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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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Examples of DNA barcodes distinguishing sister species. 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. a) Phalaropes (Phalaropus); b) Penguins (Aptenodytes); c) Goldeneyes (Bucephala).
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Figure 1: Examples of DNA barcodes distinguishing sister species. 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. a) Phalaropes (Phalaropus); b) Penguins (Aptenodytes); c) Goldeneyes (Bucephala).

Mentions: Monophyletic clusters of individuals corresponding to species were recovered in a Neighbor-joining (NJ) tree under the Kimura 2-parameter (K2P) model in all the sister-species pairs compared (Table 1, see Additional files 1, 2). Multiple diagnostic characters in the branches of the trees leading to species clusters were detected in all the pairs (see Additional file 1, Figure 1). Bootstrap support at the nodes grouping individuals of the same species varied from 55 to 100%, except for Eastern Meadowlark (Sturnella magna), with the majority of the values (93.1%) above 85% (see Additional file 1). Species with clusters of individuals supported with bootstrap levels below 85% were: Ruby-throated Hummingbird (Archilochus colubris), Black-chinned Hummingbird (Archilochus alexandri), Gunnison Sage-Grouse (Centrocercus minimus), Dusky Grouse (Dendragapus obscurus), Nuttall's Woodpecker (Picoides nuttallii), Jackass Penguin (Spheniscus demersus), and Magellanic Penguin (Spheniscus magellanicus). These species were distinguished by <10 fixed nucleotide substitutional differences or had multiple intraspecific clusters. Probabilities of chance occurrence of reciprocal monophyly arising from random-branching within a single taxon were smaller than the level of significance (α) of 5% (Table 1). Ideally, larger sample sizes are required to increase the power of the test and to confirm reciprocal monophyly over a broad geographic range.


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

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

Examples of DNA barcodes distinguishing sister species. 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. a) Phalaropes (Phalaropus); b) Penguins (Aptenodytes); c) Goldeneyes (Bucephala).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Examples of DNA barcodes distinguishing sister species. 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. a) Phalaropes (Phalaropus); b) Penguins (Aptenodytes); c) Goldeneyes (Bucephala).
Mentions: Monophyletic clusters of individuals corresponding to species were recovered in a Neighbor-joining (NJ) tree under the Kimura 2-parameter (K2P) model in all the sister-species pairs compared (Table 1, see Additional files 1, 2). Multiple diagnostic characters in the branches of the trees leading to species clusters were detected in all the pairs (see Additional file 1, Figure 1). Bootstrap support at the nodes grouping individuals of the same species varied from 55 to 100%, except for Eastern Meadowlark (Sturnella magna), with the majority of the values (93.1%) above 85% (see Additional file 1). Species with clusters of individuals supported with bootstrap levels below 85% were: Ruby-throated Hummingbird (Archilochus colubris), Black-chinned Hummingbird (Archilochus alexandri), Gunnison Sage-Grouse (Centrocercus minimus), Dusky Grouse (Dendragapus obscurus), Nuttall's Woodpecker (Picoides nuttallii), Jackass Penguin (Spheniscus demersus), and Magellanic Penguin (Spheniscus magellanicus). These species were distinguished by <10 fixed nucleotide substitutional differences or had multiple intraspecific clusters. Probabilities of chance occurrence of reciprocal monophyly arising from random-branching within a single taxon were smaller than the level of significance (α) of 5% (Table 1). Ideally, larger sample sizes are required to increase the power of the test and to confirm reciprocal monophyly over a broad geographic range.

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