Phylogenetic systematics of Vigna sensu stricto in the context of Physostigma and allies.

PREMISE: Vigna includes economically vital crops and wild species. Molecular systematic studies of Vigna species resulted in generic segregates of many New World (NW) species. However, limited Old World (OW) sampling left questions regarding inter- and intraspecific relationships in Vigna s.s. METHODS: African species, including the putative sister genus Physostigma, were comprehensively sampled within the context of NW relatives. Maximum likelihood and Bayesian inference analyses of the chloroplast matK-trnK and nuclear ribosomal ITS/5.8 S (ITS) DNA regions were undertaken to resolve OW Vigna taxonomic questions. Divergence dates were estimated using BEAST to date key nodes in the phylogeny. RESULTS: Analyses of matK and ITS data supported five clades of Vigna s.s.: subg. Lasiospron, a reduced subg. Vigna, subg. Haydonia, subg. Ceratotropis, an enlarged subg. Plectrotropis, and a clade including V. kirkii and V. stenophylla. Genome size estimates of 601 Mb for V. kirkii are near the overall mean of the genus, whereas V. stenophylla had a larger genome (810 Mb), similar to some Vigna subg. Ceratotropis or Plectrotropis species. CONCLUSIONS: Former subg. Vigna is reduced to yellow- and blue-flowered species and subg. Plectrotropis is enlarged to mostly all white-, pink-, and purple-flowered species. The age of the split between NW and OW Vigna lineages is ~6-7 Myr. Genome size estimates cannot rule out a polyploid or hybrid origin for V. stenophylla, potentially involving extinct lineage ancestors of Vigna subg. Ceratotropis or Plectrotropis, as indicated by network and phylogenetic analyses. Taxonomic revisions are suggested based on these results.

Documento de consenso sobre tabaquismo y riesgo vascular.

Consensus statement on smoking and vascular risk About 22% of the Spanish population are daily smokers. Men are more likely to smoke than women. In Spain, women between 15-25 years of age smoke as much or more than men. Every smoker should be assessed for: physical dependence on nicotine (Fagerström test), social and psychological dependence (Glover Nilsson test), level of motivation to quit (Richmond test), probability of therapy success (Henri-Mondor and Michael-Fiore tests), and stage of behavioral change development (Prochaska and DiClementi). Advice on smoking cessation is highly cost-effective and should always be provided. Smoking is an enhancer of cardiovascular risk because it acts as a pathogen agent in the development of arteriosclerosis and is associated with ischemic heart disease, stroke, and peripheral artery disease. Smoking increases the risk of chronic lung diseases (COPD) and is related to cancers of the lung, female genitalia, larynx, oropharynx, bladder, mouth, esophagus, liver and biliary tract, and stomach, among others. Combined oral contraceptives should be avoided in women smokers older than 35 years of age due to the risk of thromboembolism. In smoking cessation, the involvement of physicians, nurses, psychologists, etc. is important, and their multidisciplinary collaboration is needed. Effective pharmacological treatments for smoking cessation are available. Combined treatments are recommended when smoker's dependence is high. For individuals who are unable to quit smoking, a strategy based on tobacco damage management with a total switch to smokeless products could be a less dangerous alternative for their health than continuing to smoke.

Molecular phylogeny and divergence time of Harpalyce (Leguminosae, Papilionoideae), a lineage with amphitropical diversification in seasonally dry forests and savannas.

Our knowledge of the systematics of the papilionoid legume tribe Brongniartieae has greatly benefitted from recent advances in molecular phylogenetics. The tribe was initially described to include species marked by a strongly bilabiate calyx and an embryo with a straight radicle, but recent research has placed taxa from the distantly related core Sophoreae and Millettieae within it. Despite these advances, the most species-rich genera within the Brongniartieae are still not well studied, and their morphological and biogeographical evolution remains poorly understood. Comprising 35 species, Harpalyce is one of these poorly studied genera. In this study, we present a comprehensive, multi-locus molecular phylogeny of the Brongniartieae, with an increased sampling of Harpalyce, to investigate morphological and biogeographical evolution within the group. Our results confirm the monophyly of Harpalyce and indicate that peltate glandular trichomes and a strongly bilabiate calyx with a carinal lip and three fused lobes are synapomorphies for the genus, which is internally divided into three distinct ecologically and geographically divergent lineages, corresponding to the previously recognized sections. Our biogeographical reconstructions demonstrate that Brongniartieae originated in South America during the Eocene, with subsequent pulses of diversification in South America, Mesoamerica, and Australia. Harpalyce also originated in South America during the Miocene at around 20 Ma, with almost synchronous later diversification in South America and Mexico/Mesoamerica beginning 10 Ma, but mostly during the Pliocene. Migration of Harpalyce from South to North America was accompanied by a biome and ecological shift from savanna to seasonally dry forest.

