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Napolitano C, Clavijo C, Rojas-Bonzi V, Miño CI, González-Maya JF, Bou N, Giraldo A, Martino A, Miyaki CY, Aguirre LF, Cosacov A, Milián-García Y, Prosdocimi L, Ramírez-Bravo OE, Tovar LA, Velez-Zuazo X, Barrios M, Herrera-Fernández B, Montiel-Villalobos MG, Oliveira-Miranda MA, Pool M, Santos-Murgas A, Segovia-Salcedo MC, Cecchi F, Dans AJ, Dilchand N, Lima SMQ, Novas MC, Pelz-Serrano K, Pougy N, Rodríguez I, van der Meer L, Zapata-Ríos G. Understanding the conservation-genetics gap in Latin America: challenges and opportunities to integrate genetics into conservation practices. Front Genet 2024; 15:1425531. [PMID: 39040996 PMCID: PMC11261212 DOI: 10.3389/fgene.2024.1425531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/04/2024] [Indexed: 07/24/2024] Open
Abstract
Introduction: Integrating genetic data into conservation management decisions is a challenging task that requires strong partnerships between researchers and managers. Conservation in Latin America is of crucial relevance worldwide given the high biodiversity levels and the presence of hotspots in this region. Methods: We conducted a survey across Latin America to identify gaps and opportunities between genetic researchers and conservation managers. We aimed to better understand conservation managers' points of view and how genetic research could help conservation practitioners to achieve their goals, by implementing genetic assessments that could effectively inform conservation practices. We distributed an online survey via four regional collaborating organizations and 32 focal points based in 20 Latin American countries. The target respondents were conservation managers of species or areas in Latin America. Results: We collected a total of 468 answered questionnaires from 21 Latin American countries. Most respondents (44%) were from an academic or research institution while non-academics were mainly from non-governmental institutions (30%) and government agencies (25%). Most respondents (65%) have performed or used genetic assessments in their managed area or species, either alone, in partnership, contracting someone else or using published results. For the majority of this group, the genetic results were relevant to their conservation management goals, helping to inform management decisions. Respondents that had not performed genetic assessments (35%) were mainly from the non-academic group, and their main barriers were limited access to funds, genetic lab facilities, and trained personnel to design studies and conduct lab work. Discussion: From the findings, we describe the current situation and provide a general diagnosis of the conservation-genetics gap in Latin America. We describe the gender gap, academic-practitioner co-development of conservation questions and projects, and the nationality and residency of Latin American conservation managers in relation to the countries where they work. We discuss opportunities to co-create research questions and co-develop studies based on conservation practitioners' needs. We offer recommendations for overcoming barriers to integrate genetic information into conservation actions, and advance agendas that fit the needs and realities of the highly heterogeneous, biodiverse and challenging Latin American region.
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Affiliation(s)
- Constanza Napolitano
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
| | | | - Viviana Rojas-Bonzi
- Instituto de Investigación Biológica del Paraguay, Asuncion, Paraguay
- Wildlife Ecology and Conservation Department, University of Florida, Gainesville, FL, United States
| | - Carolina I. Miño
- Laboratorio de Genética Evolutiva - LGE, Instituto de Biología Subtropical - IBS, Consejo Nacional de Investigaciones Científicas y Técnicas - CONICET, Universidad Nacional de Misiones (UNaM), Posadas, Argentina
| | - José F. González-Maya
- Área de Biología de la Conservación, Departamento de Ciencias Ambientales, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Bogotá, Colombia
| | - Nadia Bou
- Departamento de Biodiversidad y Genética, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Alan Giraldo
- Grupo de Investigación en Ecología Animal, Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad del Valle, Cali, Colombia
| | - Angela Martino
- Centro de Investigaciones en Ecología y Zonas Aridas, Universidad Nacional Experimental Francisco de Miranda, Coro, Venezuela
| | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luis F. Aguirre
- Centro de Biodiversidad y Genética, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Andrea Cosacov
- Laboratorio de Ecología Evolutiva y Biología Floral, Instituto Multidisciplinario de Biología Vegetal, CONICET-Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Laura Prosdocimi
- Laboratorio de Ecología, Comportamiento y Mamíferos Marinos (LECyMM), Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - O. Eric Ramírez-Bravo
- Centro de Agroecología, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Eco campus Valsequillo, San Pedro Zacachimalpa, Mexico
| | - Luis Antonio Tovar
- Facultad de Ciencias Forestales, Universidad Nacional Agraria La Molina, Lima, Peru
| | - Ximena Velez-Zuazo
- Smithsonian National Zoological Park and Conservation Biology Institute, Washington, DC, United States
| | - Mercedes Barrios
- Centro de Datos para la Conservación, Centro de Estudios Conservacionistas, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
| | - Bernal Herrera-Fernández
