8 results on '"Agustín Jiménez-Ruiz"'
Search Results
2. Phylotyping and functional analysis of two ancient human microbiomes.
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Raúl Y Tito, Simone Macmil, Graham Wiley, Fares Najar, Lauren Cleeland, Chunmei Qu, Ping Wang, Frederic Romagne, Sylvain Leonard, Agustín Jiménez Ruiz, Karl Reinhard, Bruce A Roe, and Cecil M Lewis
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Medicine ,Science - Abstract
BACKGROUND: The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas. METHODOLOGY/PRINCIPAL FINDINGS: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases. CONCLUSIONS/SIGNIFICANCE: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.
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- 2008
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3. Three new species of Cytauxzoon in European wild felids
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David Modrý, Mason V. Reichard, Luciana Cătălina Panait, Angela Monica Ionică, Adnan Hodžić, Kristýna Hrazdilová, Jana Juránková, Elliott A. Zieman, Andrei Daniel Mihalca, Mike Heddergott, Clayton K. Nielsen, Georgiana Deak, Călin Mircea Gherman, Fabrizia Veronesi, and Francisco Agustín Jiménez-Ruiz
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Felidae ,Mitochondrial DNA ,040301 veterinary sciences ,Genotypes ,European wild felids ,18S ,Wild ,Zoology ,Animals, Wild ,Piroplasmids ,Cytauxzoon ,Piroplasmida ,0403 veterinary science ,03 medical and health sciences ,Species Specificity ,RNA, Ribosomal, 18S ,Animals ,Clade ,Protozoan Infections, Animal ,Phylogeny ,030304 developmental biology ,Ribosomal ,0303 health sciences ,Genetic diversity ,Genome ,Protozoan Infections ,18S rDNA ,General Veterinary ,biology ,Phylogenetic tree ,Animal ,Felis ,Cytochrome c oxidase subunit I ,Mitochondrial genes ,DNA ,04 agricultural and veterinary sciences ,General Medicine ,DNA, Protozoan ,biology.organism_classification ,Mitochondrial ,Europe ,Genome, Mitochondrial ,Protozoan ,Babesia ,RNA ,Parasitology ,Genome, Protozoan - Abstract
Protists of the genus Cytauxzoon infect a wide variety of wild and domestic felids worldwide. While the American Cytauxzoon felis has been well described, data on the European isolates of Cytauxzoon are still scant. The aim of the current study was to determine the genetic diversity of European Cytauxzoon spp. in wild felids across Europe by analyzing one nuclear and two mitochondrial genes, along with representative complete mitochondrial genomes. Overall, 106 biological samples from wild felids (92 from Felis silvestris and 14 from Lynx lynx) from Germany, Romania, Czech Republic, and Luxembourg were collected and screened for the presence of Cytauxzoon spp. using nested PCR protocols, targeting the highly conserved 18S rDNA, mitochondrial cytochrome b (CytB) and cytochrome c oxidase subunit I (COI) genes. Furthermore, 18 previously confirmed wild felid biological samples from Europe, and comparative material from USA positive for C. felis, were included in the study. In 18S rDNA sequences analyses, Cytauxzoon spp. from felids formed two separate clades of New World and Old World isolates, with a low inner diversity of the European clade. In contrast to 18S rDNA, the phylogenetic analyses of CytB and COI genes affirmatively revealed three highly supported clades, resulting in three defined genotypes. Similar intra- and interspecific variability of CytB and COI genes was observed in the case of different Babesia spp. Considering geography, host species and analyses of three genes, we conclude that the three detected genotypes of Cytauxzoon in European wild felids represent three new species, which we herein describe.
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- 2021
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4. Un registro nuevo de Atractus boettgeri (Serpentes: Colubridae), con comentarios sobre la taxonomía e historia natural de la especie
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Agustín Jiménez-Ruiz, Jorge Salazar-Bravo, Julieta Vargas, and Jay M. Savage
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Geography ,biology ,Atractus ,Colubridae ,Taxonomy (biology) ,biology.organism_classification ,Humanities ,Ecology, Evolution, Behavior and Systematics - Abstract
Se reporta una extension de en la distribucion de la especie Atractus boettgeri, una serpiente endemica de Bolivia. Esta especie se diferencia de A. taeniatus por tener un numero segmental muy por encima del intervalo descrito para A. taeniatus y por tener solo 6 dientes maxilares, en vez de 8-9 en A. taeniatus. Ademas, A. boettgeri se diferencia de A. emmeli por tener escamas supralabiales en patron 6-6 (en vez de 7-7) y tener un conteo de escamas ventrales menor en hembras (175-177 versus 181-189). Incluyendo este, todos los registros conocidos para A. boettgeri parecen estar asociados con la vegetacion del Cerrado en Bolivia. El ejemplar se encontro en el estomago del tatu comun (Dasypus novemcinctus).
