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A Comparison of Feathers and Oral Swab Samples as DNA Sources for Molecular Sexing in Companion Birds. Animals (Basel) 2023; 13:ani13030525. [PMID: 36766417 PMCID: PMC9913368 DOI: 10.3390/ani13030525] [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: 12/03/2022] [Revised: 01/17/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The early age determinism of the sex in case of monomorphic birds is very important, because most companion birds have no distinct sexual dimorphic traits. Molecular genetic sexing was proved to be one of the most accurate sex determinations in monomorphic birds. The aim of this study was to compare the results obtained by PCR performed on isolate genomic DNA from paired samples of feathers and oral swabs collected from the same individuals. Samples of oral swabs (n = 101) and feathers (n = 74) were collected from 101 companion birds from four different species (Columba livia domestica, Psittacula krameri, Neophema splendida and Agapornis spp.). The PCR was performed for the amplification of the CHD1W and CHD1Z genes in females and the CHD1Z gene in males. The overall PCR success rate of sex determination was significantly higher from oral swabs than from feathers. The PCR success rate from oral swabs was higher in juveniles and from feathers was significantly higher in adults. The similarity between the oral swab and feathers was obtained in 78.38% of the birds. Oral swabs proved to be a more reliable sample for genetic sex determination in the species tested in this study.
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Searching for genetic evidence of demographic decline in an arctic seabird: beware of overlapping generations. Heredity (Edinb) 2022; 128:364-376. [PMID: 35246618 PMCID: PMC9076905 DOI: 10.1038/s41437-022-00515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Genetic data are useful for detecting sudden population declines in species that are difficult to study in the field. Yet this indirect approach has its own drawbacks, including population structure, mutation patterns, and generation overlap. The ivory gull (Pagophila eburnea), a long-lived Arctic seabird, is currently suffering from rapid alteration of its primary habitat (i.e., sea ice), and dramatic climatic events affecting reproduction and recruitment. However, ivory gulls live in remote areas, and it is difficult to assess the population trend of the species across its distribution. Here we present complementary microsatellite- and SNP-based genetic analyses to test a recent bottleneck genetic signal in ivory gulls over a large portion of their distribution. With attention to the potential effects of population structure, mutation patterns, and sample size, we found no significant signatures of population decline worldwide. At a finer scale, we found a significant bottleneck signal at one location in Canada. These results were compared with predictions from simulations showing how generation time and generation overlap can delay and reduce the bottleneck microsatellite heterozygosity excess signal. The consistency of the results obtained with independent methods strongly indicates that the species shows no genetic evidence of an overall decline in population size. However, drawing conclusions related to the species' population trends will require a better understanding of the effect of age structure in long-lived species. In addition, estimates of the effective global population size of ivory gulls were surprisingly low (~1000 ind.), suggesting that the evolutionary potential of the species is not assured.
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Monge O, Dumas D, Baus I. Environmental DNA from avian residual saliva in fruits and its potential uses in population genetics. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-1074-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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4
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Hou X, Xu P, Lin Z, D'Urban-Jackson J, Dixon A, Bold B, Xu J, Zhan X. Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population. Integr Zool 2018; 13:553-568. [PMID: 29316314 DOI: 10.1111/1749-4877.12305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Accurate individual identification is required to estimate survival rates in avian populations. For endangered species, non-invasive methods of obtaining individual identification, such as using molted feathers as a source of DNA for microsatellite markers, are preferred because of less disturbance, easy sample preparation and high efficiency. With the availability of many avian genomes, a few pipelines isolating genome-wide microsatellites have been published, but it is still a challenge to isolate microsatellites from the reference genome efficiently. Here, we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome. We have identified over 95 000 microsatellite loci and established a system comprising 10 highly polymorphic markers (PIC value: 0.49-0.93, mean: 0.79) for an endangered species, saker falcon (Falco cherrug). These markers (except 1) were successfully amplified in 126 molted feathers, exhibiting high amplification success rates (83.9-99.7%), high quality index (0.90-0.97) and low allelic dropout rates (1-9.5%). To further assess the efficiency of this marker system in a population study, we identified individual sakers using these molted feathers (adult) and 146 plucked feathers (offspring). The use of parent and offspring samples enabled us to infer the genotype of missing samples (N = 28), and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers. Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.
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Affiliation(s)
- Xian Hou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,School of Nature Conservation, Beijing Forestry University, Beijing, China
| | | | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Andrew Dixon
- Emirates Falconers' Club, Abu Dhabi, United Arab Emirates.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China
| | - Batbayar Bold
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Wildlife Science and Conservation Center, Ulaanbaatar, Mongolia
| | - Jiliang Xu
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Grendelmeier A, Arlettaz R, Olano-Marin J, Pasinelli G. Experimentally provided conspecific cues boost bird territory density but not breeding performance. Behav Ecol 2016. [DOI: 10.1093/beheco/arw144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Lobo D, Godinho R, Álvares F, López-Bao JV, Rodríguez A. A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research. PLoS One 2015; 10:e0139765. [PMID: 26496352 PMCID: PMC4619700 DOI: 10.1371/journal.pone.0139765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022] Open
Abstract
Noninvasive samples for genetic analyses have become essential to address ecological questions. Popular noninvasive samples such as faeces contain degraded DNA which may compromise genotyping success. Saliva is an excellent alternative DNA source but scarcity of suitable collection methods makes its use anecdotal in field ecological studies. We develop a noninvasive method of collection that combines baits and porous materials able to capture saliva. We report its potential in optimal conditions, using confined dogs and collecting saliva early after deposition. DNA concentration in saliva extracts was generally high (mean 14 ng μl-1). We correctly identified individuals in 78% of samples conservatively using ten microsatellite loci, and 90% of samples using only eight loci. Consensus genotypes closely matched reference genotypes obtained from hair DNA (99% of identification successes and 91% of failures). Mean genotyping effort needed for identification using ten loci was 2.2 replicates. Genotyping errors occurred at a very low frequency (allelic dropout: 2.3%; false alleles: 1.5%). Individual identification success increased with duration of substrate handling inside dog’s mouth and the volume of saliva collected. Low identification success was associated with baits rich in DNA-oxidant polyphenols and DNA concentrations <1 ng μl-1. The procedure performed at least as well as other noninvasive methods, and could advantageously allow detection of socially low-ranked individuals underrepresented in sources of DNA that are involved in marking behaviour (faeces or urine). Once adapted and refined, there is promise for this technique to allow potentially high rates of individual identification in ecological field studies requiring noninvasive sampling of wild vertebrates.
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Affiliation(s)
- Diana Lobo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- * E-mail: (AR); (RG)
| | - Francisco Álvares
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Vairão, Portugal
| | - José V. López-Bao
- Research Unit of Biodiversity (UO/CSIC/PA), Oviedo University, Mieres, Spain
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU), Riddarhyttan, Sweden
| | - Alejandro Rodríguez
- Department of Conservation Biology, Estación Biológica de Doñana, CSIC, Sevilla, Spain
- * E-mail: (AR); (RG)
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Yannic G, Yearsley JM, Sermier R, Dufresnes C, Gilg O, Aebischer A, Gavrilo MV, Strøm H, Mallory ML, Guy Morrison RI, Gilchrist HG, Broquet T. High connectivity in a long-lived high-Arctic seabird, the ivory gull Pagophila eburnea. Polar Biol 2015. [DOI: 10.1007/s00300-015-1775-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Adam I, Scharff C, Honarmand M. Who is who? Non-invasive methods to individually sex and mark altricial chicks. J Vis Exp 2014. [PMID: 24893585 DOI: 10.3791/51429] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Many experiments require early determination of offspring's sex as well as early marking of newborns for individual recognition. According to animal welfare guidelines, non-invasive techniques should be preferred whenever applicable. In our group, we work on different species of song birds in the lab and in the field, and we successfully apply non-invasive methods to sex and individually mark chicks. This paper presents a comprehensive non-invasive tool-box. Sexing birds prior to the expression of secondary sexual traits requires the collection of DNA-bearing material for PCR. We established a quick and easy method to sex birds of any age (post hatching) by extracting DNA from buccal swabs. Results can be obtained within 3 hours. For individual marking chick's down feathers are trimmed in specific patterns allowing fast identification within the hatching order. This set of methods is easily applicable in a standard equipped lab and especially suitable for working in the field as no special equipment is required for sampling and storage. Handling of chicks is minimized and marking and sexing techniques are non-invasive thereby supporting the RRR-principle of animal welfare guidelines.
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Affiliation(s)
- Iris Adam
- Department of Animal Behavior, Freie Universität Berlin;
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Monteiro NM, Silva RM, Cunha M, Antunes A, Jones AG, Vieira MN. Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers. Mol Ecol Resour 2013; 14:150-6. [DOI: 10.1111/1755-0998.12151] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 06/13/2013] [Accepted: 07/02/2013] [Indexed: 11/27/2022]
Affiliation(s)
- N. M. Monteiro
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Rua Padre Armando Quintas Vairão 4485-661 Portugal
- Faculdade de Ciências da Saúde; CEBIMED; Universidade Fernando Pessoa; Rua Carlos da Maia 296 Porto 4200-150 Portugal
| | - R. M. Silva
- Departamento de Clínicas Veterinárias; ICBAS; Instituto Ciências Biomédicas Abel Salazar da Universidade do Porto; Rua de Jorge Viterbo Ferreira 228 Porto 4050-313 Portugal
| | - M. Cunha
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Rua Padre Armando Quintas Vairão 4485-661 Portugal
| | - A. Antunes
- CIIMAR/CIMAR; Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 289 Porto 4050-123 Portugal
- Departamento de Biologia; FCUP; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre Porto 4169-007 Portugal
| | - A. G. Jones
- Department of Biology; Texas A&M University; 3258 TAMU College Station TX 77843 USA
| | - M. N. Vieira
- CIIMAR/CIMAR; Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 289 Porto 4050-123 Portugal
- Departamento de Biologia; FCUP; Faculdade de Ciências da Universidade do Porto; Rua do Campo Alegre Porto 4169-007 Portugal
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