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Gutiérrez EG, Ortega J, Savoie A, Baeza JA. The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates. BMC Genomics 2023; 24:527. [PMID: 37674108 PMCID: PMC10481570 DOI: 10.1186/s12864-023-09596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The harsh conditions of high-altitude environments are known to drive the evolution of physiological and morphological traits in endothermic animals. These conditions are expected to result in the adaptive evolution of protein coding genes encoded in mitochondrial genomes that are vital for the oxidative phosphorylation pathway. In this study, we formally tested for signatures of adaptive evolution on mitochondrial protein coding genes in Tapirus pinchaque and other odd-toed ungulates inhabiting high-elevation environments. RESULTS The AT-rich mitochondrial genome of T. pinchaque is 16,750 bp long. A phylomitogenomic analysis supports the monophyly of the genus Tapirus and families in the Perissodactyla. The ratio of non-synonymous to synonymous substitutions demonstrated that all mitochondrial genes undergo purifying selection in T. pinchaque and other odd ungulates living at high elevations. Over this negative background selection, Branch Models suggested that cox3 and nad6 might be undergoing stronger purifying selection than other mitochondrial protein coding genes. Furthermore, Site Models suggested that one and four sites in nad2 and nad5, respectively, could be experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation of selection strength in nad6, evidence of episodic diversifying selection in cob, and revealed episodic positive/diversifying selection signatures for two sites in nad1, and one site each in nad2 and nad4. CONCLUSION The mitochondrial genome of T. pinchaque is an important genomic resource for conservation of this species and this study contributes to the understanding of adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates inhabiting high-altitude environments.
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Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala S/N, Col. Santo Tomás, Ciudad de México, C.P. 11340, Mexico
| | - Avery Savoie
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA
| | - J Antonio Baeza
- Department of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC, 29634, USA.
- Smithsonian Marine Station at Fort Pierce, 701 Seaway Drive, Fort Pierce, FL, 34949, USA.
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile.
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Saldaña CZ, Gutiérrez EG, Carlos ZC, Jose CA, Jean AV, Alejandro LP, Lopez CS. [Factors associated with prolonged hospital-stay after appendectomy during the SARS-CoV-2 pandemic]. Khirurgiia (Mosk) 2023:47-52. [PMID: 37916557 DOI: 10.17116/hirurgia202310147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
OBJECTIVE To determine the factors associated with prolonged hospital-stay after appendectomy in SARS-CoV-2 pandemic. MATERIAL AND METHODS A retrospective observational cohort study included 420 patients after surgery for acute appendicitis between March 2019 and March 2020, April 2020 and April 2021. There were 336 patients before the SARS-COV-2 pandemic, and 84 ones underwent surgery during the pandemic. RESULTS Incidence of prolonged hospital stay was 15% and 26%, respectively (RR 1.76). RR is more than 1 and assumes SARS-CoV-2 infection as a risk factor. CONCLUSION There is an association between SARS-CoV-2 infection and prolonged hospital-stay after surgery for acute appendicitis (RR 1.76).
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Affiliation(s)
- C Z Saldaña
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
| | - E G Gutiérrez
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
| | - Z C Carlos
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
| | - C-A Jose
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
| | - A V Jean
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
| | - L P Alejandro
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
| | - C S Lopez
- School of Medicine, Antenor Orrego Private University, Trujillo, Peru
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Espinoza-Gómez A, Moreno-Santillán DD, Juárez-Maldonado R, Gutiérrez EG, Salazar MI, Alonso-Palomares LA, López-Vidal JC, Elizalde-Arellano C, Ortega J. Identification of viral RNA sequences in vampire bats (Desmodus rotundus) from central Mexico. REV MEX BIODIVERS 2022. [DOI: 10.22201/ib.20078706e.2022.93.4021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Bats are important reservoirs of viral entities that cause diverse economical and health problems in several sectors. The purpose of this study was to determine the prevalence of the rabies virus in vampire bats. We also tested for 3 other zoonotic viruses in the collected tissue. We captured 45 vampire bats (Desmodus rotundus), which were measured and sexed under standard parameters. We followed an RT-PCR reaction to amplify the viral products of four virus types: chikungunya (CHIKV), dengue (DENV), rabies (RABV) and Zika virus (ZIKV) from cerebral tissue. We obtained an amplicon of 100 bp for ZIKV in 2 samples, representing a prevalence of 4.4%. An amplicon of 581 bp for RABV was observed in 9 individuals, which is equivalent to 20% of our sample. We obtained 4 different haplotypes for RABV and a single haplotype for ZIKV. We did not record the presence of DENV and CHIKV. We corroborated the presence of the family Rhabdoviridae in the vampire bat and recorded the presence of ZIKV for the first time in this bat species.
