Person: Medina Bujalance, Rafael
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First Name
Rafael
Last Name
Medina Bujalance
Affiliation
Universidad Complutense de Madrid
Faculty / Institute
Ciencias Biológicas
Department
Biodiversidad, Ecología y Evolución
Area
Botánica
Identifiers
5 results
Search Results
Now showing 1 - 5 of 5
Item Phylogenomic delineation of Physcomitrium (Bryophyta: Funariaceae) based on targeted sequencing of nuclear exons and their flanking regions rejects the retention of Physcomitrella, Physcomitridium and Aphanorrhegma(Journal of Systematics and Evolution, 2019) Medina Bujalance, Rafael; Johnson, Matthew G.; Liu, Yang ; Wickett, Norman J. ; Shaw, A. Jonathan ; Goffinet, BernardSelection on spore dispersal mechanisms in mosses is thought to shape the transformation of the sporophyte. The majority of extant mosses develop a sporangium that dehisces through the loss of an operculum, and regulates spore release through the movement of articulate teeth, the peristome, lining the capsule mouth. Such complexity was acquired by the Mesozoic Era, but was lost in some groups during subsequent diversification events, challenging the resolution of the affinities for taxa with reduced architectures. The Funariaceae are a cosmopolitan and diverse lineage of mostly annual mosses, and exhibit variable sporophyte complexities, spanning from long, exerted, operculate capsules with two rings of well-developed teeth, to capsules immersed among maternal leaves, lacking a differentiated line of dehiscence (i.e., inoperculate) and without peristomes. The family underwent a rapid diversification, and the relationships of taxa with reduced sporophytes remain ambiguous. Here, we infer the relationships of five taxa with highly reduced sporophytes based on 648 nuclear loci (exons complemented by their flanking regions), based on inferences from concatenated data and concordance analysis of single gene trees. Physcomitrellopsis is resolved as nested within one clade of Entosthodon. Physcomitrella s. l., is resolved as a polyphyletic assemblage and, along with its putative relative Aphanorrhegma, nested within Physcomitrium. We propose a new monophyletic delineation of Physcomitrium, which accommodates species of Physcomitrella and Aphanorrhegma. The monophyly of Physcomitrium s. l. is supported by a small plurality of exons, but a majority of trees inferred from exons and their adjacent non-coding regions.Item HybPiper: Extracting coding sequence and introns for phylogenetics from high‐throughput sequencing reads using target enrichment(Application in Plant Sciences, 2016) G. Johnson, Matthew ; Gardner, Elliot M. ; Liu, Yang; Medina Bujalance, Rafael; Goffinet, Bernard; Shaw, A. Jonathan; Zerega, Nyree J. C.; Wickett, Norman J.Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of highthroughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a userfriendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.Item Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes(NAture Communications, 2019) Liu, Yang ; Johnson, Matthew G. ; Cox, Cymon J. ; Medina Bujalance, Rafael; Devos, Nicolas ; Vanderpoorten, Alain ; Hedenäs, Lars ; Bell, Neil E. ; Shevock, James R. ; Aguero, Blanka ; Quandt, Dietmar; Wickett, Norman J. ; Shaw, A. Jonathan ; Goffinet, BernardMosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.Item Lewinskya, a new genus to accommodate the phaneroporous and monoicous taxa of Orthotrichum (Bryophyta, Orthotrichaceae)(Cryptogamie, Bryologie, 2016) Lara, Francisco; Garilleti, Ricardo; Goffinet, Bernard; Draper, Isabel; Medina Bujalance, Rafael; Vigalondo, Beatriz; Mazimpaka, VicenteMolecular analyses have consistently evidenced the phylogenetic heterogeneity of Orthotrichum Hedw., and suggested the need to segregate the species with superficial stomata in a separate genus. A recent proposal has been made to accommodate the monoicous species with such stomata in the genus Dorcadion Adans. ex Lindb., which is, however, an illegitimate name according to the current Code of nomenclature of algae, fungi and plants. Consequently a new name is required, and the generic name Lewinskya F.Lara, Garilleti & Goffinet is proposed. New combinations are made for all the species included in the new genus. Given the long history of the genus Orthotrichum and the similarities between this genus and Lewinskya, the morphological and geographic circumscriptions of both genera are provided to define them accurately. The taxa remaining in Orthotrichum s.str. are also listedItem 350 My of Mitochondrial Genome Stasis in Mosses, an Early Land Plant Lineage(Molecular Biology and Evolution, 2014) Liu, Yang; Medina Bujalance, Rafael; Goffinet, BernardAmong land plants, angiosperms have the structurally most labile mitochondrial (mt) genomes. In contrast, the so-called early land plants (e.g., mosses) seem to have completely static mt chromosomes. We assembled the complete mt genomes from 12 mosses spanning the moss tree of life, to assess 1) the phylogenetic depth of the conserved mt gene content and order and 2) the correlation between scattered sequence repeats and gene order lability in land plants. The mt genome of most mosses is approximately 100 kb in size, and thereby the smallest among land plants. Based on divergence time estimates, moss mt genome structure has remained virtually frozen for 350 My, with only two independent gene losses and a single gene relocation detected across the macroevolutionary tree. This is the longest period of mt genome stasis demonstrated to date in a plant lineage. The complete lack of intergenic repeat sequences, considered to be essential for intragenomic recombinations, likely accounts for the evolutionary stability of moss mt genomes.