Revision of the genus Agrostis (Poaceae, Pooideae, Poeae) in Megamexico.

Agrostis is one of the most diverse genera of the Poaceae, including ca. 198 species, principally distributed in cold and temperate regions of the world, but also found in the high mountains of the tropics. We present a revision based on morphoanatomical evidence, for the biogeographic region known as Megamexico 3 (i.e., Mexico including the desert areas of southern USA and the Central America territory, to northern Nicaragua). We include taxonomic descriptions and an identification key for the found taxa, maps with the known geographical distribution of the species, and figures with the morphoanatomical characteristics, elevation and phenology. Agrostis is represented in the study zone by 20 species, of which four are endemic and three are introduced. Most records of the genus are distributed in the mountains, above 1500 m a.s.l., in open areas of temperate forests, with conifers and Quercus. Specimens with spikelets occur year round, but most records occur during the wet season, in the months of July to October. We propose a preliminary conservation assessment for each species in the study zone, according to the International Union for Conservation of Nature categories: one with Deficient Data (DD), six as Endangered (EN), two as Vulnerable (VU), and 11 as Least Concern (LC).

ResumenAgrostis es uno de los géneros más diversos de las Poaceae, con ca. 198 especies, principalmente distribuidas en regiones frías y templadas del mundo, aunque también se pueden encontrar en grandes elevaciones de los trópicos. En este trabajo se presenta una revisión basada en evidencia morfoanatómica para la región biogeográfica conocida como Megaméxico 3 (i.e., México incluyendo las áreas desérticas del sur de los EUA y el territorio de Centroamérica hasta el norte de Nicaragua). Se incluyen descripciones taxonómicas y una clave de identificación para los taxones encontrados, mapas con la distribución geográfica conocida de las especies, así como figuras con las características morfoanatómicas, elevación y fenología. Agrostis está representado en la zona de estudio por 20 especies, cuatro de las cuales son endémicas y tres son introducidas. La mayoría de los registros del género se distribuyen en regiones montañosas, por arriba de los 1500 de elevación, en áreas abiertas de bosques templados, con coníferas y Quercus. Es posible encontrar ejemplares con espiguillas durante todo el año, pero la mayoría de los registros ocurren durante la época lluviosa, durante los meses de julio a octubre. Se propone una evaluación preliminar de conservación para cada especie en la zona de estudio, de acuerdo con las categorías de la Union Internacional para la Conservación de la Naturaleza: una con Datos Deficientes (DD), seis como Amenzadas (EN), dos como Vulnerables (VU) y 11 de Preocupación Menor (LC).

Incorporating evolutionary and threat processes into crop wild relatives conservation.

Crop wild relatives (CWR) intra- and interspecific diversity is essential for crop breeding and food security. However, intraspecific genetic diversity, which is central given the idiosyncratic threats to species in landscapes, is usually not considered in planning frameworks. Here, we introduce an approach to develop proxies of genetic differentiation to identify conservation areas, applying systematic conservation planning tools that produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa-specific tolerance to human-modified habitats, and their extinction risk status. Our analyses can be used as inputs for developing national action plans for the conservation and use of CWR. Our results also inform public policy to mitigate threat processes to CWR (like crops living modified organisms or agriculture subsidies), and could advise future research (e.g. for potential germplasm collecting). Although we focus on Mesoamerican CWR within Mexico, our methodology offers opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.

Patterns of chromosomal variation in Mexican species of Aeschynomene (Fabaceae, Papilionoideae) and their evolutionary and taxonomic implications.

A cytogenetic analysis of sixteen taxa of the genus Aeschynomene Linnaeus, 1753, which includes species belonging to both subgenera Aeschynomene (Léonard, 1954) and Ochopodium (Vogel, 1838) J. Léonard, 1954, was performed. All studied species had the same chromosome number (2n = 20) but exhibited karyotype diversity originating in different combinations of metacentric, submetacentric and subtelocentric chromosomes, chromosome size and number of SAT chromosomes. The plasticity of the genomes included the observation in a taxon belonging to the subgenus Aeschynomene of an isolated spherical structure similar in appearance to the extra chromosomal circular DNA observed in other plant genera. By superimposing the karyotypes in a recent phylogenetic tree, a correspondence between morphology, phylogeny and cytogenetic characteristics of the taxa included in the subgenus Aeschynomene is observed. Unlike subgenus Aeschynomene, the species of Ochopodium exhibit notable karyotype heterogeneity. However the limited cytogenetic information recorded prevents us from supporting the proposal of their taxonomic separation and raise it to the genus category. It is shown that karyotype information is useful in the taxonomic delimitation of Aeschynomene and that the diversity in the diploid level preceded the hybridization/polyploidization demonstrated in the genus. The systematic implications of our results and their value can be extended to other Dalbergieae genera as knowledge about the chromosomal structure and its evolution increases.