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Gutiérrez EG, Rodríguez-Herrera B, Baeza JA, Isabel Salazar M, Ortega J. Genetic Analyses Reveal High Connectivity among Populations of the Honduran White Bat Ectophylla alba in the Caribbean Lowlands of Central Eastern Costa Rica. Acta Chiropterologica 2022. [DOI: 10.3161/15081109acc2022.24.1.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Edgar G. Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340,
| | - Bernal Rodríguez-Herrera
- Escuela de Biología y Centro de Investigación en Biodiversidad y Ecología Tropical, Universidad de Costa Rica, 11501-2060, San Pedro de Montes de Oca, San José, Costa Rica
| | - J. Antonio Baeza
- Departament of Biological Sciences, 132 Long Hall, Clemson University, Clemson, SC 29634, USA
| | - Ma. Isabel Salazar
- Laboratorio de Virología e Inmunovirología, Posgrado en Ciencias Químicobiológicas, Posgrado de Inmunología, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Químicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomás, C.P. 11340,
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Gutiérrez EG, Vivas-Toro I, Carmona-Ruíz D, Villalobos-Chaves D, Rodríguez-Herrera B, Real-Monroy MD, León-Avila G, Ortega J. Socio-spatial organization reveals paternity and low kinship in the Honduran white bat (Ectophylla alba) in Costa Rica. Integr Zool 2021; 16:646-658. [PMID: 33411951 DOI: 10.1111/1749-4877.12514] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ectophylla alba is a tent-making bat that roosts in mixed-sex clusters comprising adults and offspring. Our goal was to determine the genetic identity of individuals belonging to different roosting groups. We tested the hypothesis of kin selection as a major force structuring group composition. We used 9 microsatellites designed for E. alba to determine the genetic identity and probability of parentage of individuals. We analyzed parentage and kinship using the software ML-Relate, GenAIEx, and Cervus. The obtained relationship probabilities (0.5) revealed a clear maternal relationship between female adults and offspring with allele compatibility, and at least 5 relationships between male adults and pups. We found a low degree of relatedness within roosting groups. Between roosting groups at different sites, the mean probability of a half-sibling relationship ranged from 0.214 to 0.244 and, for full-sibling relationship, from 0.383 to 0.553. Genetically, adult individuals were poorly related within clusters, and kinship as an evolutionary force could not explain group membership.
