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da Silva LP, Mata VA, Lopes PB, Pinho CJ, Chaves C, Correia E, Pinto J, Heleno RH, Timoteo S, Beja P. Dietary metabarcoding reveals the simplification of bird-pest interaction networks across a gradient of agricultural cover. Mol Ecol 2024; 33:e17324. [PMID: 38506491 DOI: 10.1111/mec.17324] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024]
Abstract
Agriculture is vital for supporting human populations, but its intensification often leads to landscape homogenization and a decline in non-provisioning ecosystem services. Ecological intensification and multifunctional landscapes are suggested as nature-based alternatives to intensive agriculture, using ecological processes like natural pest regulation to maximize food production. Birds are recognized for their role in increasing crop yields by consuming invertebrate pests in several agroecosystems. However, the understanding of how bird species, their traits and agricultural land cover influence the structure of bird-pest interactions remains limited. We sampled bird-pest interactions monthly for 1 year, at four sites within a multifunctional landscape, following a gradient of increasing agricultural land cover. We analysed 2583 droppings of 55 bird species with DNA metabarcoding and detected 225 pest species in 1139 samples of 42 bird species. As expected, bird-pest interactions were highly variable across bird species. Dietary pest richness was lower in the fully agricultural site, while predation frequency remained consistent across the agricultural land cover gradient. Network analysis revealed a reduction in the complexity of bird-pest interactions as agricultural coverage increased. Bird species abundance affected the bird's contribution to the network structure more than any of the bird traits analysed (weight, phenology, invertebrate frequency in diet and foraging strata), with more common birds being more important to network structure. Overall, our results show that increasing agricultural land cover increases the homogenization of bird-pest interactions. This shows the importance of maintaining natural patches within agricultural landscapes for biodiversity conservation and enhanced biocontrol.
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Affiliation(s)
- Luis P da Silva
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Vanessa A Mata
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Pedro B Lopes
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Catarina J Pinho
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Catia Chaves
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Edna Correia
- Departamento de Biologia Animal, Centro de Estudos Do Ambiente e Do Mar, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Joana Pinto
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Ruben H Heleno
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, University of Coimbra, Coimbra, Portugal
| | - Sergio Timoteo
- Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, University of Coimbra, Coimbra, Portugal
| | - Pedro Beja
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- CIBIO, Centro de Investigação Em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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da Silva LP, Mata VA, Lopes PB, Lopes RJ, Beja P. High-resolution multi-marker DNA metabarcoding reveals sexual dietary differentiation in a bird with minor dimorphism. Ecol Evol 2020; 10:10364-10373. [PMID: 33072265 PMCID: PMC7548197 DOI: 10.1002/ece3.6687] [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: 04/21/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 11/11/2022] Open
Abstract
Although sexual dietary differentiation is well known in birds, it is usually linked with significant morphological dimorphism between males and females, with lower differentiation reported in sexually monomorphic or only slightly dimorphic species. However, this may be an artifact of poor taxonomic resolution achieved in most conventional dietary studies, which may be unable to detect subtle intraspecific differentiation in prey consumption. Here, we show the power of multi‐marker metabarcoding to address these issues, focusing on a slightly dimorphic generalist passerine, the black wheatear Oenanthe leucura. Using markers from four genomic regions (18S, 16S, COI, and trnL), we analyzed fecal droppings collected from 93 adult black wheatears during the breeding season. We found that sexes were rather similar in bill and body features, though males had a slightly thicker bill and longer wings and tail than females. Diet was dominated in both sexes by a very wide range of arthropod species and a few fleshy fruits, but the overall diet diversity was higher for males than females, and there was a much higher frequency of occurrence of ants in female (58%) than male (29%) diets. We hypothesize that the observed sexual differentiation was likely related to females foraging closer to their offspring on abundant prey, while males consumed a wider variety of prey while foraging more widely. Overall, our results suggest that dietary sexual differentiation in birds may be more widespread than recognized at present and that multi‐marker DNA metabarcoding is a particularly powerful tool to unveiling such differences.
