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Schlautmann J, Rehling F, Albrecht J, Jaroszewicz B, Schabo DG, Farwig N. Observing frugivores or collecting scats: a method comparison to construct quantitative seed dispersal networks. OIKOS 2021. [DOI: 10.1111/oik.08175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jan Schlautmann
- Conservation Ecology, Dept of Biology, Univ. of Marburg Germany
| | - Finn Rehling
- Conservation Ecology, Dept of Biology, Univ. of Marburg Germany
| | - Jörg Albrecht
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F) Frankfurt/Main Germany
| | - Bogdan Jaroszewicz
- Białowieża Geobotanical Station, Faculty of Biology, Univ. of Warsaw Białowieża Poland
| | - Dana G. Schabo
- Conservation Ecology, Dept of Biology, Univ. of Marburg Germany
| | - Nina Farwig
- Conservation Ecology, Dept of Biology, Univ. of Marburg Germany
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2
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DNA barcoding exposes the need to control the illegal trade of eggs of non-threatened parrots in Brazil. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01209-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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3
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Torrontegi O, Alvarez V, Hurtado A, Sevilla IA, Höfle U, Barral M. Naturally Avian Influenza Virus-Infected Wild Birds Are More Likely to Test Positive for Mycobacterium spp. and Salmonella spp. Avian Dis 2020; 63:131-137. [PMID: 31131569 DOI: 10.1637/11866-042518-reg.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/20/2018] [Indexed: 11/05/2022]
Abstract
Wild birds often harbor infectious microorganisms. Some of these infectious microorganisms may present a risk to domestic animals and humans through spillover events. Detections of certain microorganisms have been shown to increase host susceptibility to infections by other microorganisms, leading to coinfections and altered host-to-host transmission patterns. However, little is known about the frequency of coinfections and its impact on wild bird populations. In order to verify whether avian influenza virus (AIV) natural infection in wild waterbirds was related to the excretion of other microorganisms, 73 AIV-positive samples (feces and cloacal swabs) were coupled with 73 AIV-negative samples of the same sampling characteristics and tested by real-time PCR specific for the following microorganisms: West Nile virus, avian avulavirus 1, Salmonella spp., Yersinia enterocolitica, Yersinia pseudotuberculosis, Mycobacterium avium subspecies, Mycobacterium tuberculosis complex, and Mycobacterium spp. Concurrent detections were found in 47.9% (35/73) of the AIV-positive samples and in 23.3% (17/73) of the AIV-negative samples (P = 0.003). Mycobacterium spp. and Salmonella spp. were found to be significantly more prevalent among the AIV-positive samples than among the AIV-negative samples (42.9% vs. 22.8%; P = 0.024 and 15.2% vs. 0.0%; P = 0.0015, respectively). Prevalence of concurrent detections differed significantly among sampling years (P = 0.001), host families (P = 0.002), host species (P = 0.003), AIV subtypes (P = 0.003), and type of sample (P = 0.009). Multiple concurrent detections (more than one of the tested microorganisms excluding AIV) were found in 9.6% (7/73) of all the AIV-positive samples, accounting for 20% (7/35) of the concurrent detection cases. In contrast, in AIV-negative samples we never detected more than one of the selected microorganisms. These results show that AIV detection was associated with the detection of the monitored microorganisms. Further studies of a larger field sample set or under experimental conditions are necessary to infer causality in these trends.
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Affiliation(s)
- Olalla Torrontegi
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio (Bizkaia), Spain
| | - Vega Alvarez
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio (Bizkaia), Spain
| | - Ana Hurtado
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio (Bizkaia), Spain
| | - Iker A Sevilla
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio (Bizkaia), Spain
| | - Ursula Höfle
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos (IREC), CSIC-UCLM-JCCM, Ronda de Toledo 13005 Ciudad Real, Spain.,Escuela de Ingenieros Agrónomos, Ronda de Calatrava, 13071 Ciudad Real, Spain
| | - Marta Barral
- NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Animal Health Department, Bizkaia Science and Technology Park 812L, 48160 Derio (Bizkaia), Spain,
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4
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Kopuchian C, Campagna L, Lijtmaer DA, Cabanne GS, García NC, Lavinia PD, Tubaro PL, Lovette I, Di Giacomo AS. A test of the riverine barrier hypothesis in the largest subtropical river basin in the Neotropics. Mol Ecol 2020; 29:2137-2149. [DOI: 10.1111/mec.15384] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Cecilia Kopuchian
- Laboratorio de Biología de la ConservaciónCECOAL (Centro de Ecología Aplicada del Litoral) CONICET Corrientes Argentina
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program Cornell Laboratory of Ornithology Cornell University Ithaca New York USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Darío A. Lijtmaer
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Gustavo S. Cabanne
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Natalia C. García
- Fuller Evolutionary Biology Program Cornell Laboratory of Ornithology Cornell University Ithaca New York USA
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Pablo D. Lavinia
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Pablo L. Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” MACN‐CONICETCiudad Autónoma de Buenos Aires Buenos Aires Argentina
| | - Irby Lovette
- Fuller Evolutionary Biology Program Cornell Laboratory of Ornithology Cornell University Ithaca New York USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Adrián S. Di Giacomo
- Laboratorio de Biología de la ConservaciónCECOAL (Centro de Ecología Aplicada del Litoral) CONICET Corrientes Argentina
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5
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Zou R, Liang C, Dai M, Wang X, Zhang X, Song Z. DNA barcoding and phylogenetic analysis of bagrid catfish in China based on mitochondrial COI gene. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:73-80. [PMID: 32126856 DOI: 10.1080/24701394.2020.1735379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The family Bagridae is a collection of species widely distributed in Africa and Asia with a high diversity of morphology. The species identification and phylogenetic relationship in this family have been confused and controversial. In order to explore the effectiveness of DNA barcoding in species identification of Bagridae, sequences of mitochondrial cytochrome c oxidase I (COI) gene of 20 species in four genera of Bagridae were used to analyse barcoding gap and to reconstruct phylogenetic relationship. Both the barcoding gap and the phylogenetic tree analysis showed that the COI gene-based DNA barcoding is an effective molecular technique for most species recognition of Chinese Bagridae. However, the rapid speciation and incomplete lineage sorting may affect the accuracy of DNA barcoding in species identification in certain species, and adding additional genes, such as nuclear gene, may help to achieve accurate identification of these species. The phylogenetic tree showed that the monophyly of genera Pelteobagrus, Leiocassis and Pseudobagrus did not exist, which supports that the species of genera Pelteobagrus, Pseudobagrus and Leiocassis distributed in China should be revised into one genus.
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Affiliation(s)
- Rui Zou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Cong Liang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mengmeng Dai
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaodong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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6
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Avigliano E, Rosso JJ, Lijtmaer D, Ondarza P, Piacentini L, Izquierdo M, Cirigliano A, Romano G, Nuñez Bustos E, Porta A, Mabragaña E, Grassi E, Palermo J, Bukowski B, Tubaro P, Schenone N. Biodiversity and threats in non-protected areas: A multidisciplinary and multi-taxa approach focused on the Atlantic Forest. Heliyon 2019; 5:e02292. [PMID: 31497670 PMCID: PMC6722266 DOI: 10.1016/j.heliyon.2019.e02292] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/04/2019] [Accepted: 08/08/2019] [Indexed: 01/15/2023] Open
Abstract
Along many decades, protected environments were targeted by the scientific community for ecological research and for the collection of scientific information related to environmental aspects and biodiversity. However, most of the territory in hotspot regions with weak or even non legal protection has been left aside. These non-protected areas (NPA) could host high biodiversity values. This paper addresses how scientific effort on a NPA (CIAR) of 700 ha from the Atlantic Rain Forest, generates new information and tools for large-scale environmental and biodiversity management in NPAs. Information published during the last decade was summarized and complemented with subsequent novel data about biodiversity (new species, first records, DNA and chemical analyses, etc.). The results showed: 1 new genus (arachnid), 6 new species and several putative new species (fish and arthropod), 6 vulnerable species (bird and mammal) and 36 first records for Argentina (fish, arthropod, platyhelminth and fungi). When compared with protected natural areas of the same biome, the CIAR showed highly valuable aspects for fauna and environment conservation, positioning this NPA as a worldwide hotspot for some taxa. Indeed, when compared to international hotspots in a coordinated Malaise trap program, the CIAR showed 8,651 different barcode index numbers (∼species) of arthropods, 80% of which had not been previously barcoded. Molecules like Inoscavin A, with antifungal activity against phytopathogens, was isolated for the first time in Phellinus merrillii fungi. The study of major threats derived from anthropic activities measured 20 trace elements, 18 pesticides (i.e. endosulfans, chlorpyrifos, DDTs, HCHs) and 27 pharmaceuticals and drugs (i.e. benzoylecgonine and norfluoxetine) in different biotic and abiotic matrices (water, sediment, fish and air biomonitors). This integrated data analysis shows that biodiversity research in NPA is being undervalued and how multidisciplinary and multi-taxa surveys creates a new arena for research and a pathway towards sustainable development in emerging countries with biodiversity hotspots.