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Affiliation(s)
- Edgar G Gutiérrez
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Isabela Vivas-Toro
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Daniela Carmona-Ruíz
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | | | | | - Melina Del Real-Monroy
- Laboratorio de Genómica Evolutiva, Doctorado en Ciencias Básicas, Universidad Autónoma de Zacatecas, Zacatecas, Zac., México
| | - Gloria León-Avila
- Laboratorio de Genética, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Jorge Ortega
- Laboratorio de Bioconservación y Manejo, Posgrado en Ciencias Quimicobiológicas, Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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Zamora‐Gutierrez V, Ortega J, Avila‐Flores R, Aguilar‐Rodríguez PA, Alarcón‐Montano M, Avila‐Torresagatón LG, Ayala‐Berdón J, Bolívar‐Cimé B, Briones‐Salas M, Chan‐Noh M, Chávez‐Cauich M, Chávez C, Cortés‐Calva P, Cruzado J, Cuevas JC, Del Real‐Monroy M, Elizalde‐Arellano C, García‐Luis M, García‐Morales R, Guerrero JA, Guevara‐Carrizales AA, Gutiérrez EG, Hernández‐Mijangos LA, Ibarra‐López MP, Iñiguez‐Dávalos LI, León‐Madrazo R, López‐González C, López‐Téllez MC, López‐Vidal JC, Martínez‐Balvanera S, Montiel‐Reyes F, Murrieta‐Galindo R, Orozco‐Lugo CL, Pech‐Canché JM, Pérez‐Pérez L, Ramírez‐Martínez MM, Rizo‐Aguilar A, Robredo‐Esquivelzeta E, Rodas‐Martínez AZ, Rojo‐Cruz MA, Selem‐Salas CI, Uribe‐Bencomo E, Vargas‐Contreras JA, MacSwiney G. MC. The Sonozotz project: Assembling an echolocation call library for bats in a megadiverse country. Ecol Evol 2020; 10:4928-4943. [PMID: 32551071 PMCID: PMC7297765 DOI: 10.1002/ece3.6245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 11/23/2022] Open
Abstract
Bat acoustic libraries are important tools that assemble echolocation calls to allow the comparison and discrimination to confirm species identifications. The Sonozotz project represents the first nation-wide library of bat echolocation calls for a megadiverse country. It was assembled following a standardized recording protocol that aimed to cover different recording habitats, recording techniques, and call variation inherent to individuals. The Sonozotz project included 69 species of echolocating bats, a high species richness that represents 50% of bat species found in the country. We include recommendations on how the database can be used and how the sampling methods can be potentially replicated in countries with similar environmental and geographic conditions. To our knowledge, this represents the most exhaustive effort to date to document and compile the diversity of bat echolocation calls for a megadiverse country. This database will be useful to address a range of ecological questions including the effects of anthropogenic activities on bat communities through the analysis of bat sound.
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Affiliation(s)
- Veronica Zamora‐Gutierrez
- CONACYT—Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Durango (CIIDIR)Instituto Politécnico NacionalDurangoMéxico
| | - Jorge Ortega
- Departamento de ZoologíaEscuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalCiudad de MéxicoMéxico
| | - Rafael Avila‐Flores
- División Académica de Ciencias BiológicasUniversidad Juárez Autónoma de TabascoVillahermosaMéxico
| | - Pedro Adrián Aguilar‐Rodríguez
- Centro de Investigaciones TropicalesUniversidad VeracruzanaXalapaMéxico
- Universidad Autónoma de TlaxcalaTlaxcala de XicohténcatlMéxico
| | | | | | | | | | - Miguel Briones‐Salas
- Centro Interdisciplinario de Investigación para el Desarrollo Integral RegionalUnidad Oaxaca (CIIDIR)Instituto Politécnico NacionalOaxacaMéxico
| | - Martha Chan‐Noh
- Campus de Ciencias Biológicas‐AgropecuariasUniversidad Autónoma de YucatánMéridaMéxico
| | - Manuel Chávez‐Cauich
- Campus de Ciencias Biológicas‐AgropecuariasUniversidad Autónoma de YucatánMéridaMéxico
| | - Cuauhtémoc Chávez
- Departamento de Ciencias AmbientalesUniversidad Autónoma Metropolitana‐Unidad LermaLermaMéxico
| | - Patricia Cortés‐Calva
- Programa de Planeación Ambiental y ConservaciónCentro de Investigaciones Biológicas del Noroeste, S.C.La PazMéxico
| | | | - Jesús Carlo Cuevas
- Ingeniería en Recursos Naturales y AgropecuariosUniversidad de GuadalajaraAutlánMéxico
| | | | - Cynthia Elizalde‐Arellano
- Departamento de ZoologíaEscuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalCiudad de MéxicoMéxico