- Instituto Internacional de Conservación y Manejo de Vida Silvestre (ICOMVIS), Universidad Nacional, Heredia, Costa Rica
| | | | | | - Monique Pool
- Green Heritage Fund Suriname, Paramaribo, Suriname
| | - Alonso Santos-Murgas
- Departamento de Zoología, Facultad de Ciencias Naturales Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá. Estación Científica Coiba AIP, Ciudad del Saber, Panama
| | | | - Felipe Cecchi
- Grupo Antropología de la Conservación, Universidad de Los Lagos, Osorno, Chile
| | - Armando J. Dans
- Departamento de Ciencias Ambientales y Producción Sostenible, Universidad de las Regiones Autónomas de la Costa Caribe Nicaragüense, Bluefields, Nicaragua
| | - Nelanie Dilchand
- Aquatic and Terrestrial Pioneers Consulting Services, Georgetown, Guyana
| | - Sergio M. Q. Lima
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - María Caridad Novas
- División de Conservación, Departamento de Botánica, Jardín Botánico Nacional Dr. Rafael María Moscoso, Santo Domingo, Dominican Republic
| | - Karla Pelz-Serrano
- Departamento de Ciencias Ambientales, División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma, Lerma, Mexico
| | - Nina Pougy
- Departamento de Desenvolvimento Científico, Museu do Amanhã, Instituto de Desenvolvimento e Gestão - IDG, Rio de Janeiro, Brazil
| | - Iris Rodríguez
- Escuela de Biología, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
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Bourret A, Nozères C, Parent E, Parent GJ. Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.98539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.
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Identifying the Genetic Distance Threshold for Entiminae (Coleoptera: Curculionidae) Species Delimitation via COI Barcodes. INSECTS 2022; 13:insects13030261. [PMID: 35323559 PMCID: PMC8953793 DOI: 10.3390/insects13030261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/27/2022] [Accepted: 03/03/2022] [Indexed: 02/01/2023]
Abstract
The subfamily Entiminae is the largest group in the family Curculionidae, and it has long represented a challenge in traditional and molecular classification. Here, we analyzed intra- and interspecific genetic distances of 621 public COI barcode sequences (658bp) from 39 genera and 110 species of Entiminae, to determine parameters most congruent in retaining established species. We found that the mean intraspecific genetic distance (3.07%) was much smaller than the mean interspecific one (21.96%), but there is a wide range of overlap between intra- and interspecific genetic distances (0.77−18.01%), indicating that there is no consistent, universal barcoding gap. Specifically, DNA barcoding gap analysis for morphospecies revealed that 102 of 110 morphospecies had barcoding gaps, and 9.18% was the optimum threshold of genetic distances for 97 species delimitation. We further confirmed this threshold with barcodes from 27 morphologically identified specimens (including 21 newly reported barcodes) sequenced from five genera and seven species. We also identified thresholds to delimit congeneric species within 14 selected genera (species > 2), which varied from 7.42% (Trichalophus) to 13.48% (Barypeithes). We herein present optimal parameters for species identification in the Entiminae. Our study suggests that despite no universal genetic distance threshold value in subfamily Entiminae, 9.18% is optimal for most species. We recommend a wider sampling of geographic populations to better account for intraspecific distance variation, and that genetic distance thresholds for species delimitation should be refined at the genus level.
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Radulovici AE, Vieira PE, Duarte S, Teixeira MAL, Borges LMS, Deagle BE, Majaneva S, Redmond N, Schultz JA, Costa FO. Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.67862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.
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DNA Barcoding of Marine Mollusks Associated with Corallina officinalis Turfs in Southern Istria (Adriatic Sea). DIVERSITY 2021. [DOI: 10.3390/d13050196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Presence of mollusk assemblages was studied within red coralligenous algae Corallina officinalis L. along the southern Istrian coast. C. officinalis turfs can be considered a biodiversity reservoir, as they shelter numerous invertebrate species. The aim of this study was to identify mollusk species within these settlements using DNA barcoding as a method for detailed identification of mollusks. Nine locations and 18 localities with algal coverage range above 90% were chosen at four research areas. From 54 collected samples of C. officinalis turfs, a total of 46 mollusk species were identified. Molecular methods helped identify 16 gastropod, 14 bivalve and one polyplacophoran species. COI sequences for two bivalve species (Musculus cf. costulatus (Risso, 1826) and Gregariella semigranata (Reeve, 1858)) and seven gastropod species (Megastomia winfriedi Peñas & Rolán, 1999, Eatonina sp. Thiele, 1912, Eatonina cossurae (Calcara, 1841), Crisilla cf. maculata (Monterosato, 1869), Alvania cf. carinata (da Costa, 1778), Vitreolina antiflexa (Monterosato, 1884) and Odostomia plicata (Montagu, 1803)) represent new BINs in BOLD database. This study contributes to new findings related to the high biodiversity of mollusks associated with widespread C. officinalis settlements along the southern coastal area of Istria.
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