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Affiliation(s)
- Esteban Avigliano
- Centro de Investigaciones Antonia Ramos (CIAR), Fundación Bosques Nativos Argentinos, Camino Balneario s/n, Villa Bonita, Misiones, Argentina
- Instituto de Investigaciones en Producción Animal (INPA-CONICET-UBA), Universidad de Buenos Aires, Av. Chorroarín 280, (C1427CWO), Buenos Aires, Argentina
| | - Juan Jose Rosso
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Dario Lijtmaer
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Paola Ondarza
- Laboratorio de Ecotoxicología y Contaminación Ambiental, Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Luis Piacentini
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Matías Izquierdo
- Laboratorio de Biología Reproductiva y Evolución, Instituto de Diversidad y Ecología Animal (IDEA-UNC-CONICET), Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba. Av. Velez Sarsfield 299 (X5000 JJC), Córdoba, Argentina
| | - Adriana Cirigliano
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, (1428), Buenos Aires, Argentina
| | - Gonzalo Romano
- Departamento de Biología, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (CONICET), Ruta 259 km 16.4, (9000), Esquel, Chubut, Argentina
| | - Ezequiel Nuñez Bustos
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Andres Porta
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y Molecular de Peces (BIMOPE), Instituto de Investigaciones Marinas y Costeras, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata (CONICET), Dean Funes 3350, (B7600), Mar del Plata, Argentina
| | - Emanuel Grassi
- Instituto Misionero de Biodiversidad (IMiBio), Ruta N12 km 5, (N3370), Puerto Iguazú, Misiones, Argentina
| | - Jorge Palermo
- Departamento de Biología, Facultad de Ciencias Naturales, Universidad Nacional de la Patagonia San Juan Bosco (CONICET), Ruta 259 km 16.4, (9000), Esquel, Chubut, Argentina
- Unidad de Microanálisis y Métodos Físicos en Química Orgánica (UMYMFOR-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, (1428), Buenos Aires, Argentina
| | - Belen Bukowski
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Pablo Tubaro
- Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN-CONICET), Av. Angel Gallardo 470, (C1405DJR), Buenos Aires, Argentina
| | - Nahuel Schenone
- Centro de Investigaciones Antonia Ramos (CIAR), Fundación Bosques Nativos Argentinos, Camino Balneario s/n, Villa Bonita, Misiones, Argentina
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7
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Torrontegi O, Alvarez V, Acevedo P, Gerrikagoitia X, Höfle U, Barral M. Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community. Vet Res 2019; 50:4. [PMID: 30654831 PMCID: PMC6337815 DOI: 10.1186/s13567-019-0623-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Abstract
During 2007-2009 and 2012-2014, avian influenza virus (AIV) was studied in a wild avian community of a northern Spanish wetland using non-invasive sampling methods and host identification by COI barcoding. The aim of this longitudinal study was to evaluate AIV dynamics in a natural wetland ecosystem, taking into account both virological aspects and ecological traits of hosts. Global AIV prevalence decreased significantly during the second sampling period (0.3%) compared to the first (6.6%). Circulating subtype distributions were also different between periods, with a noteworthy H5 and H7 subtype richness during the first sampling period. Mallard Anas platyrhynchos was identified as the main AIV host, although not all positive samples could be ascribed to the host. We modelled AIV prevalence with regard to the avian host community composition and meteorological data from the wetland. Statistical analysis revealed seasonal differences in AIV detection, with higher prevalence during the breeding season compared to other phenological events. The model also shows that the lower AIV prevalence during the second study period was associated with a significant reduction of breeding Anseriformes in the wetland, revealing a long-term fluctuation of AIV prevalence driven by the breeding Anseriformes community. This longitudinal study on AIV epidemiology in a natural ecosystem reveals that although prevalence follows seasonal and annual patterns, long-term prevalence fluctuation is linked to the breeding community composition and size. These results are relevant to understanding the influence of host ecology on pathogen transmission for preventing and managing influenza emergence.
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Affiliation(s)
- Olalla Torrontegi
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Vega Alvarez
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Pelayo Acevedo
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Xeider Gerrikagoitia
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Ursula Höfle
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Marta Barral
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
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8
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González-Varo JP, Arroyo JM, Jordano P. The timing of frugivore-mediated seed dispersal effectiveness. Mol Ecol 2018; 28:219-231. [PMID: 30151871 PMCID: PMC6905405 DOI: 10.1111/mec.14850] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/08/2018] [Accepted: 08/15/2018] [Indexed: 12/01/2022]
Abstract
The seed dispersal effectiveness framework allows assessing mutualistic services from frugivorous animals in terms of quantity and quality. Quantity accounts for the number of seeds dispersed and quality for the probability of recruitment of dispersed seeds. Research on this topic has largely focused on the spatial patterns of seed deposition because seed fates often vary between microhabitats due to differences in biotic and abiotic factors. However, the temporal dimension has remained completely overlooked despite these factors-and even local disperser assemblages-can change dramatically during long fruiting periods. Here, we test timing effects on seed dispersal effectiveness, using as study case a keystone shrub species dispersed by frugivorous birds and with a fruiting period of 9 months. We evaluated quantity and quality in different microhabitats of a Mediterranean forest and different periods of the fruiting phenophase. We identified the bird species responsible for seed deposition through DNA barcoding and evaluated the probability of seedling recruitment through a series of field experiments on sequential demographic processes. We found that timing matters: The disperser assemblage was temporally structured, seed viability decreased markedly during the plant's fruiting phenophase, and germination was lower for viable seeds dispersed in the fruiting peak. We show how small contributions to seed deposition by transient migratory species can result in a relevant effectiveness if they disperse seeds in a high-quality period for seedling recruitment. This study expands our understanding of seed dispersal effectiveness, highlighting the importance of timing and infrequent interactions for population and community dynamics.
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Affiliation(s)
- Juan P González-Varo
- Integrative Ecology Group, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain.,Terrestrial Ecology Group, Instituto Mediterráneo de Estudios Avanzados, UIB-CSIC, Esporles, Spain
| | - Juan M Arroyo
- Integrative Ecology Group, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Pedro Jordano
- Integrative Ecology Group, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
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9
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González-Varo JP, Carvalho CS, Arroyo JM, Jordano P. Unravelling seed dispersal through fragmented landscapes: Frugivore species operate unevenly as mobile links. Mol Ecol 2017; 26:4309-4321. [PMID: 28503829 DOI: 10.1111/mec.14181] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 11/27/2022]
Abstract
Seed dispersal constitutes a pivotal process in an increasingly fragmented world, promoting population connectivity, colonization and range shifts in plants. Unveiling how multiple frugivore species disperse seeds through fragmented landscapes, operating as mobile links, has remained elusive owing to methodological constraints for monitoring seed dispersal events. We combine for the first time DNA barcoding and DNA microsatellites to identify, respectively, the frugivore species and the source trees of animal-dispersed seeds in forest and matrix of a fragmented landscape. We found a high functional complementarity among frugivores in terms of seed deposition at different habitats (forest vs. matrix), perches (isolated trees vs. electricity pylons) and matrix sectors (close vs. far from the forest edge), cross-habitat seed fluxes, dispersal distances and canopy-cover dependency. Seed rain at the landscape-scale, from forest to distant matrix sectors, was characterized by turnovers in the contribution of frugivores and source-tree habitats: open-habitat frugivores replaced forest-dependent frugivores, whereas matrix trees replaced forest trees. As a result of such turnovers, the magnitude of seed rain was evenly distributed between habitats and landscape sectors. We thus uncover key mechanisms behind "biodiversity-ecosystem function" relationships, in this case, the relationship between frugivore diversity and landscape-scale seed dispersal. Our results reveal the importance of open-habitat frugivores, isolated fruiting trees and anthropogenic perching sites (infrastructures) in generating seed dispersal events far from the remnant forest, highlighting their potential to drive regeneration dynamics through the matrix. This study helps to broaden the "mobile-link" concept in seed dispersal studies by providing a comprehensive and integrative view of the way in which multiple frugivore species disseminate seeds through real-world landscapes.
