RaBoT: a rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-06-07

AUTHORS

Ivan Scotti, William Montaigne, Klára Cseke, Stéphane Traissac

ABSTRACT

ContextNo efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary.AimsWe developed a method to compare genome-wide diversity estimates while taking into account—and factoring out—variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels.MethodsAn approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers.ResultsRaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots.ConclusionRaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms). More... »

PAGES

631-635

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/s13595-013-0302-z

DOI

http://dx.doi.org/10.1007/s13595-013-0302-z

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1050265193


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/07", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Agricultural and Veterinary Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0705", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Forestry Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Unit\u00e9 Mixte de Recherche \u201cEcologie des For\u00eats de Guyane\u201d (EcoFoG), INRA\u2014Institut National de la Recherche Agronomique, BP 709, 97387, Kourou Cedex, French Guiana, France", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Unit\u00e9 Mixte de Recherche \u201cEcologie des For\u00eats de Guyane\u201d (EcoFoG), INRA\u2014Institut National de la Recherche Agronomique, BP 709, 97387, Kourou Cedex, French Guiana, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Scotti", 
        "givenName": "Ivan", 
        "id": "sg:person.01032345662.28", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032345662.28"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Unit\u00e9 Mixte de Recherche \u201cEcologie des For\u00eats de Guyane\u201d (EcoFoG), Universit\u00e9 des Antilles et de la Guyane, Kourou, French Guiana, France", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Unit\u00e9 Mixte de Recherche \u201cEcologie des For\u00eats de Guyane\u201d (EcoFoG), Universit\u00e9 des Antilles et de la Guyane, Kourou, French Guiana, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Montaigne", 
        "givenName": "William", 
        "id": "sg:person.013311223257.18", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013311223257.18"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Department of Forest Tree Breeding, Experiment Station and Arboretum, Forest Research Institute, S\u00e1rv\u00e1r, Hungary", 
          "id": "http://www.grid.ac/institutes/grid.481832.4", 
          "name": [
            "Department of Forest Tree Breeding, Experiment Station and Arboretum, Forest Research Institute, S\u00e1rv\u00e1r, Hungary"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Cseke", 
        "givenName": "Kl\u00e1ra", 
        "id": "sg:person.0717320463.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717320463.89"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Unit\u00e9 Mixte de Recherche \u201cEcologie des For\u00eats de Guyane\u201d (EcoFoG), AgroParisTech, Kourou, French Guiana, France", 
          "id": "http://www.grid.ac/institutes/None", 
          "name": [
            "Unit\u00e9 Mixte de Recherche \u201cEcologie des For\u00eats de Guyane\u201d (EcoFoG), AgroParisTech, Kourou, French Guiana, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Traissac", 
        "givenName": "St\u00e9phane", 
        "id": "sg:person.015351344143.09", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015351344143.09"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1038/163688a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011831556", 
          "https://doi.org/10.1038/163688a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00122-003-1262-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035152188", 
          "https://doi.org/10.1007/s00122-003-1262-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/a:1024025331750", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012869488", 
          "https://doi.org/10.1023/a:1024025331750"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1023/b:coge.0000041021.91777.1a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005924155", 
          "https://doi.org/10.1023/b:coge.0000041021.91777.1a"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2013-06-07", 
    "datePublishedReg": "2013-06-07", 
    "description": "ContextNo efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary.AimsWe developed a method to compare genome-wide diversity estimates while taking into account\u2014and factoring out\u2014variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels.MethodsAn approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers.ResultsRaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots.ConclusionRaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).", 
    "genre": "article", 
    "id": "sg:pub.10.1007/s13595-013-0302-z", 
    "inLanguage": "en", 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1034834", 
        "issn": [
          "1286-4560", 
          "1297-966X"
        ], 
        "name": "Annals of Forest Science", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "6", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "70"
      }
    ], 
    "keywords": [
      "genetic diversity", 
      "diversity levels", 
      "undisturbed populations", 
      "multi-locus estimates", 
      "multi-locus level", 
      "multi-locus comparisons", 
      "genome-wide level", 
      "fragment length polymorphism (AFLP) markers", 
      "low genetic diversity", 
      "genome scan approach", 
      "high genetic diversity", 
      "length polymorphism (AFLP) markers", 
      "comparison of populations", 
      "diversity estimates", 
      "census size", 
      "polymorphism markers", 
      "codominant markers", 
      "Virola michelii", 
      "dominant markers", 
      "diversity", 
      "genotype level", 
      "undisturbed plots", 
      "corresponding adult population", 
      "scan approach", 
      "michelii", 
      "seedlings", 
      "markers", 
      "population", 
      "stochastic variance", 
      "high levels", 
      "allele level", 
      "large number", 
      "levels", 
      "empirical data", 
      "rarefaction", 
      "false positives", 
      "plots", 
      "sensitive method", 
      "differences", 
      "development", 
      "efficient method", 
      "variance", 
      "significance", 
      "data", 
      "number", 
      "significance of differences", 
      "comparison", 
      "size", 
      "advent", 
      "estimates", 
      "such tests", 
      "false negatives", 
      "approach", 
      "positives", 
      "negatives", 
      "method", 
      "adult population", 
      "use", 
      "subgroups", 
      "properties", 
      "test", 
      "bootstrap", 
      "account", 
      "bootstrap method", 
      "AimsWe", 
      "ContextNo efficient method", 
      "inter-population stochastic variance", 
      "genome-wide diversity estimates", 
      "inter-locus variance", 
      "MethodsAn approach", 
      "ResultsRaBoT", 
      "ConclusionRaBoT", 
      "biallelic codominant markers"
    ], 
    "name": "RaBoT: a rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity", 
    "pagination": "631-635", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1050265193"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1007/s13595-013-0302-z"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1007/s13595-013-0302-z", 
      "https://app.dimensions.ai/details/publication/pub.1050265193"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2021-11-01T18:21", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_614.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1007/s13595-013-0302-z"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s13595-013-0302-z'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s13595-013-0302-z'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s13595-013-0302-z'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s13595-013-0302-z'


