Examinando por Autor "Villaverde, Tamara"

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A new classification of Carex (Cyperaceae) subgenera supported by a HybSeq backbone phylogenetic tree
(The Linnean Society of London, 2020-05-29) Villaverde, Tamara; Jimenez-Mejias, Pedro; Luceño, Modesto; Waterway, Marcia J.; Kim, Sangtae; Lee, Bora; Rincón-Barrado, Mario; Hahn, Marlene; Maguilla, Enrique; Roalson, Eric H.; Hipp, Andrew L.; Global Carex Group
The field of systematics is experiencing a new molecular revolution driven by the increased availability of high-throughput sequencing technologies. As these techniques become more affordable, the increased genomic resources have increasingly far-reaching implications for our understanding of the Tree of Life. With c. 2000 species, Carex (Cyperaceae) is one of the five largest genera of angiosperms and one of the two largest among monocots, but the phylogenetic relationships between the main lineages are still poorly understood. We designed a Cyperaceae-specific HybSeq bait kit using transcriptomic data of Carex siderosticta and Cyperus papyrus. We identified 554 low-copy nuclear orthologous loci, targeting a total length of c. 1 Mbp. Our Cyperaceae-specific kit shared loci with a recently published angiosperm-specific Anchored Hybrid Enrichment kit, which enabled us to include and compile data from different sources. We used our Cyperaceae kit to sequence 88 Carex spp., including samples of all the five major clades in the genus. For the first time, we present a phylogenetic tree of Carex based on hundreds of loci (308 nuclear exon matrices, 543 nuclear intron matrices and 66 plastid exon matrices), demonstrating that there are six strongly supported main lineages in Carex: the Siderostictae, Schoenoxiphium, Unispicate, Uncinia, Vignea and Core Carex clades. Based on our results, we suggest a revised subgeneric treatment and provide lists of the species belonging to each of the subgenera. Our results will inform future biogeographic, taxonomic, molecular dating and evolutionary studies in Carex and provide the step towards a revised classification that seems likely to stand the test of time.
An NGS-Based Phylogeny of Orthotricheae (Orthotrichaceae, Bryophyta) With the Proposal of the New Genus Rehubryum From Zealandia
(Frontiers Media, 2022-05-12) Draper, Isabel; Villaverde, Tamara; Garilleti, Ricardo; Burleigh, J. Gordon; McDaniel, Stuart F.; Mazimpaka, Vicente; Calleja, Juan A.; Lara, Francisco
Phylogenomic data increase the possibilities of resolving the evolutionary and systematic relationships among taxa. This is especially valuable in groups with few and homoplasious morphological characters, in which systematic and taxonomical delimitations have been traditionally difficult. Such is the case of several lineages within Bryophyta, like Orthotrichaceae, the second most diverse family of mosses. Members of tribe Orthotricheae are common in temperate and cold regions, as well as in high tropical mountains. In extratropical areas, they represent one of the main components of epiphytic communities, both in dry and oceanic or hyperoceanic conditions. The epiphytic environment is considered a hostile one for plant development, mainly due to its low capacity of moisture retention. Thus, the diversification of the Orthotrichaceae in this environment could be seen as striking. Over the last two decades, great taxonomic and systematic progresses have led to a rearrangement at the generic level in this tribe, providing a new framework to link environment to patterns of diversification. Here, we use nuclear loci targeted with the GoFlag 408 enrichment probe set to generate a well-sampled phylogeny with well-supported suprageneric taxa and increasing the phylogenetic resolution within the two recognized subtribes. Specifically, we show that several genera with Ulota-like morphology jointly constitute an independent lineage. Within this lineage, the recently described Atlantichella from Macaronesia and Western Europe appears as the sister group of Ulota bellii from Zealandia. This latter species is here segregated in the new genus Rehubryum. Assessment of the ecological and biogeographical affinities of the species within the phylogenetic framework suggests that niche adaptation (including climate and substrate) may be a key evolutionary driver that shaped the high diversification of Orthotricheae.
Assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors in a RAD‐seq phylogeny of Carex section Schoenoxiphium
(Wiley, 2021-02-19) Villaverde, Tamara; Maguilla, Enrique; Luceño, Modesto; Hipp, Andrew L.
Restriction site-associated DNA sequencing (RAD-seq) and related methods have become relatively common approaches to resolve species-level phylogeny. It is not clear, however, whether RAD-seq data matrices are well suited to relaxed clock inference of divergence times, given the size of the matrices and the abundance of missing data. We investigated the sensitivity of Bayesian relaxed clock estimates of divergence times to alternative analytical decisions on an empirical RAD-seq phylogenetic matrix. We explored the relative contribution of secondary calibration strategies, amount of missing data, and the data partition analyzed to overall variance in divergence times inferred using BEAST MCMC analyses of Carex section Schoenoxiphium (Cyperaceae)-a recent radiation for which we have nearly complete species sampling of RAD-seq data. The crown node for Schoenoxiphium was estimated to be 15.22 (9.56-21.18) Ma using a single calibration point and low missing data, 11.93 (8.07-16.03) Ma using multiple calibration points and low missing data, and 8.34 (5.41-11.22) using multiple calibrations but high missing data. We found that using matrices with more than half of the individuals with missing data inferred younger mean ages for all nodes. Moreover, we have found that our molecular clock estimates are sensitive to the positions of the calibration(s) in our phylogenetic tree (using matrices with low missing data), especially when only a single calibration was applied to estimate divergence times. These results argue for sensitivity analyses and caution in interpreting divergence time estimates from RAD-seq data.
