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Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects

Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known... Full description

Journal Title: Systematic biology 2006-08, Vol.55 (4), p.595-609
Main Author: Pons, Joan
Other Authors: Barraclough, Timothy G , Gomez-Zurita, Jesus , Cardoso, Anabela , Duran, Daniel P , Hazell, Steaphan , Kamoun, Sophien , Sumlin, William D , Vogler, Alfried P , Hedin, Marshal
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
Quelle: Alma/SFX Local Collection
Publisher: England: Society of Systematic Zoology
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/16967577
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title: Sequence-Based Species Delimitation for the DNA Taxonomy of Undescribed Insects
format: Article
creator:
  • Pons, Joan
  • Barraclough, Timothy G
  • Gomez-Zurita, Jesus
  • Cardoso, Anabela
  • Duran, Daniel P
  • Hazell, Steaphan
  • Kamoun, Sophien
  • Sumlin, William D
  • Vogler, Alfried P
  • Hedin, Marshal
subjects:
  • Animals
  • Australia
  • Base Sequence
  • Biological taxonomies
  • Cicindelidae
  • Classification - methods
  • Climate
  • coalescence
  • Coleoptera - genetics
  • DNA
  • DNA, Mitochondrial - genetics
  • Evolution, Molecular
  • Evolutionary biology
  • Genetic Variation
  • Geography
  • Insect genetics
  • Insects
  • Likelihood Functions
  • Mitochondrial DNA
  • Models, Genetic
  • Molecular Sequence Data
  • mtDNA
  • paleoclimate
  • Parametric models
  • Parsimony
  • Phylogenetic species concept
  • Phylogenetics
  • Phylogeny
  • Sequence Analysis, DNA
  • Speciation
  • Species
  • Species Specificity
  • Taxonomy
ispartof: Systematic biology, 2006-08, Vol.55 (4), p.595-609
description: Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique (“diagnostic”) characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionCataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique (“diagnostic”) characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
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subjectAnimals ; Australia ; Base Sequence ; Biological taxonomies ; Cicindelidae ; Classification - methods ; Climate ; coalescence ; Coleoptera - genetics ; DNA ; DNA, Mitochondrial - genetics ; Evolution, Molecular ; Evolutionary biology ; Genetic Variation ; Geography ; Insect genetics ; Insects ; Likelihood Functions ; Mitochondrial DNA ; Models, Genetic ; Molecular Sequence Data ; mtDNA ; paleoclimate ; Parametric models ; Parsimony ; Phylogenetic species concept ; Phylogenetics ; Phylogeny ; Sequence Analysis, DNA ; Speciation ; Species ; Species Specificity ; Taxonomy
ispartofSystematic biology, 2006-08, Vol.55 (4), p.595-609
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descriptionCataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique (“diagnostic”) characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
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6Climate
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14Geography
15Insect genetics
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17Likelihood Functions
18Mitochondrial DNA
19Models, Genetic
20Molecular Sequence Data
21mtDNA
22paleoclimate
23Parametric models
24Parsimony
25Phylogenetic species concept
26Phylogenetics
27Phylogeny
28Sequence Analysis, DNA
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30Species
31Species Specificity
32Taxonomy
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notesPresent Address: Area de Biología Animal, Departamento de Zoología y Antropología Física, Facultad de Biología, Universidad de Murcia–Campus de Espinardo, Murcia, 30071, Spain
abstractCataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique (“diagnostic”) characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
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