 

This table displays all metadata directly associated to this object as RDF triples.

175 TRIPLES      22 PREDICATES      102 URIs      90 LITERALS      6 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1007/s13595-013-0302-z schema:about anzsrc-for:07
2 anzsrc-for:0705
3 schema:author N1aaf15d978c94e1399bda80f80378c11
4 schema:citation sg:pub.10.1007/s00122-003-1262-8
5 sg:pub.10.1023/a:1024025331750
6 sg:pub.10.1023/b:coge.0000041021.91777.1a
7 sg:pub.10.1038/163688a0
8 schema:datePublished 2013-06-07
9 schema:datePublishedReg 2013-06-07
10 schema:description ContextNo efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary.AimsWe developed a method to compare genome-wide diversity estimates while taking into account—and factoring out—variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels.MethodsAn approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers.ResultsRaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots.ConclusionRaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
11 schema:genre article
12 schema:inLanguage en
13 schema:isAccessibleForFree true
14 schema:isPartOf N2ff1c7de2e204678afaf216c56667e65
15 Ne04863de0ecc49d68d1bce51a26ca6b0
16 sg:journal.1034834
17 schema:keywords AimsWe
18 ConclusionRaBoT
19 ContextNo efficient method
20 MethodsAn approach
21 ResultsRaBoT
22 Virola michelii
23 account
24 adult population
25 advent
26 allele level
27 approach
28 biallelic codominant markers
29 bootstrap
30 bootstrap method
31 census size
32 codominant markers
33 comparison
34 comparison of populations
35 corresponding adult population
36 data
37 development
38 differences
39 diversity
40 diversity estimates
41 diversity levels
42 dominant markers
43 efficient method
44 empirical data
45 estimates
46 false negatives
47 false positives
48 fragment length polymorphism (AFLP) markers
49 genetic diversity
50 genome scan approach
51 genome-wide diversity estimates
52 genome-wide level
53 genotype level
54 high genetic diversity
55 high levels
56 inter-locus variance
57 inter-population stochastic variance
58 large number
59 length polymorphism (AFLP) markers
60 levels
61 low genetic diversity
62 markers
63 method
64 michelii
65 multi-locus comparisons
66 multi-locus estimates
67 multi-locus level
68 negatives
69 number
70 plots
71 polymorphism markers
72 population
73 positives
74 properties
75 rarefaction
76 scan approach
77 seedlings
78 sensitive method
79 significance
80 significance of differences
81 size
82 stochastic variance
83 subgroups
84 such tests
85 test
86 undisturbed plots
87 undisturbed populations
88 use
89 variance
90 schema:name RaBoT: a rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity
91 schema:pagination 631-635
92 schema:productId N2a1f2fb2fe8744b1925ca8fe3f5c8d79
93 Ne76442bb1ae149ec9b6977985669f012
94 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050265193
95 https://doi.org/10.1007/s13595-013-0302-z
96 schema:sdDatePublished 2021-11-01T18:21
97 schema:sdLicense https://scigraph.springernature.com/explorer/license/
98 schema:sdPublisher N734ddbbe200b4388b4598d8eb389ff5e
99 schema:url https://doi.org/10.1007/s13595-013-0302-z
100 sgo:license sg:explorer/license/
101 sgo:sdDataset articles
102 rdf:type schema:ScholarlyArticle
103 N07bd3002a5af4e8fbdb5eac3d0541c23 rdf:first sg:person.015351344143.09
104 rdf:rest rdf:nil
105 N0f5ded4bf060499c8684d403b1a64dd7 rdf:first sg:person.013311223257.18
106 rdf:rest N1a4032c9f2c94468a7423545050261d3
107 N1a4032c9f2c94468a7423545050261d3 rdf:first sg:person.0717320463.89
108 rdf:rest N07bd3002a5af4e8fbdb5eac3d0541c23
109 N1aaf15d978c94e1399bda80f80378c11 rdf:first sg:person.01032345662.28
110 rdf:rest N0f5ded4bf060499c8684d403b1a64dd7
111 N2a1f2fb2fe8744b1925ca8fe3f5c8d79 schema:name dimensions_id
112 schema:value pub.1050265193
113 rdf:type schema:PropertyValue