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Affiliation(s)
- Luís P da Silva
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Vanessa A Mata
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | | | - Ricardo J Lopes
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal
| | - Pedro Beja
- CIBIO-InBIO Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal.,CIBIO-InBIO Research Center in Biodiversity and Genetic Resources Institute of Agronomy University of Lisbon Lisbon Portugal
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Ferreira S, Tierno de Figueroa JM, Martins FMS, Verissimo J, Quaglietta L, Grosso-Silva JM, Lopes PB, Sousa P, Paupério J, Fonseca NA, Beja P. The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera. Biodivers Data J 2020; 8:e55137. [PMID: 32821214 PMCID: PMC7403161 DOI: 10.3897/bdj.8.e55137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/05/2020] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The use of DNA barcoding allows unprecedented advances in biodiversity assessments and monitoring schemes of freshwater ecosystems; nevertheless, it requires the construction of comprehensive reference collections of DNA sequences that represent the existing biodiversity. Plecoptera are considered particularly good ecological indicators and one of the most endangered groups of insects, but very limited information on their DNA barcodes is available in public databases. Currently, less than 50% of the Iberian species are represented in BOLD. NEW INFORMATION The InBIO Barcoding Initiative Database: contribution to the knowledge on DNA barcodes of Iberian Plecoptera dataset contains records of 71 specimens of Plecoptera. All specimens have been morphologically identified to species level and belong to 29 species in total. This dataset contributes to the knowledge on the DNA barcodes and distribution of Plecoptera from the Iberian Peninsula and it is one of the IBI database public releases that makes available genetic and distribution data for a series of taxa.The species represented in this dataset correspond to an addition to public databases of 17 species and 21 BINs. Fifty-eight specimens were collected in Portugal and 18 in Spain during the period of 2004 to 2018. All specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD) online database. The distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).
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Affiliation(s)
- Sonia Ferreira
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
| | | | - Filipa MS Martins
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do PortoPortoPortugal
| | - Joana Verissimo
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, PortugalDepartamento de Biologia, Faculdade de Ciências, Universidade do PortoPortoPortugal
| | - Lorenzo Quaglietta
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Lisboa, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de AgronomiaLisboaPortugal
| | - José Manuel Grosso-Silva
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Pedro B Lopes
- Rua do Torgal nº16, Trigais - Covilhã, 6215-295 Erada, Covilhã, PortugalRua do Torgal nº16, Trigais - Covilhã, 6215-295 EradaCovilhãPortugal
| | - Pedro Sousa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
| | - Joana Paupério
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
| | - Nuno A Fonseca
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
| | - Pedro Beja
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoVairãoPortugal
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de Agronomia, Lisboa, PortugalCIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Instituto Superior de AgronomiaLisboaPortugal
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da Silva LP, Mata VA, Lopes PB, Pereira P, Jarman SN, Lopes RJ, Beja P. Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists. Mol Ecol Resour 2019; 19:1420-1432. [PMID: 31332947 PMCID: PMC6899665 DOI: 10.1111/1755-0998.13060] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 11/27/2018] [Revised: 06/16/2019] [Accepted: 06/19/2019] [Indexed: 01/01/2023]
Abstract
The application of DNA metabarcoding to dietary analysis of trophic generalists requires using multiple markers in order to overcome problems of primer specificity and bias. However, limited attention has been given to the integration of information from multiple markers, particularly when they partly overlap in the taxa amplified, and vary in taxonomic resolution and biases. Here, we test the use of a mix of universal and specific markers, provide criteria to integrate multi‐marker metabarcoding data and a python script to implement such criteria and produce a single list of taxa ingested per sample. We then compare the results of dietary analysis based on morphological methods, single markers, and the proposed combination of multiple markers. The study was based on the analysis of 115 faeces from a small passerine, the Black Wheatears (Oenanthe leucura). Morphological analysis detected far fewer plant taxa (12) than either a universal 18S marker (57) or the plant trnL marker (124). This may partly reflect the detection of secondary ingestion by molecular methods. Morphological identification also detected far fewer taxa (23) than when using 18S (91) or the arthropod markers IN16STK (244) and ZBJ (231), though each method missed or underestimated some prey items. Integration of multi‐marker data provided far more detailed dietary information than any single marker and estimated higher frequencies of occurrence of all taxa. Overall, our results show the value of integrating data from multiple, taxonomically overlapping markers in an example dietary data set.
