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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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Levels of intraspecific and interspecific distances of sister-species of birds. a) Frequency distribution of K2P intraspecific and interspecific genetic distances between sister-species. b) Frequency distribution of the ratios of K2P interspecific: intraspecific distances in sister species of birds.
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Figure 3: Levels of intraspecific and interspecific distances of sister-species of birds. a) Frequency distribution of K2P intraspecific and interspecific genetic distances between sister-species. b) Frequency distribution of the ratios of K2P interspecific: intraspecific distances in sister species of birds.

Mentions: Mean among sister-species distances of mtDNA barcodes varied from 0.78% to 11.77%, with 20 out of 60 (28.6%) distances smaller than the 2.7% threshold used to flag potential new species of birds. Among-species distances overlapped maximum within-species distances in 39 of 60 (65%) sister-species pairs. Excluding cases that are likely to represent overlooked species based on other attributes, the overlap was observed in 21 of 60 sister-species pairs (35%, Figure 3A). However, COI sequences in several species were structured in NJ trees into clades that represent geographically structured populations, recognized subspecies or possibly cryptic species (Table 3). The ratios of among-species to within-species distances were above 1 except for western and eastern populations of Eastern Meadowlark (Sturnella magna) which are thought to be two species [11,25] (Figure 3B).


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

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

Levels of intraspecific and interspecific distances of sister-species of birds. a) Frequency distribution of K2P intraspecific and interspecific genetic distances between sister-species. b) Frequency distribution of the ratios of K2P interspecific: intraspecific distances in sister species of birds.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Levels of intraspecific and interspecific distances of sister-species of birds. a) Frequency distribution of K2P intraspecific and interspecific genetic distances between sister-species. b) Frequency distribution of the ratios of K2P interspecific: intraspecific distances in sister species of birds.
Mentions: Mean among sister-species distances of mtDNA barcodes varied from 0.78% to 11.77%, with 20 out of 60 (28.6%) distances smaller than the 2.7% threshold used to flag potential new species of birds. Among-species distances overlapped maximum within-species distances in 39 of 60 (65%) sister-species pairs. Excluding cases that are likely to represent overlooked species based on other attributes, the overlap was observed in 21 of 60 sister-species pairs (35%, Figure 3A). However, COI sequences in several species were structured in NJ trees into clades that represent geographically structured populations, recognized subspecies or possibly cryptic species (Table 3). The ratios of among-species to within-species distances were above 1 except for western and eastern populations of Eastern Meadowlark (Sturnella magna) which are thought to be two species [11,25] (Figure 3B).

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