Alfonso Delgado-Salinas

Phylogeny of the Genus Phaseolus (Leguminosae): A Recent Diversification in an Ancient Landscape

Abstract A combined parsimony analysis of the species of Phaseolus and closely related New World genera was performed with sequences from the nuclear ribosomal ITS/5.8 S and plastid trnK loci. Species relationships are resolved with high parsimony bootstrap support at all hierarchical levels. All species of Phaseolus, except five enigmatic ones, belong to one of eight clades. These eight clades show some morphological, ecological, or biogeographical distinction, and are informally recognized in a phylogenetic classification. The five enigmatic species, Phaseolus glabellus, P. macrolepis, P. microcarpus, P. oaxacanus, and P. talamancensis are weakly resolved as the sister clade to the Tuerckheimii group. An evolutionary rates analysis that biases for old age estimates suggests that the Phaseolus stem clade is the same age as the New World Phaseolinae crown clade with a maximum age of ca. 8 Ma. The Phaseolus crown is estimated to be no older than ca. 6 Ma, and the average age of the eight well supported crown clades within Phaseolus is ca. 2 Ma. The maximum age estimate of a Late Pliocene to Pleistocene diversification of Phaseolus post-dates the major tectonic activity in Mexico where Phaseolus diversity is centered.

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.

A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica

Lack of introgression or divergent selection may be responsible for the maintenance of phenotypic differences between sympatric populations of crops and their wild progenitors. To distinguish between these hypotheses, amplified fragment length polymorphism markers were located on a molecular linkage map of Phaseolus vulgaris relative to genes for the domestication syndrome and other traits. Diversity for these same markers was then analyzed in two samples of wild and domesticated populations from Mesoamerica. Differentiation between wild and domesticated populations was significantly higher in parapatric and allopatric populations compared to sympatric populations. It was also significantly higher near genes for domestication compared to those away from these genes. Concurrently, the differences in genetic diversity between wild and domesticated populations were strongest around such genes. These data suggest that selection in the presence of introgression appears to be a major evolutionary factor maintaining the identity of wild and domesticated populations in sympatric situations. Furthermore, alleles from domesticated populations appear to have displaced alleles in sympatric wild populations, thus leading to a reduction in genetic diversity in such populations. These results also provide a possible experimental framework for assessing the long-term risk of transgene escape and the targeting of transgenes inside the genome to minimize the survival of these transgenes into wild populations following introduction by gene flow.

Plant diversity patterns in neotropical dry forests and their conservation implications

Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale.

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

BackgroundLegumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes.ResultsWe report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools.ConclusionsThe genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.

Karyotypic studies on species of Phaseolus (Fabaceae: Phaseolinae).

Ten karyotypes of Phaseolus were analyzed. Possible directions of karyological evolution of those species are suggested. All species studied have karyotypes composed exclusively of metacentric and submetacentric chromosomes, except P. filiformis with all metacentrics, and P. chiapasanus with one pair of subtelocentric chromosomes. Secondary constrictions and satellites are common among species studied. Phaseolus leptostachyus, P. micranthus, and P. macvaughii are considered as aneuploids with 2n= 20, whereas the rest of the species have 2n= 22.

Vigna (Leguminosae) sensu lato: The names and identities of the American segregate genera

PREMISE OF STUDY The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. METHODS The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. KEY RESULTS The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. CONCLUSIONS American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.

LOCATING EVOLUTIONARY PRECURSORS ON A PHYLOGENETIC TREE

Conspicuous innovations in the history of life are often preceded by more cryptic genetic and developmental precursors. In many cases, these appear to be associated with recurring origins of very similar traits in close relatives (parallelisms) or striking convergences separated by deep time (deep homologies). Although the phylogenetic distribution of gain and loss of traits hints strongly at the existence of such precursors, no models of trait evolution currently permit inference about their location on a tree. Here we develop a new stochastic model, which explicitly captures the dependency implied by a precursor and permits estimation of precursor locations. We apply it to the evolution of extrafloral nectaries (EFNs), an ecologically significant trait mediating a widespread mutualism between plants and ants. In legumes, a species‐rich clade with morphologically diverse EFNs, the precursor model fits the data on EFN occurrences significantly better than conventional models. The model generates explicit hypotheses about the phylogenetic location of hypothetical precursors, which may help guide future studies of molecular genetic pathways underlying nectary position, development, and function.