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Affiliation(s)
- Juan P González-Varo
- Integrative Ecology Group, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain.,Department of Zoology, Conservation Science Group, University of Cambridge, Cambridge, UK
| | - Carolina S Carvalho
- Departamento de Ecologia, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Juan M Arroyo
- Integrative Ecology Group, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Pedro Jordano
- Integrative Ecology Group, Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
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10
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More RP, Mane RC, Purohit HJ. matK-QR classifier: a patterns based approach for plant species identification. BioData Min 2016; 9:39. [PMID: 27990177 PMCID: PMC5148893 DOI: 10.1186/s13040-016-0120-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 12/02/2016] [Indexed: 12/24/2022] Open
Abstract
Background DNA barcoding is widely used and most efficient approach that facilitates rapid and accurate identification of plant species based on the short standardized segment of the genome. The nucleotide sequences of maturaseK (matK) and ribulose-1, 5-bisphosphate carboxylase (rbcL) marker loci are commonly used in plant species identification. Here, we present a new and highly efficient approach for identifying a unique set of discriminating nucleotide patterns to generate a signature (i.e. regular expression) for plant species identification. Methods In order to generate molecular signatures, we used matK and rbcL loci datasets, which encompass 125 plant species in 52 genera reported by the CBOL plant working group. Initially, we performed Multiple Sequence Alignment (MSA) of all species followed by Position Specific Scoring Matrix (PSSM) for both loci to achieve a percentage of discrimination among species. Further, we detected Discriminating Patterns (DP) at genus and species level using PSSM for the matK dataset. Combining DP and consecutive pattern distances, we generated molecular signatures for each species. Finally, we performed a comparative assessment of these signatures with the existing methods including BLASTn, Support Vector Machines (SVM), Jrip-RIPPER, J48 (C4.5 algorithm), and the Naïve Bayes (NB) methods against NCBI-GenBank matK dataset. Results Due to the higher discrimination success obtained with the matK as compared to the rbcL, we selected matK gene for signature generation. We generated signatures for 60 species based on identified discriminating patterns at genus and species level. Our comparative assessment results suggest that a total of 46 out of 60 species could be correctly identified using generated signatures, followed by BLASTn (34 species), SVM (18 species), C4.5 (7 species), NB (4 species) and RIPPER (3 species) methods As a final outcome of this study, we converted signatures into QR codes and developed a software matK-QR Classifier (http://www.neeri.res.in/matk_classifier/index.htm), which search signatures in the query matK gene sequences and predict corresponding plant species. Conclusions This novel approach of employing pattern-based signatures opens new avenues for the classification of species. In addition to existing methods, we believe that matK-QR Classifier would be a valuable tool for molecular taxonomists enabling precise identification of plant species. Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0120-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ravi Prabhakar More
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020 Maharashtra India ; Present Institute: Division of Molecular Entomology, ICAR- National Bureau of Agricultural Insect Resources (NBAIR), Hebbal, Bengaluru, 560024 Karnataka India
| | | | - Hemant J Purohit
- Environmental Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020 Maharashtra India
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11
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Morales-Contreras J, Escalante P, Martínez-Ruíz M, Matías-Ferrer N. Black hawk-eagle(Spizaetus tyrannus)identified by DNA from a feather recovered in the rain-forest region of Veracruz. SOUTHWEST NAT 2016. [DOI: 10.1894/0038-4909-61.2.137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tin MMY, Rheindt FE, Cros E, Mikheyev AS. Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy. Mol Ecol Resour 2014; 15:329-36. [PMID: 25132578 DOI: 10.1111/1755-0998.12314] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 08/06/2014] [Accepted: 08/06/2014] [Indexed: 11/26/2022]
Abstract