| | - Margarita García‐Luis
- Centro Interdisciplinario de Investigación para el Desarrollo Integral RegionalUnidad Oaxaca (CIIDIR)Instituto Politécnico NacionalOaxacaMéxico
- Instituto Tecnológico del Valle de OaxacaXoxocotlánMéxico
| | | | - José Antonio Guerrero
- Facultad de Ciencias BiológicasUniversidad Autónoma del Estado de MorelosCuernavacaMéxico
| | | | - Edgar G. Gutiérrez
- Departamento de ZoologíaEscuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalCiudad de MéxicoMéxico
| | | | | | | | - Rafael León‐Madrazo
- División Académica de Ciencias BiológicasUniversidad Juárez Autónoma de TabascoVillahermosaMéxico
| | - Celia López‐González
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Durango (CIIDIR)Instituto Politécnico NacionalDurangoMéxico
| | | | - Juan Carlos López‐Vidal
- Departamento de ZoologíaEscuela Nacional de Ciencias BiológicasInstituto Politécnico NacionalCiudad de MéxicoMéxico
| | | | - Fernando Montiel‐Reyes
- Centro Interdisciplinario de Investigación para el Desarrollo Integral Regional Unidad Durango (CIIDIR)Instituto Politécnico NacionalDurangoMéxico
| | | | - Carmen Lorena Orozco‐Lugo
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMéxico
| | - Juan M. Pech‐Canché
- Facultad de Ciencias Biológicas y AgropecuariasUniversidad VeracruzanaTuxpanMéxico
| | - Lucio Pérez‐Pérez
- División Académica de Ciencias BiológicasUniversidad Juárez Autónoma de TabascoVillahermosaMéxico
| | | | - Areli Rizo‐Aguilar
- Facultad de Ciencias Químicas e IngenieríaUniversidad Autónoma del Estado de MorelosCuernavacaMéxico
| | | | - Alba Z. Rodas‐Martínez
- División Académica de Ciencias BiológicasUniversidad Juárez Autónoma de TabascoVillahermosaMéxico
| | | | | | - Elena Uribe‐Bencomo
- Campus de Ciencias Biológicas‐AgropecuariasUniversidad Autónoma de YucatánMéridaMéxico
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Gutiérrez EG, Hernández Canchola G, León Paniagua LS, Martínez Méndez N, Ortega J. Isolation and characterization of microsatellite markers for Sturnira parvidens and cross-species amplification in Sturnira species. PeerJ 2017; 5:e3367. [PMID: 28560110 PMCID: PMC5445947 DOI: 10.7717/peerj.3367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/28/2017] [Indexed: 11/20/2022] Open
Abstract
Background Sturnira is one of the most species-rich genera in the Neotropics, and it is found from Mexico and the Lesser Antilles to Argentina. This genus forms a well-supported monophyletic clade with at least twenty-one recognized species, as well as several others under taxonomic review. Sturnira parvidens is a widespread frugivorous bat of the deciduous forests of the Neotropics, is highly abundant, and is a major component in fruit dispersal to regenerate ecosystems. Methods We used a technique based on Illumina paired-end sequencing of a library highly enriched for microsatellite repeats to develop loci for S. parvidens. We analyzed millions of resulting reads with specialized software to extract those reads that contained di-, tri-, tetra-, penta-, and hexanucleotide microsatellites. Results We selected and tested 14 polymorphic (di, tri, and tetra) microsatellites. All markers were genotyped on 26 different individuals from distinct locations of the distributional area of S. parvidens. We observed medium—high genetic variation across most loci, but only 12 were functionally polymorphic. Levels of expected heterozygosity across all markers were high to medium (mean HE = 0.79, mean HO = 0.72). We examined ascertainment bias in twelve bats of the genus, obtaining null/monomorphic/polymorphic amplifications. Discussion The Illumina paired-end sequencing system is capable of identifying massive numbers of microsatellite loci, while expending little time, reducing costs, and providing a large amount of data. The described polymorphic loci for S. parvidens in particular, and for the genus in general, could be suitable for further genetic analysis, including taxonomic inconsistencies, parentage/relatedness analysis, and population genetics assessments.
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Affiliation(s)
- Edgar G Gutiérrez
- Department of Zoología, Instituto Politécnico Nacional/ENCB, CDMX, CDMX, México
| | | | | | | | - Jorge Ortega
- Department of Zoología, Instituto Politécnico Nacional/ENCB, CDMX, CDMX, México
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