A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research
Publication Date
October 23, 2015
Journal
PLOS ONE
Authors
Diana Lobo, Raquel Godinho, Francisco Álvares, José V. López Bao, et al
Volume
10
Issue
10
Pages
e0139765
DOI
https://dx.plos.org/10.1371/journal.pone.0139765
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0139765
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26496352
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619700
Europe PMC
http://europepmc.org/abstract/MED/26496352
Web of Science
000363309200008
Scopus
84949844981
Mendeley
http://www.mendeley.com/research/new-method-noninvasive-genetic-sampling-saliva-ecological-research
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2370458"], "description"=>"<p>Successful identification means complete agreement with 10-loci genotypes obtained from hair samples.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583712, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequencies_of_dog_individual_identification_across_classes_of_the_amount_of_saliva_attached_to_the_substrate_/1583712", "title"=>"Frequencies of dog individual identification across classes of the amount of saliva attached to the substrate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370456"], "description"=>"<p>Means and 95% CI are shown for every combination of substrate and bait, once records >60 ng μl<sup>-1</sup> were excluded.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583710, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Log_transformed_DNA_concentration_ng_l_1_in_saliva_extracts_/1583710", "title"=>"Log-transformed DNA concentration (ng μl<sup>-1</sup>) in saliva extracts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370464"], "description"=>"<div><p>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<sup>-1</sup>). 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<sup>-1</sup>. 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.</p></div>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583718, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_New_Method_for_Noninvasive_Genetic_Sampling_of_Saliva_in_Ecological_Research_/1583718", "title"=>"A New Method for Noninvasive Genetic Sampling of Saliva in Ecological Research", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370461"], "description"=>"<p>The amount of saliva attached to substrates after being handled by dogs, DNA concentration in saliva extracts, identification success, and number of genotyping replicates needed for individual identification are shown (sample size in brackets). Individual identification is expressed as the proportion of dogs matching all ten loci with the reference genotype (either hair genotype or consensus genotype) and as the percentage of correct loci per dog. Values represent means ± SE (upper half of the table) and proportions (lower half).</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583715, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Performance_of_substrates_and_baits_/1583715", "title"=>"Performance of substrates and baits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370460"], "description"=>"<p>For substrates, Tukey contrasts for pairs of means were indicated by shared superscripts: <sup>a</sup><i>P</i><0.001, <sup>b</sup><i>P</i> = 0.023, <sup>c</sup><i>P</i> = 0.084, <sup>d</sup><i>P</i> = 0.002.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583714, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variation_in_dog_handling_behaviour_across_types_of_substrates_and_baits_/1583714", "title"=>"Variation in dog handling behaviour across types of substrates and baits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370455"], "description"=>"<p>Bars indicate the distribution of substrates among classes of collected amount of saliva, from absence (class 1) to saturation (class 4). Data from all five experimental sessions are shown. Cork, <i>n</i> = 58; styrofoam, <i>n</i> = 54; wood, <i>n</i> = 58.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583709, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.g002", "stats"=>{"downloads"=>5, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amount_of_saliva_attached_to_three_types_of_substrate_after_dog_handling_/1583709", "title"=>"Amount of saliva attached to three types of substrate after dog handling.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370454"], "description"=>"<p>A: Porous substrates (cork, styrofoam, wood) in a bag after sterilization. B: Cork substrates covered with meat, ready for delivery.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583708, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Porous_substrates_cork_styrofoam_wood_in_a_bag_after_sterilization_B_Cork_substrates_covered_with_meat_ready_for_delivery_/1583708", "title"=>"A: Porous substrates (cork, styrofoam, wood) in a bag after sterilization. B: Cork substrates covered with meat, ready for delivery.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370463"], "description"=>"<p>Parameter estimates of fixed effects are shown. For the effects of substrate, bait, dog sex and dog size the levels styrofoam, meat, female, and small, respectively, are included in the intercept. All models contain the random effects of dog identity nested within experimental session.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583717, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.t004", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Minimal_adequate_binomial_GLMMs_for_dog_identification_success_expressed_as_the_percentage_of_correct_loci_/1583717", "title"=>"Minimal adequate binomial GLMMs for dog identification success expressed as the percentage of correct loci.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370462"], "description"=>"<p>Parameter estimates of fixed effects influencing the quantity of saliva attached to substrates, DNA concentration in saliva extracts (ng µl<sup>-1</sup>), and dog identification success expressed as a perfect match for 10 loci are shown. Levels styrofoam (substrate), meat (bait), female (sex), and small (dog size) are included in the intercept. All models contain the random effects of dog identity nested within experimental session. Errors: normal (saliva score, DNA concentration), binomial (species and individual identification) and Poisson (number of genotyping attempts needed for a correct identification). S*B: substrate-bait interaction.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583716, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.t003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effects_included_in_minimal_adequate_Generalized_Linear_Mixed_Models_/1583716", "title"=>"Effects included in minimal adequate Generalized Linear Mixed Models.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370459"], "description"=>"<p>Individual identification success across different classes of DNA concentration in saliva extracts.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583713, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Individual_identification_success_across_different_classes_of_DNA_concentration_in_saliva_extracts_/1583713", "title"=>"Individual identification success across different classes of DNA concentration in saliva extracts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-23 03:06:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2370457"], "description"=>"<p>Species identification success across different classes of DNA concentration in saliva extracts.</p>", "links"=>[], "tags"=>["collection methods", "Noninvasive Genetic Sampling", "Low identification success", "noninvasive methods", "New Method", "noninvasive method", "reference genotypes", "saliva extracts", "Allelic dropout", "noninvasive sampling", "DNA concentration", "2.2 replicates", "Popular noninvasive samples", "genotyping effort", "Ecological Research Noninvasive samples", "field studies", "substrate handling", "Genotyping errors", "alternative DNA source", "DNA concentrations", "microsatellite loci", "identification successes", "identification success", "genotyping success", "consensus genotypes"], "article_id"=>1583711, "categories"=>["Uncategorised"], "users"=>["Diana Lobo", "Raquel Godinho", "Francisco Álvares", "José V. López-Bao", "Alejandro Rodriguez"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139765.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_identification_success_across_different_classes_of_DNA_concentration_in_saliva_extracts_/1583711", "title"=>"Species identification success across different classes of DNA concentration in saliva extracts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-23 03:06:08"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"11", "full-text"=>"11", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"10", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"9", "full-text"=>"5", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"16", "full-text"=>"18", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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