Inexpensive Graphene Oxide Heaters Lithographed by Laser.

In this paper, we present a simple and inexpensive method for the fabrication of high-performance graphene-based heaters on different large-scale substrates through the laser photothermal reduction of graphene oxide (laser-reduced graphene-oxide, LrGO). This method allows an efficient and localized high level of reduction and therefore a good electrical conductivity of the treated films. The performance of the heaters is studied in terms of steady-state temperature, power consumption, and time response for different substrates and sizes. The results show that the LrGO heaters can achieve stable steady-state temperatures higher than 200 °C when a voltage of 15 V is applied, featuring a time constant of around 4 s and a heat transfer coefficient of ~200 °C cm2/W. These characteristics are compared with other technologies in this field, demonstrating that the fabrication approach described in this work is competitive and promising to fabricate large-scale flexible heaters with a very fast response and high steady-state temperatures in a cost-effective way. This technology can be easily combined with other fabrication methods, such as screen printing or spray-deposition, for the manufacturing of complete sensing systems where the temperature control is required to adjust functionalities or to tune sensitivity or selectivity.

Leaf adaptations and species boundaries in North American Cercis: implications for the evolution of dry floras.

PREMISE OF THE STUDY: The North American Cercis clade spans dry to mesic climates and exhibits complex morphological variation. We tested various proposed species classifications of this group and whether aspects of leaf morphology, particularly the "drip-tip" in some regional populations, are adaptive and/or linked with phylogeny. METHODS: We made measurements on over 1100 herbarium specimens from throughout North America and analyzed the data with univariate and multivariate approaches. We analyzed phylogenetically DNA sequence data from nuclear ITS and three plastid regions from 40 samples, and estimated divergence times with a relaxed-clock Bayesian analysis. We used climate and geographic position data to predict the variation observed in leaf size and shape by using stepwise multiple linear regressions. KEY RESULTS: Morphometric analyses yielded a pattern of continuous and often clinal character variation across North America, without correlated gaps in character states. Conversely, phylogenetic and divergence time analyses yielded distinct clades from California, the interior west, and eastern North America separated by between ~12 and 16 million years. Multiple regressions yielded highly significant correlations between leaf apex shape and precipitation of the warmest quarter. CONCLUSIONS: Despite a pattern of continuous morphological character variation, the long period of geographic and presumably genetic isolation warrants the delimitation of three species. Predictive modeling supports the adaptive value of acuminate apices or "drip-tips" in mesic habitats. This suggests that Cercis leaves change more rapidly than inferred from parsimony reconstruction, which has implications for the evolution of the dry floras of North America and Eurasia.

Domestication Genomics of the Open-Pollinated Scarlet Runner Bean (Phaseolus coccineus L.).

The runner bean is a legume species from Mesoamerica closely related to common bean (Phaseolus vulgaris). It is a perennial species, but it is usually cultivated in small-scale agriculture as an annual crop for its dry seeds and edible immature pods. Unlike the common bean, P. coccineus has received little attention from a genetic standpoint. In this work we aim to (1) provide information about the domestication history and domestication events of P. coccineus; (2) examine the distribution and level of genetic diversity in wild and cultivated Mexican populations of this species; and, (3) identify candidate loci to natural and artificial selection. For this, we generated genotyping by sequencing data (42,548 SNPs) from 242 individuals of P. coccineus and the domesticated forms of the closely related species P. vulgaris (20) and P. dumosus (35). Eight genetic clusters were detected, of which half corresponds to wild populations and the rest to domesticated plants. The cultivated populations conform a monophyletic clade, suggesting that only one domestication event occurred in Mexico, and that it took place around populations of the Trans-Mexican Volcanic Belt. No difference between wild and domesticated levels of genetic diversity was detected and effective population sizes are relatively high, supporting a weak genetic bottleneck during domestication. Most populations presented an excess of heterozygotes, probably due to inbreeding depression. One population of P. coccineus subsp. striatus had the greatest excess and seems to be genetically isolated despite being geographically close to other wild populations. Contrasting with previous studies, we did not find evidence of recent gene flow between wild and cultivated populations. Based on outlier detection methods, we identified 24 domestication-related SNPs, 13 related to cultivar diversification and eight under natural selection. Few of these SNPs fell within annotated loci, but the annotated domestication-related SNPs are highly expressed in flowers and pods. Our results contribute to the understanding of the domestication history of P. coccineus, and highlight how the genetic signatures of domestication can be substantially different between closely related species.

Genomic history of the origin and domestication of common bean unveils its closest sister species.

BACKGROUND: Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. RESULTS: We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. CONCLUSIONS: We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the "wild ancestor" of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes.

The papilionoid legume tribe Brongniartieae comprises a collection of 15 genera with disparate morphologies that were previously positioned in at least four remotely related tribes. The Brongniartieae displays a wide geographical disjunction between Australia and the New World and previous phylogenetic studies had provided conflicting results about the relationships between the American and Australian genera. We carry out phylogenetic analyses of (1) a plastid matK dataset extensively sampled across legumes to solve the enigmatic relationship of the Cuban-endemic monospecific genus Behaimia; and (2) multilocus datasets with focus on all genera ever referred to Brongniartieae. These analyses resulted in a well-resolved and strongly-supported phylogenetic tree of the Brongniartieae. The monophyly of all American genera of Brongniartieae is strongly supported. The doubtful position of the Australian genus Plagiocarpus is resolved within a clade comprising all Australian genera. Behaimia has been traditionally classified in tribe Millettieae, but our new molecular data and re-assessment of morphological traits have resolved the genus within the early-branching papilionoid tribe Brongniartieae. Characters including the pinnately multifoliolate (vs. unifoliolate) leaves, a sessile (vs. stipitate) ovary, and an indehiscent or late dehiscent one-seeded pod distinguish Behaimia from its closer relatives, the South American genera Cyclolobium and Limadendron.

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.

BACKGROUND: Legumes 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. RESULTS: We 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. CONCLUSIONS: The 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.

Symbiont shift towards Rhizobium nodulation in a group of phylogenetically related Phaseolus species.

Bean plants from the Phaseolus genus are widely consumed and represent a nitrogen source for human nutrition. They provide biological fertilization by establishing root nodule symbiosis with nitrogen-fixing bacteria. To establish a successful interaction, bean plants and their symbiotic bacteria need to synchronize a proper molecular crosstalk. Within the Phaseolus genus, P. vulgaris has been the prominent species to study nodulation with Rhizobium symbionts. However the Phaseolus genus comprises diverse species whose symbionts have not been analyzed. Here we identified and studied nodule bacteria from representative Phaseolus species not previously analyzed and from all the described wild species related to P. vulgaris. We found Bradyrhizobium in nodules from most species representing all Phaseolus clades except in five phylogenetically related species from the P. vulgaris clade. Therefore we propose that Bradyrhizobium nodulation is common in Phaseolus and that there was a symbiont preference shift to Rhizobium nodulation in few related species. This work sets the basis to further study the genetic basis of this symbiont substitution.

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.

Genome sequence of Rhizobium sp. strain CCGE510, a symbiont isolated from nodules of the endangered wild bean Phaseolus albescens.

We present the genome sequence of Rhizobium sp. strain CCGE510, a nitrogen fixing bacterium taxonomically affiliated with the R. leguminosarum-R. etli group, isolated from wild Phaseolus albescens nodules grown in native pine forests in western Mexico. P. albescens is an endangered bean species phylogenetically related to P. vulgaris. In spite of the close host relatedness, Rhizobium sp. CCGE510 does not establish an efficient symbiosis with P. vulgaris. This is the first genome of a Rhizobium symbiont from a Phaseolus species other than P. vulgaris, and it will provide valuable new insights about symbiont-host specificity.

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.

Neotropical mutualism between Acacia and Pseudomyrmex: phylogeny and divergence times.

The interaction between Acacia and Pseudomyrmex is a textbook example of mutualism between ants and plants, nevertheless aspects of its evolutionary biology have not been formally explored. In this paper we analyze primarily the phylogenies of both New World Acacia and of their associated species of ants, and the geographic origin of this mutualism. Until now, there has been no molecular analysis of this relationship in terms of its origin and age. We analyzed three chloroplast markers (matK, psaB-rps14, and trnL-trnF) on a total of 70 taxa of legumes from the subfamily Mimosoideae, and two nuclear regions (long-wavelength rhodopsine and wingless) on a total of 43 taxa of ants from subfamily Pseudomyrmecinae. The monophyly of subgenus Acacia and within the New World lineages that of the myrmecophilous Acacia group was established. In addition, our results supported the monophyly of the genus Pseudomyrmex and of the associated acacia-ants P. ferrugineus group. Using Bayesian methods and calibration data, the estimated divergence times for the groups involved in the mutualism are: 5.44+/-1.93 My for the myrmecophilous acacias and 4.58+/-0.82 My for their associated ant species, implying that their relationship originated in Mesoamerica between the late Miocene to the middle Pliocene, with eventual diversification of both groups in Mexico.