Phylogeny and Biogeography of Wajira (Leguminosae): A Monophyletic Segregate of Vigna Centered in the Horn of Africa Region

Abstract Evidence from chloroplast trnK and nuclear ribosomal ITS sequences and morphological data reveals that the monotypic legume genus Wajira is nested within a clade comprising the species of Vigna subgen. Macrorhynchus. This Wajira-containing clade is basally branching in a larger clade that contains many of the genera traditionally referred to as tribe Phaseoleae subtribe Phaseolinae. Wajira is thus recircumscribed to include Vigna subgen. Macrorhynchus. Given the heterogeneity of floral morphology of its constituent species, Wajira is apomorphically diagnosed by woody stems and a pollen brush that comprises an introrse linear array of unicellular hairs. This recircumscribed genus now comprises five species, one of which is described as new, Wajira danissana. Three species require new nomenclatural combinations, Wajira grahamiana, Wajira praecox, and Wajira virescens. Wajira albescens, W. danissana, W. praecox, and W. virescens are woody climbers that are each narrowly distributed in the arid Somalia-Masai region characterized by sparse ground cover not subjected to seasonal burning. Wajira grahamiana has a thick woody subterranean rootstock that resprouts stems, and is widespread in the Sudano-Zambezian Region, southern India, and Sri Lanka, where grasslands subjected to seasonal burning predominate. This species is resolved in all phylogenetic analyses as derived from within the Somalia-Masai clade. An evolutionary rates analysis of trnK sequences suggests that the Wajira stem clade diverged from its closest relatives just over 10 million years ago, the extant diversification of the genus began around 6–7 million years ago, and Wajira grahamiana attained its widespread distribution during the last 2 million years.

Chloroplast DNA Phylogenetic Studies in New World Phaseolinae (Leguminosae: Papilionoideae: Phaseoleae)

Chloroplast DNA restriction site variation was examined in several species of Pha- seolus, Vigna, and Ramirezella, and in four potential outgroups (Dipogon, Macroptilium, Oxyrhynchus and Strophostyles) of the Phaseolus-Vigna complex. Cladistic analyses of restriction site characters yielded 22 equally parsimonious trees with a consistency index of 0.60. Results of the chloroplast DNA analysis are consistent with current hypotheses from morphological studies in suggesting that Phaseolus is monophyletic, but that Vigna is polyphyletic. The Vigna plastomes are divided into two clades. One consists of all the Old World subgenera surveyed and the New World subg. Lasiospron, supporting morphological evidence that this distinct New World subgenus may be more closely related to the Old World groups than to other New World subgenera. The second clade is strictly New World and comprises Vigna subg. Srgmotdotropts, V. populnea, Ramirezella and Oxyrhynchus. The close relationship of Ramirezella chloroplast DNAs with New World Vigna and Oxyrhynchus plastomes follows recent cladistic analyses of morphological characters. Relationships of plastomes of the New World clade to the mostly Old World Vigna clade depends on rooting of the tree. Within Phaseolus, species from three small and distinct Mexican endemic sections have monophyletic chlo- roplast DNAs. Plastomes of the larger sect. Phaseolus are not monophyletic, but subgroups within the section follow relationships proposed by non-molecular studies. If rooted with Dipogon, the chloroplast DNA gene tree places Phaseolus, along with Macroptilium and Strophostyles, as sister group to the New World Vigna clade. Otherwise, if rooted with the Macroptilium and Strophostyles plastomes, Phaseolus chloroplast DNAs are sister group to plastomes of both Vigna clades and of Dipogon.