Bridging the micro‐and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above
(Wiley, 2018-07-17) Villaverde, Tamara; Pokorny, Lisa; Olsson, Sanna; Rincón-Barrado, Mario; Johnson, Matthew G.; Gardner, Elliot M.; Wickett, Norman J.; Riina, Ricarda; Sanmartin, Isabel
Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above species to within populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case study. Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times. Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern. We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths.
Phylogenomics sheds new light on the drivers behind a long-lasting systematic riddle: the figwort family Scrophulariaceae
(Wiley, 2023) Villaverde, Tamara; Larridon, Isabel; Shah, Toral; Fowler, Rachael M.; Chau, John H.; Olmstead, Richard G.; Sanmartín, Isabel
The figwort family, Scrophulariaceae, comprises c. 2000 species whose evolutionary relationships at the tribal level have proven difficult to resolve, hindering our ability to understand their origin and diversification.We designed a specific probe kit for Scrophulariaceae, targeting 849 nuclear loci and obtaining plastid regions as by-products. We sampled c. 87% of the genera described in the family and use the nuclear dataset to estimate evolutionary relationships, timing of diversification, and biogeographic patterns.Ten tribes, including two new tribes, Androyeae and Camptolomeae, are supported, and the phylogenetic positions of Androya, Camptoloma, and Phygelius are unveiled. Our study reveals a major diversification at c. 60 million yr ago in some Gondwanan landmasses, where two different lineages diversified, one of which gave rise to nearly 81% of extant species. A Southern African origin is estimated for most modern-day tribes, with two exceptions, the American Leucophylleae, and the mainly Australian Myoporeae. The rapid mid-Eocene diversification is aligned with geographic expansion within southern Africa in most tribes, followed by range expansion to tropical Africa and multiple dispersals out of Africa.Our robust phylogeny provides a framework for future studies aimed at understanding the role of macroevolutionary patterns and processes that generated Scrophulariaceae diversity.
Rare and widespread: integrating Bayesian MCMC approaches, Sanger sequencing and Hyb-Seq phylogenomics to reconstruct the origin of the enigmatic Rand Flora genus Camptoloma
(Wiley, 2021-10-02) Culshaw, Victoria; Villaverde, Tamara; Mairal, Mario; Olsson, Sanna; Sanmartin, Isabel
Premise Genera that are widespread, with geographically discontinuous distributions and represented by few species, are intriguing. Is their achieved disjunct distribution recent or ancient in origin? Why are they species-poor? The Rand Flora is a continental-scale pattern in which closely related species appear codistributed in isolated regions over the continental margins of Africa. Genus Camptoloma (Scrophulariaceae) is the most notable example, comprising three species isolated from each other on the northwest, eastern, and southwest Africa. Methods We employed Sanger sequencing of nuclear and plastid markers, together with genomic target sequencing of 2190 low-copy nuclear genes, to infer interspecies relationships and the position of Camptoloma within Scrophulariaceae by using supermatrix and multispecies-coalescent approaches. Lineage divergence times and ancestral ranges were inferred with Bayesian Markov chain Monte Carlo (MCMC) approaches. The population history was estimated with phylogeographic coalescent methods. Results Camptoloma rotundifolium, restricted to Southern Africa, was shown to be a sister species to the disjunct clade formed by C. canariense, endemic to the Canary Islands, and C. lyperiiflorum, distributed in the Horn of Africa-Southern Arabia. Camptoloma was inferred to be sister to the mostly South African tribes Teedieae and Buddlejeae. Stem divergence was dated in the Late Miocene, while the origin of the extant disjunction was inferred as Early Pliocene. Conclusions The current disjunct distribution of Camptoloma across Africa was likely the result of fragmentation and extinction and/or population bottlenecking events associated with historical aridification cycles during the Neogene; the pattern of species divergence, from south to north, is consistent with the "climatic refugia" Rand Flora hypothesis.
State of the World's Plants and Fungi, 2023
(Royal Botanic Gardens, Kew, 2023) Antonelli, A.; Fry, C.; Villaverde, Tamara; et.al.
El quinto informe de State of the World’s elaborado por el Real Jardín Botánico de Kew (en adelante Kew o Kew Gardens), publicado hoy, expone la condición actual de las plantas y hongos del mundo a nivel mundial. Basado en el trabajo de 200 investigadores internacionales, abarca el contenido de más de 25 artículos científicos de vanguardia en sus 11 capítulos. El nuevo informe examina los ejes impulsores y patrones globales de la biodiversidad, así como las lagunas críticas de conocimiento y cómo abordarlas.
Tackling Rapid Radiations With Targeted Sequencing
(Frontiers, 2020-01-09) Larridon, Isabel; Villaverde, Tamara; Zuntini, Alexandre R.; Pokorny, Lisa; Brewer, Grace E.; Epitawalage, Niroshini; Fairlie, Isabel; Hahn, Marlene; Kim, Jan; Maguilla, Enrique; Maurin, Olivier; Xanthos, Martin; Hipp, Andrew L.; Forest, Felix; Baker, William J.
In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations.