economically important tropical forage tree L. leucocephala, are discussed. Heterogeneous ITS copy types, including 26 putative pseudogene sequences, were found within individuals of four of the five tetraploid and one diploid species. Potential pseudogenes were identified using two pairwise comparison approaches as well as a tree-based method that compares observed and expected proportions of total ITS variation contributed by the 5.8S subunit optimized onto branches of one of the ITS gene trees. Inclusion of putative pseudogene sequences in the analysis provided evidence that some pseudogenes in allopolyploid L. leucocephala are not the result of post-allopolyploidization gene silencing, but were inherited from its putative diploid maternal progenitor L. pulverulenta.

Arabidopsis thaliana Leaf Form Evolved via Loss of KNOX Expression in Leaves in Association with a Selective Sweep

Morphological diversity is often caused by altered gene expression of key developmental regulators. However, the precise developmental trajectories through which morphologies evolved remain poorly understood. It is also unclear to what degree genetic changes contributing to morphological divergence were fixed by natural selection. Here we investigate these problems in the context of evolutionary developmental transitions that produced the simple unlobed leaf of the model species Arabidopsis thaliana. We demonstrate that A. thaliana leaf shape likely derived from a more complex lobed ancestral state that persists in extant Arabidopsis species. We also show that evolution of the unlobed leaf form in A. thaliana involved loss of expression of the knotted1-like homeobox gene SHOOTMERISTEMLESS (STM) in leaves and that cis-regulatory divergence contributed to this process. Further, we provide evidence for a selective sweep at the A. thaliana STM locus, indicating that loss of STM expression in A. thaliana leaves may have been fixed by positive selection. In summary, our data provide key information as to when and how the characteristic leaf form of A. thaliana evolved.

Serendipitous backyard hybridization and the origin of crops

Backyard gardens, dump heaps, and kitchen middens are thought to have provided important venues for early crop domestication via generation of hybrids between otherwise isolated plant species. However, this process has rarely been demonstrated empirically. For the majority of polyploid crops, it remains uncertain to what extent hybridization and polyploidization preceded domestication or were precipitated by human activities. Using archaeological, ethnobotanical, geographical, and genetic data, we investigate the extent and significance of predomestication cultivation, backyard sympatry, and spontaneous hybridization for the Mimosoid legume tree Leucaena, which is used as a food crop throughout south-central Mexico. We show that predomestication cultivation was widespread, involved numerous independent transitions from the wild to cultivation, and resulted in extensive artificial sympatry of 2–6 species locally and 13 species in total. Using chloroplast and rapidly evolving nuclear-encoded DNA sequences, we demonstrate that hybridization in Leucaena has been extensive and complex, spawning a diverse set of novel hybrids as a result of juxtaposition of species in cultivation. The scale and complexity of hybridization in Leucaena is significantly greater than that documented for any other Mexican plant domesticates so far. However, there are striking parallels between Leucaena and the other major Mexican perennial domesticates Agave and Opuntia, which show very similar domestication via backyard hybridization pathways. Our results suggest that backyard hybridization has played a central role in Mesoamerican crop domestication and demonstrate that the simple step of bringing species together in cultivation can provide a potent trigger for domestication.

Systematics of the Halimolobine Brassicaceae: Evidence from Three Loci and Morphology

Abstract Relationships among Halimolobos, Mancoa, Pennellia, and Sphaerocardamum have been controversial. Higher level studies, using cpDNA data from the chloroplast encoded ndhF and trnL intron, suggested that some species of these genera represent a monophyletic group: the halimolobine clade. The research presented here focuses on the halimolobine clade with denser intra and inter-specific sampling. The primary aims of the project were: (1) to further test the monophyly of the halimolobine clade; (2) to test the monophyly Halimolobos, Mancoa, Pennellia, and Sphaerocardamum; and (3) to study the evolution of morphological characters in the clade. Data were generated from the trnL-F region, nrDNA ITS, pistillata intron one, and 17 non-molecular characters. The difficulties associated with incorporating these data into simultaneous analyses are discussed and a strategy is presented. Separate and simultaneous analysis confirmed a monophyletic core group of halimolobine species. The strict consensus tree contained five well-supported halimolobine subclades: Sphaerocardamum, Pennellia plus Arabis tricornuta, Mancoa bracteata plus M. foliosa, a narrowly defined Halimolobos, and a clade consisting of a subset of Halimolobos and Mancoa species. Individual morphological characters vary in their utility for classification of the group. However, the majority of the characters provide some grouping information within the halimolobine clade. Communicating Editor: Paul Wilson

DOES HYBRIDIZATION DRIVE THE TRANSITION TO ASEXUALITY IN DIPLOID BOECHERA

Gametophytic apomixis is a common form of asexual reproduction in plants. Virtually all gametophytic apomicts are polyploids, and some view polyploidy as a prerequisite for the transition to apomixis. However, any causal link between apomixis and polyploidy is complicated by the fact that most apomictic polyploids are allopolyploids, leading some to speculate that hybridization, rather than polyploidy, enables apomixis. Diploid apomixis presents a rare opportunity to isolate the role of hybridization, and a number of diploid apomicts have been documented in the genus Boechera (Brassicaceae). Here, we present the results of a microsatellite study of 1393 morphologically and geographically diverse diploid individuals, evaluating the hypothesis that diploid Boechera apomicts are hybrids. This genus‐wide dataset was made possible by the applicability of a core set of microsatellite loci in 69 of the 70 diploid Boechera species and by our ability to successfully genotype herbarium specimens of widely varying ages. With few exceptions, diploid apomicts exhibited markedly high levels of heterozygosity resulting from the combination of disparate genomes. This strongly suggests that most apomictic diploid Boechera lineages are of hybrid origin, and that the genomic consequences of hybridization allow for the transition to gametophytic apomixis in this genus.

Using RAPDs to Identify DNA Sequence Loci for Species Level Phylogeny Reconstruction: an Example from Leucaena (Fabaceae)

Abstract Resolving phylogenies among closely related species remains a perplexing problem in plant systematics. All too often cpDNA and nrDNA ITS are insufficiently variable to provide desired resolution or support. In the present study, we have adopted a RAPD-based approach to develop sequence-characterized regions, from the nuclear genome, with levels of DNA sequence variation appropriate for resolving relationships within subclades of Leucaena (Fabaceae). RAPDs were used to amplify a set of seven Leucaena accessions. Equal length fragments amplified in two or more species were sequenced and compared. Specific primers were designed for aligned product sets displaying similar or greater levels of variation than have been found in previous ITS studies. Two regions whose DNA sequences provided greater resolution and bootstrap support than ITS or cpDNA RFLP restriction site data sets for the same sample of Leucaena species are discussed in detail.

Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids

To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.