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- 2010
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5. Litomosoides (Nemata: Filarioidea) of Bats from Bolivia with Records for Three Known Species and the Description of a New Species
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Juliana Notarnicola, F. Agustín Jiménez Ruiz, and Scott Lyell Gardner
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Sympatry ,Male ,Bolivia ,Biodiversity ,Zoology ,Ciencias Biológicas ,Common species ,Chiroptera ,Nearctic ecozone ,Bats ,Prevalence ,Animals ,Ecology, Evolution, Behavior and Systematics ,Filarioidea ,Filarioids ,Lasiurus ,biology ,Amazon rainforest ,Ecology ,Zoología, Ornitología, Entomología, Etología ,Thorn forest ,biology.organism_classification ,Filariasis ,Onchocercidae ,Parasitology ,Taxonomy (biology) ,Female ,CIENCIAS NATURALES Y EXACTAS - Abstract
Herein, we describe Litomosoides salazari n. sp. collected from the body cavity of the yellow bat, Lasiurus ega, from Bolivia. This new species of filarioid nematode is most closely related to the carinii group and is characterized by its relatively small size with the vulva located slightly posterior to the esophago-intestinal junction; an arrow-shaped buccal capsule; and a short, rounded tail. New host and locality records for both Litomosoides hamletti and L. chandleri in phyllostomid bats, and L. brasiliensis occurring in both phyllostomid and vespertilionid bats, are provided. The morphological variability of the specimens is documented by providing comparative measurements of 3 known species. Litomosoides brasiliensis occurs in 6 species of bats from Bolivia and was the most common species of filarioid nematode encountered. All 4 species of nematodes, including the new species, were found in sympatry at Chijchijpa, a locality in the Yungas of Bolivia. Bolivia is a country of great biological diversity (Anderson, 1997), with more than 300 species of mammals occurring there. Of these, approximately 5% are endemic, occurring nowhere else (Anderson, 1997). More than 100 species of bats have been identified from within the country (Anderson, 1997; Simmons, 2005). This great diversity is a result of a confluence of several biomes conjoining in the area, including high-altitude Andes and Puna-Altiplano, the Yungas in the eastern foothills of the Andes, Amazon tropical forest in the northeast, and a mixture of grassland and chaco thorn forest coming in from the southern and eastern lowlands (Unzueta, 1975). Filarioid nematodes of Litomosoides Chandler, 1931 occur in the body cavities of bats, marsupials, and sigmodontine and hystricognath rodents throughout the Neotropical and southern Nearctic regions. Showing relatively high taxonomic diversity with approximately 30 described species, these nemas exhibit an indirect pattern of transmission between mammalian hosts, with all known life cycles requiring an arthropod vector or interme- diate host to transfer microfilariae between and among definitive hosts (Bain et al., 1980). As a result of the continuing work on the biodiversity of mammals of Bolivia as part of the Bolivian Parasite Biodiversity Project, we report herein the results of our work on the filarioid nematodes of bats from Bolivia. This work, funded by the National Science Foundation, was undertaken as a collaborative
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- 2010
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6. A new record of Atractus boettgeri (Serpentes: Colubridae), with notes on taxonomy and natural history Un registro nuevo de Atractus boettgeri (Serpentes: Colubridae), con comentarios sobre la taxonomía e historia natural de la especie
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Jorge Salazar-Bravo, Julieta Vargas, Agustín Jimenez-Ruiz, and Jay M. Savage
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Atractus boettgeri ,Atractus taeniatus ,Atractus emmeli ,Bolivia ,Biology (General) ,QH301-705.5 - Abstract
We report a range extension of Atractus boettgeri, a rare snake endemic to Bolivia. This species differs from Atractus taeniatus by a higher segmental count (well outside the range for A. taeniatus) and by having only 6 maxillary teeth as opposed to 8-9 in A. taeniatus. In addition, A. boettgeri differs from A. emmeli in having 6-6 supralabials (versus 7-7) and fewer ventrals (175-177 versus 181-189 in females). All known records of A. boettgeri indicate an association between this species and the Cerrado vegetation of central Bolivia. This report is also unique in that the specimen reported herein was found in the stomach of a Common Long-Nosed Armadillo (Dasypus novemcinctus).Se reporta una extensión de en la distribución de la especie Atractus boettgeri, una serpiente endémica de Bolivia. Esta especie se diferencia de A. taeniatus por tener un número segmental muy por encima del intervalo descrito para A. taeniatus y por tener sólo 6 dientes maxilares, en vez de 8-9 en A. taeniatus. Además, A. boettgeri se diferencia de A. emmeli por tener escamas supralabiales en patrón 6-6 (en vez de 7-7) y tener un conteo de escamas ventrales menor en hembras (175-177 versus 181-189). Incluyendo éste, todos los registros conocidos para A. boettgeri parecen estar asociados con la vegetación del Cerrado en Bolivia. El ejemplar se encontró en el estómago del tatú común (Dasypus novemcinctus).
- Published
- 2010
7. Helminth parasites of garter snakes and mud turtles from several localities of the Mesa Central of Mexico
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Gerardo Pérez-Ponce de León, Agustín Jiménez-Ruiz, F., Mendoza-Garfias, B., and García-Prieto, L.
8. Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans
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Hendrik N. Poinar, Fabien L. Condamine, Frédéric Delsuc, Mariella Superina, Melanie Kuch, Jacob Enk, Gillian C. Gibb, Nadia Moraes-Barros, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, University of Alberta, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden, McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada, Instituto de Biociências, Universidade de São Paulo (USP), Instituto de Biociências, Universidade de São Paulo, Biological Science Department, University of New Orleans, New Orleans, This work largely benefited from the help of the following individuals and institutions who provided tissue samples: François Catzeflis (Institut des Sciences de l’Evolution, Montpellier, France), Jean-François Mauffrey, Philippe Gaucher, Eric Hansen, François Ouhoud-Renoux, Jean-Christophe Vié, Philippe Cerdan, Michel Blanc, and Rodolphe Paowé (French Guiana), Sergio Vizcaíno (Museo de La Plata, La Plata, Argentina), Jorge Omar García and Rodolfo Rearte (Complejo Ecológico Municipal, Presidencia Roque Sáenz Peña, Argentina), Daniel Hernández (Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay), John Trupkiewicz (Philadelphia Zoo, USA), Darrin Lunde (National Museum of Natural History, Washington, USA), Jim Patton and Yuri Leite (Museum of Vertebrate Zoology, Berkeley, USA), Ross MacPhee (American Museum of Natural History, New York, USA), Jonathan Dunnum and Joseph Cook (Museum of Southwestern Biology, Albuquerque, USA), Donna Dittman and Mark Hafner (Louisiana State University Museum of Natural Science, Baton Rouge, USA), Gerhard Haszprunar and Michael Hiermeier (Zoologische Staatssammlung München, Munich, Germany), Géraldine Véron (Museum National d’Histoire Naturelle, Paris, France), Agustín Jiménez-Ruiz, Guido Valverde, and Guillermo Pérez-Jimeno. Our thanks also extend to Trish McLenachan and David Penny who sequenced and made freely available the first sloth mitogenomes, Lionel Hautier and Philippe Gaubert for taxonomical advice, and two anonymous referees for helpful comments. This work was supported by grants from the EU’s Seventh Framework Programme (No 286431) to N.M.-B., the Centre National de la Recherche Scientifique (CNRS), the Scientific Council of Université Montpellier 2 (UM2), and Investissement d’Avenir of the Agence Nationale de la Recherche (CEBA: ANR-10-LABX-25-01) to F.D., and the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Canada Research Chairs program to H.N.P. This is contribution ISEM 2015-227-S of the Institut des Sciences de l’Evolution de Montpellier, ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), University of Gothenburg (GU), McMaster Ancient DNA Center [Hamilton, Ontario], McMaster University [Hamilton, Ontario], and University of New Orleans
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0106 biological sciences ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Lineage (evolution) ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,01 natural sciences ,molecular phylogenetics ,purl.org/becyt/ford/1 [https] ,Clade ,Phylogeny ,shotgun Illumina sequencing ,Mammals ,biology ,Phylogenetic tree ,Ecology ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,High-Throughput Nucleotide Sequencing ,Genomics ,Biological Evolution ,mitochondrial genomes ,Molecular phylogenetics ,CIENCIAS NATURALES Y EXACTAS ,Systematics ,Otras Ciencias Biológicas ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,010603 evolutionary biology ,Ciencias Biológicas ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,[SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology ,Genetics ,Animals ,mammals ,purl.org/becyt/ford/1.6 [https] ,molecular dating ,Molecular Biology ,Discoveries ,Ecology, Evolution, Behavior and Systematics ,Computational Biology ,Bayes Theorem ,Xenarthra ,15. Life on land ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Genome, Mitochondrial ,Dasypus - Abstract
Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos in two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 million years ago. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 million years. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guianan shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats. Fil: Gibb, Gillian C.. Universite de Montpellier; Francia. Massey Universit; Nueva Zelanda Fil: Condamine, Fabien L.. University of Gothenburg; Suecia. Universite de Montpellier; Francia. University of Alberta; Canadá Fil: Kuch, Melanie. McMaster University; Canadá Fil: Enk, Jacob. McMaster University; Canadá Fil: Moraes Barros, Nadia. Universidade Do Porto; Portugal. Universidade de Sao Paulo; Brasil Fil: Superina, Mariella. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; Argentina Fil: Poinar, Hendrik N.. McMaster University; Canadá Fil: Delsuc, Frederic. Universite de Montpellier; Francia
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- 2015
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