Molecular evolution and phylogenetics of caecilian amphibians (Gymnophiona)

Tesis doctoral inédita leida en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura:01-12-200

A new species of sand racer, Psammodromus (Squamata: Lacertidae), from the Western Iberian Peninsula

[EN] A new species of lacertid lizard of the genus Psammodromus is described from the Iberian Peninsula. Genetic and recently published phenotypic data support the differentiation of Psammodromus hispanicus into three, and not as previously sug-gested two, distinct lineages. Age estimates, lineage allopatry, the lack of mitochondrial and nuclear haplotype sharing between lineages, ecological niche divergence, and the current biogeographic distribution, indicated that the three lineages correspond to three independent species. Here, we describe a new species, Psammodromus occidentalis sp. n., which is genetically different from the other sand racers and differentiated by the number of femoral pores, number of throat scales, snout shape, head ratio, green nuptial coloration, and number of supralabial scales below the subocular scale. We also pro-pose to upgrade the two previously recognized subspecies, Psammodromus hispanicus hispanicus Fitzinger, 1826 from central Spain and Psammodromus hispanicus edwardsianus (Dugès, 1829) from eastern Spain, to the species level: Psam-modromus hispanicus stat. nov. and Psammodromus edwardsianus stat. nov. Given that the holotype of Psammodromus hispanicus was lost, we designate a neotype. We also analysed museum specimens of P. blanci, P. microdactylus and P. algirus to describe differentiation of the Psammodromus hispanicus lineages/species from their closest relatives. Copyright © 2011 Magnolia Press.Peer Reviewe

Integrative analyses of speciation and divergence in Psammodromus hispanicus (Squamata: Lacertidae)

BackgroundGenetic, phenotypic and ecological divergence within a lineage is the result of past and ongoing evolutionary processes, which lead ultimately to diversification and speciation. Integrative analyses allow linking diversification to geological, climatic, and ecological events, and thus disentangling the relative importance of different evolutionary drivers in generating and maintaining current species richness.ResultsHere, we use phylogenetic, phenotypic, geographic, and environmental data to investigate diversification in the Spanish sand racer (Psammodromus hispanicus). Phylogenetic, molecular clock dating, and phenotypic analyses show that P. hispanicus consists of three lineages. One lineage from Western Spain diverged 8.3 (2.9-14.7) Mya from the ancestor of Psammodromus hispanicus edwardsianus and P. hispanicus hispanicus Central lineage. The latter diverged 4.8 (1.5-8.7) Mya. Molecular clock dating, together with population genetic analyses, indicate that the three lineages experienced northward range expansions from southern Iberian refugia during Pleistocene glacial periods. Ecological niche modelling shows that suitable habitat of the Western lineage and P. h. edwardsianus overlap over vast areas, but that a barrier may hinder dispersal and genetic mixing of populations of both lineages. P. h. hispanicus Central lineage inhabits an ecological niche that overlaps marginally with the other two lineages.ConclusionsOur results provide evidence for divergence in allopatry and niche conservatism between the Western lineage and the ancestor of P. h. edwardsianus and P. h. hispanicus Central lineage, whereas they suggest that niche divergence is involved in the origin of the latter two lineages. Both processes were temporally separated and may be responsible for the here documented genetic and phenotypic diversity of P. hispanicus. The temporal pattern is in line with those proposed for other animal lineages. It suggests that geographic isolation and vicariance played an important role in the early diversification of the group, and that lineage diversification was further amplified through ecological divergence

Historia general de los religiosos descalzos del orden de los ermitaños del gran padre, y doctor de la Iglesia San Agustin, de la Congregacion de España, y de las Indias

Copia digital : Junta de Castilla y León. Consejería de Cultura y Turismo, 2014Sign. : []4, 2[parágrafo]-3[parágrafo]4, 2A-2Z4, 3A-3Z4, 4A-4B4, 5C6.Grab. calcográfico en [parágrafo]3 de "Valls Del. Sculp. Barcin."Texto a dos col.Port. con orla tip.Port. frontispicia grab. calc. "Pº a Villa franca Sculptor Regis, scupsit Matriti, 1663

What Lies Beneath? Molecular Evolution During the Radiation of Caecilian Amphibians

Background: Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians. Results: A total of 8540 candidate groups of orthologous genes from transcriptomic data of five species of caecilian amphibians and the genome of the frog Xenopus tropicalis were analysed in order to investigate the genetic machinery behind caecilian diversification. We found a total of 168 protein-coding genes with signatures of positive selection at different evolutionary times during the radiation of caecilians. The majority of these genes were related to functional elements of the cell membrane and extracellular matrix with expression in several different tissues. The first colonization of the tropical soils was connected to the largest number of protein-coding genes under positive selection in our analysis. From the results of our study, we highlighted molecular changes in genes involved in perception, reduction-oxidation processes, and aging that likely were involved in the adaptation to different soil strata. Conclusions: The genes inferred to have been under positive selection provide valuable insights into caecilian evolution, potentially underpin adaptations of caecilians to their extreme environments, and contribute to a better understanding of fossorial adaptations and molecular evolution in vertebrates

Inadvertent paralog inclusion drives artifactual topologies and timetree estimates in phylogenomics

Increasingly, large phylogenomic datasets include transcriptomic data from non-model organisms. This has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. While this may be expected to result in decreased phylogenetic support it is not clear if it could also drive highly supported artefactual relationships. Many groups, including the hyper-diverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events, small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated datasets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasises the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa

What lies beneath? Molecular evolution during the radiation of caecilian amphibians

Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecilians (order Gymnophiona), probably the least known of the major lineages of vertebrates, are limbless tropical amphibians, with adults of most species burrowing in soils (fossoriality). This enigmatic order of amphibians are very distinct phenotypically from other extant amphibians and likely from the ancestor of Lissamphibia, but little to nothing is known about the molecular changes underpinning their radiation. We hypothesised that colonization of various depths of tropical soils and of freshwater habitats presented new ecological opportunities to caecilians

Next-generation mitogenomics: A comparison of approaches applied to caecilian amphibian phylogeny

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing platforms (Illumina's HiSeq and MiSeq, Roche's 454 GS FLX, and Life Technologies' Ion Torrent) to produce seven (near-) complete mitogenomes from six species that form a small radiation of caecilian amphibians from the Seychelles. The fastest, most accurate method of obtaining mitogenome sequences that we tested was direct sequencing of genomic DNA (shotgun sequencing) using the MiSeq platform. Bayesian inference and maximum likelihood analyses using seven different partitioning strategies were unable to resolve compellingly all phylogenetic relationships among the Seychelles caecilian species, indicating the need for additional data in this case

Dejó un pedazo de vida y se marchó…

En el marco de la Cátedra de Fundamentos Estéticos, cursada 2016, abordamos el análisis de una producción artística en relación a los conceptos de identidad y representación entre otros. El documental “Jorge Hidalgo”, con guión por Manuela Baigorria, fue nuestro objeto de pesquisa. Nadie elige venir al mundo, simplemente nace. El azar nos antecede y nos trasciende. Lo que logramos ser está sujeto a decisiones y acciones que no son sólo propias, a una red de existencias que también por azar van construyendo una red de vínculos y afectos que conforman el territorio en el que viviremos. Como lo dijo Heidegger somos “dasein”, ser-ahí, en constante construcción en cuanto ente del mundo y cuando alcanzamos nuestra finitud lo que dejamos son huellas de nuestra existencia. Las personas construimos nuestra identidad tanto individual como colectiva valiéndonos de nuestro entorno, el ser se construye identificando aquello que lo determina, no existe un sujeto sin los otros, que son quienes operan de manera decisiva en su propia construcción identitaria. Cuando nos relacionamos con la comunidad y también con nuestra propia familia, construimos nuestro ser y nuestro hacer, en definitiva no valemos de estas relaciones para forjar nuestra identidad.Facultad de Bellas Arte

Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families

RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation & diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians