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Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds.

Tavares ES, Baker AJ - BMC Evol. Biol. (2008)

Bottom Line: However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds.This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Canada. erika.tavares@utoronto.ca

ABSTRACT

Background: DNA barcoding of life using a standardized COI sequence was proposed as a species identification system, and as a method for detecting putative new species. Previous tests in birds showed that individuals can be correctly assigned to species in ~94% of the cases and suggested a threshold of 10x mean intraspecific difference to detect potential new species. However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.

Results: To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds. In all pairs, individuals of each species were monophyletic in a neighbor-joining (NJ) tree, and each species possessed fixed mutational differences distinguishing them from their sister species. Consequently, individuals were correctly assigned to species using a statistical coalescent framework. A coalescent test of taxonomic distinctiveness based on chance occurrence of reciprocal monophyly in two lineages was verified in known sister species, and used to identify recently separated lineages that represent putative species. This approach avoids the use of a universal distance cutoff which is invalidated by variation in times to common ancestry of sister species and in rates of evolution.

Conclusion: Closely related sister species of birds can be identified reliably by barcodes of fixed diagnostic substitutions in COI sequences, verifying coalescent-based statistical tests of reciprocal monophyly for taxonomic distinctiveness. Contrary to recent criticisms, a single DNA barcode is a rapid way to discover monophyletic lineages within a metapopulation that might represent undiscovered cryptic species, as envisaged in the unified species concept. This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.

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Assignment of unknowns. Neighbor-joining tree constructed with K2P genetic distances. Fixed substitutions are represented by coloured boxes, with corresponding character positions relative to the beginning of COI. Query specimens used in the test of assignment are indicated in red, with additional information in Table 2. a) Okarito Brown Kiwi (Apteryx rowi); b) Ruby-throated Hummingbird (Archilochus colubris); c) Sandwich Tern (Thalasseus sandvicensis).
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Figure 2: Assignment of unknowns. Neighbor-joining tree constructed with K2P genetic distances. Fixed substitutions are represented by coloured boxes, with corresponding character positions relative to the beginning of COI. Query specimens used in the test of assignment are indicated in red, with additional information in Table 2. a) Okarito Brown Kiwi (Apteryx rowi); b) Ruby-throated Hummingbird (Archilochus colubris); c) Sandwich Tern (Thalasseus sandvicensis).

Mentions: Individuals from the six species-pairs with adequate samples sizes were picked randomly to query whether they could be assigned correctly to their species using clustering in a NJ tree, fixed mutations, and a statistical test of assignment based on coalescent theory [24] (Table 2, Figure 2). In all the cases the query individual was correctly assigned to species with posterior probability of 1.0 and correspondingly tiny risk of misassignment (Table 2, Figure 2). When species barcodes were comprised of more than one intraspecific cluster, as in Southern Brown Kiwi (Apteryx australis, Figure 2A), Gull-billed Tern (Gelochelidon nilotica) and Gentoo Penguin (Pygoscelis papua), the query individual was assigned correctly to the each intraspecific cluster (Table 2).


Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds.

Tavares ES, Baker AJ - BMC Evol. Biol. (2008)

Assignment of unknowns. Neighbor-joining tree constructed with K2P genetic distances. Fixed substitutions are represented by coloured boxes, with corresponding character positions relative to the beginning of COI. Query specimens used in the test of assignment are indicated in red, with additional information in Table 2. a) Okarito Brown Kiwi (Apteryx rowi); b) Ruby-throated Hummingbird (Archilochus colubris); c) Sandwich Tern (Thalasseus sandvicensis).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279116&req=5

Figure 2: Assignment of unknowns. Neighbor-joining tree constructed with K2P genetic distances. Fixed substitutions are represented by coloured boxes, with corresponding character positions relative to the beginning of COI. Query specimens used in the test of assignment are indicated in red, with additional information in Table 2. a) Okarito Brown Kiwi (Apteryx rowi); b) Ruby-throated Hummingbird (Archilochus colubris); c) Sandwich Tern (Thalasseus sandvicensis).
Mentions: Individuals from the six species-pairs with adequate samples sizes were picked randomly to query whether they could be assigned correctly to their species using clustering in a NJ tree, fixed mutations, and a statistical test of assignment based on coalescent theory [24] (Table 2, Figure 2). In all the cases the query individual was correctly assigned to species with posterior probability of 1.0 and correspondingly tiny risk of misassignment (Table 2, Figure 2). When species barcodes were comprised of more than one intraspecific cluster, as in Southern Brown Kiwi (Apteryx australis, Figure 2A), Gull-billed Tern (Gelochelidon nilotica) and Gentoo Penguin (Pygoscelis papua), the query individual was assigned correctly to the each intraspecific cluster (Table 2).

Bottom Line: However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds.This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, Canada. erika.tavares@utoronto.ca

ABSTRACT

Background: DNA barcoding of life using a standardized COI sequence was proposed as a species identification system, and as a method for detecting putative new species. Previous tests in birds showed that individuals can be correctly assigned to species in ~94% of the cases and suggested a threshold of 10x mean intraspecific difference to detect potential new species. However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.

Results: To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds. In all pairs, individuals of each species were monophyletic in a neighbor-joining (NJ) tree, and each species possessed fixed mutational differences distinguishing them from their sister species. Consequently, individuals were correctly assigned to species using a statistical coalescent framework. A coalescent test of taxonomic distinctiveness based on chance occurrence of reciprocal monophyly in two lineages was verified in known sister species, and used to identify recently separated lineages that represent putative species. This approach avoids the use of a universal distance cutoff which is invalidated by variation in times to common ancestry of sister species and in rates of evolution.

Conclusion: Closely related sister species of birds can be identified reliably by barcodes of fixed diagnostic substitutions in COI sequences, verifying coalescent-based statistical tests of reciprocal monophyly for taxonomic distinctiveness. Contrary to recent criticisms, a single DNA barcode is a rapid way to discover monophyletic lineages within a metapopulation that might represent undiscovered cryptic species, as envisaged in the unified species concept. This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.

Show MeSH
Related in: MedlinePlus