114 N2ff1c7de2e204678afaf216c56667e65 schema:volumeNumber 70
115 rdf:type schema:PublicationVolume
116 N734ddbbe200b4388b4598d8eb389ff5e schema:name Springer Nature - SN SciGraph project
117 rdf:type schema:Organization
118 Ne04863de0ecc49d68d1bce51a26ca6b0 schema:issueNumber 6
119 rdf:type schema:PublicationIssue
120 Ne76442bb1ae149ec9b6977985669f012 schema:name doi
121 schema:value 10.1007/s13595-013-0302-z
122 rdf:type schema:PropertyValue
123 anzsrc-for:07 schema:inDefinedTermSet anzsrc-for:
124 schema:name Agricultural and Veterinary Sciences
125 rdf:type schema:DefinedTerm
126 anzsrc-for:0705 schema:inDefinedTermSet anzsrc-for:
127 schema:name Forestry Sciences
128 rdf:type schema:DefinedTerm
129 sg:journal.1034834 schema:issn 1286-4560
130 1297-966X
131 schema:name Annals of Forest Science
132 schema:publisher Springer Nature
133 rdf:type schema:Periodical
134 sg:person.01032345662.28 schema:affiliation grid-institutes:None
135 schema:familyName Scotti
136 schema:givenName Ivan
137 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01032345662.28
138 rdf:type schema:Person
139 sg:person.013311223257.18 schema:affiliation grid-institutes:None
140 schema:familyName Montaigne
141 schema:givenName William
142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013311223257.18
143 rdf:type schema:Person
144 sg:person.015351344143.09 schema:affiliation grid-institutes:None
145 schema:familyName Traissac
146 schema:givenName Stéphane
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015351344143.09
148 rdf:type schema:Person
149 sg:person.0717320463.89 schema:affiliation grid-institutes:grid.481832.4
150 schema:familyName Cseke
151 schema:givenName Klára
152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717320463.89
153 rdf:type schema:Person
154 sg:pub.10.1007/s00122-003-1262-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035152188
155 https://doi.org/10.1007/s00122-003-1262-8
156 rdf:type schema:CreativeWork
157 sg:pub.10.1023/a:1024025331750 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012869488
158 https://doi.org/10.1023/a:1024025331750
159 rdf:type schema:CreativeWork
160 sg:pub.10.1023/b:coge.0000041021.91777.1a schema:sameAs https://app.dimensions.ai/details/publication/pub.1005924155
161 https://doi.org/10.1023/b:coge.0000041021.91777.1a
162 rdf:type schema:CreativeWork
163 sg:pub.10.1038/163688a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011831556
164 https://doi.org/10.1038/163688a0
165 rdf:type schema:CreativeWork
166 grid-institutes:None schema:alternateName Unité Mixte de Recherche “Ecologie des Forêts de Guyane” (EcoFoG), AgroParisTech, Kourou, French Guiana, France
167 Unité Mixte de Recherche “Ecologie des Forêts de Guyane” (EcoFoG), INRA—Institut National de la Recherche Agronomique, BP 709, 97387, Kourou Cedex, French Guiana, France
168 Unité Mixte de Recherche “Ecologie des Forêts de Guyane” (EcoFoG), Université des Antilles et de la Guyane, Kourou, French Guiana, France
169 schema:name Unité Mixte de Recherche “Ecologie des Forêts de Guyane” (EcoFoG), AgroParisTech, Kourou, French Guiana, France
170 Unité Mixte de Recherche “Ecologie des Forêts de Guyane” (EcoFoG), INRA—Institut National de la Recherche Agronomique, BP 709, 97387, Kourou Cedex, French Guiana, France
171 Unité Mixte de Recherche “Ecologie des Forêts de Guyane” (EcoFoG), Université des Antilles et de la Guyane, Kourou, French Guiana, France
172 rdf:type schema:Organization
173 grid-institutes:grid.481832.4 schema:alternateName Department of Forest Tree Breeding, Experiment Station and Arboretum, Forest Research Institute, Sárvár, Hungary
174 schema:name Department of Forest Tree Breeding, Experiment Station and Arboretum, Forest Research Institute, Sárvár, Hungary
175 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...