RAD-tag is a powerful tool for high-throughput genotyping. It relies on PCR amplification of the starting material, following enzymatic digestion and sequencing adaptor ligation. Amplification introduces duplicate reads into the data, which arise from the same template molecule and are statistically nonindependent, potentially introducing errors into genotype calling. In shotgun sequencing, data duplicates are removed by filtering reads starting at the same position in the alignment. However, restriction enzymes target specific locations within the genome, causing reads to start in the same place, and making it difficult to estimate the extent of PCR duplication. Here, we introduce a slight change to the Illumina sequencing adaptor chemistry, appending a unique four-base tag to the first index read, which allows duplicate discrimination in aligned data. This approach was validated on the Illumina MiSeq platform, using double-digest libraries of ants (Wasmannia auropunctata) and yeast (Saccharomyces cerevisiae) with known genotypes, producing modest though statistically significant gains in the odds of calling a genotype accurately. More importantly, removing duplicates also corrected for strong sample-to-sample variability of genotype calling accuracy seen in the ant samples. For libraries prepared from low-input degraded museum bird samples (Mixornis gularis), which had low complexity, having been generated from relatively few starting molecules, adaptor tags show that virtually all of the genotypes were called with inflated confidence as a result of PCR duplicates. Quantification of library complexity by adaptor tagging does not significantly increase the difficulty of the overall workflow or its cost, but corrects for differences in quality between samples and permits analysis of low-input material.
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Affiliation(s)
- M M Y Tin
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
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Aliabadian M, Beentjes KK, Roselaar C(K, van Brandwijk H, Nijman V, Vonk R. DNA barcoding of Dutch birds. Zookeys 2013; 365:25-48. [PMID: 24453549 PMCID: PMC3890669 DOI: 10.3897/zookeys.365.6287] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 12/06/2013] [Indexed: 12/01/2022] Open
Abstract
The mitochondrial cytochrome c oxidase subunit I (COI) can serve as a fast and accurate marker for the identification of animal species, and has been applied in a number of studies on birds. We here sequenced the COI gene for 387 individuals of 147 species of birds from the Netherlands, with 83 species being represented by > 2 sequences. The Netherlands occupies a small geographic area and 95% of all samples were collected within a 50 km radius from one another. The intraspecific divergences averaged 0.29% among this assemblage, but most values were lower; the interspecific divergences averaged 9.54%. In all, 95% of species were represented by a unique barcode, with 6 species of gulls and skua (Larus and Stercorarius) having at least one shared barcode. This is best explained by these species representing recent radiations with ongoing hybridization. In contrast, one species, the Lesser Whitethroat Sylvia curruca showed deep divergences, averaging 5.76% and up to 8.68% between individuals. These possibly represent two distinct taxa, S. curruca and S. blythi, both clearly separated in a haplotype network analysis. Our study adds to a growing body of DNA barcodes that have become available for birds, and shows that a DNA barcoding approach enables to identify known Dutch bird species with a very high resolution. In addition some species were flagged up for further detailed taxonomic investigation, illustrating that even in ornithologically well-known areas such as the Netherlands, more is to be learned about the birds that are present.
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Affiliation(s)
- Mansour Aliabadian
- Department of Biology, Ferdowsi University of Mashhad, Mashhad, Iran
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | | | | | | | - Vincent Nijman
- Department of Social Sciences, Oxford Brookes University, Oxford, UK
| | - Ronald Vonk
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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Arrieta RS, Lijtmaer DA, Tubaro PL. Evolution of postzygotic reproductive isolation in galliform birds: analysis of first and second hybrid generations and backcrosses. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Ramiro S. Arrieta
- División Ornitología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’; Avenida Ángel Gallardo 470; Buenos Aires; C1405DJR; Argentina
| | - Darío A. Lijtmaer
- División Ornitología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’; Avenida Ángel Gallardo 470; Buenos Aires; C1405DJR; Argentina
| | - Pablo L. Tubaro
- División Ornitología; Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’; Avenida Ángel Gallardo 470; Buenos Aires; C1405DJR; Argentina
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