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Affiliation(s)
- Luís P da Silva
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,CEF, Center for Functional Ecology - Science for People & the Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Vanessa A Mata
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | | | - Paulo Pereira
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Simon N Jarman
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,School of Biological Sciences, University of Western Australia, Perth, WA, Australia.,Environomics Future Science Platform, CSIRO National Collections and Marine Infrastructure, Crawley, WA, Australia
| | - Ricardo J Lopes
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Pedro Beja
- CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal.,CIBIO-InBIO, Research Center in Biodiversity and Genetic Resources, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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5
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Norte AC, da Silva LP, Tenreiro PJQ, Felgueiras MS, Araújo PM, Lopes PB, Matos C, Rosa A, Ferreira PJSG, Encarnação P, Rocha A, Escudero R, Anda P, Núncio MS, Lopes de Carvalho I. Patterns of tick infestation and their Borrelia burgdorferi s.l. infection in wild birds in Portugal. Ticks Tick Borne Dis 2015; 6:743-50. [PMID: 26159798 DOI: 10.1016/j.ttbdis.2015.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 10/23/2022]
Abstract
Wild birds may act as reservoirs for zoonotic pathogens and may be mechanical carriers of pathogen infected vector ticks through long distances during migration. The aim of this study was to assess tick infestation patterns in birds in Portugal and the prevalence of tick infection by Borrelia burgdorferi s.l. using PCR techniques. Seven tick species were collected from birds including Haemaphysalis punctata, Hyalomma spp., Ixodes acuminatus, Ixodes arboricola, Ixodes frontalis, Ixodes ricinus and Ixodes ventalloi. We found that I. frontalis and Hyalomma spp. were the most common ticks infesting birds of several species and that they were widespread in Portugal. Turdus merula was the bird species that presented the highest diversity of infesting ticks and had one of the highest infestation intensities. B. burgdorferi s.l. was detected in 7.3% (37/505) of Ixodidae ticks derived from birds. The most common genospecies was Borrelia turdi (6.9%), detected in ticks collected from Parus major, T. merula and Turdus philomelos, but Borrelia valaisiana (0.2%) and one Borrelia sp. (0.2%) similar to Borrelia bissettii (96% of similarity of the flaB gene in Blastn) were also detected. This study contributed to a better knowledge of the Ixodidae tick fauna parasitizing birds in Western Europe and to the assessment of the prevalence of B. burgdorferi s.l. associated with birds and their ticks.
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Affiliation(s)
- A C Norte
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Largo Marquês de Pombal, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal; Centre for Vector and Infectious Diseases Research, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal.
| | - L P da Silva
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Largo Marquês de Pombal, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal; CFE - Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - P J Q Tenreiro
- Instituto da Conservação da Natureza e das Florestas, IP, DCNFC-DGOV, Mata Nacional do Choupal, 3000-611 Coimbra, Portugal
| | - M S Felgueiras
- A ROCHA - Associação Cristã de Estudo e Defesa do Ambiente, Apartado 41, 8501-903 Mexilhoeira Grande, Portugal
| | - P M Araújo
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Largo Marquês de Pombal, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - P B Lopes
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Largo Marquês de Pombal, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - C Matos
- Rua da capela, n°13, 7630-711 Bicos, Odemira, Portugal
| | - A Rosa
- Casais da Estrada, 2000-335 Achete, Santarém, Portugal
| | | | - P Encarnação
- Instituto da Conservação da Natureza e das Florestas, IP, Estação Ornitológica do Monte do Outeirão - Apartado 139, 7500-999 Vila Nova Santo André, Portugal
| | - A Rocha
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Largo Marquês de Pombal, Faculty of Sciences and Technology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - R Escudero
- Laboratorio de Espiroquetas y Patógenos Especiales, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - P Anda
- Laboratorio de Espiroquetas y Patógenos Especiales, Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - M S Núncio
- Centre for Vector and Infectious Diseases Research, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal
| | - I Lopes de Carvalho
- Centre for Vector and Infectious Diseases Research, National Institute of Health Doutor Ricardo Jorge, Águas de Moura, Portugal; Emergence Response and Biopreparadness Unit, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Pfeifer LI, Silva DBR, Lopes PB, Matsukura TS, Santos JLF, Pinto MPP. Social support provided to caregivers of children with cerebral palsy. Child Care Health Dev 2014; 40:363-9. [PMID: 23734935 DOI: 10.1111/cch.12077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To describe the perception of caregivers of children with cerebral palsy (CP) concerning social support received and to verify how the characteristics of the children (i.e. type of CP and severity of motor impairment) and those of their caregivers (i.e. age, level of education, occupation, income and number of children) are significantly related to this perception. METHOD A total of 50 children with CP aged between 3 and 12 years and their respective caregivers participated in this study. Children were grouped in terms of type of CP and according to the severity of motor impairment through the Gross Motor Function Classification System (GMFCS). The Social Support Questionnaire (SSQ) was used to evaluate the perception of caregivers concerning the social support they receive (number of people offering support - SSQ-N index, and level of satisfaction concerning such support - SSQ-S index). RESULTS The caregivers reported receiving support from a mean of 1.67 people. Core and extended family members (i.e. husband, mother, siblings) and friends are the most common providers of support. In regard to level of satisfaction, caregivers considered the support they received to be positive, obtaining a mean of 5.52 out of a total of six points. Children's and caregivers' characteristics were not significantly related to the SSQ-N and SSQ-S indexes. CONCLUSION Family members are the caregivers' primary source of social support and caregivers reported being satisfied with the support they received.
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Affiliation(s)
- L I Pfeifer
- Department of Neurosciences and Behavioral Sciences, Division of Occupational Therapy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, S.P., Brazil
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