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

is a journal article

BMC evolutionary biology 8: (2008)
 E S  Tavares   A J  Baker 

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.

Taxon/gene matrix

Table lens view of sequences, grouped by taxon and gene feature. Click on accession number to see details for sequence. Note that if more than one sequence exists for the same gene for the same taxon, only one will be displayed here.

Features

Sequence features (such as genes) in this study

 COI 

Taxa

Taxa sequenced in thius study

 Acridotheres ginginianus   Acridotheres tristis   Actitis hypoleucos   Actitis macularia   Aethia cristatella   Cyclorrhynchus psittacula   Aethia pygmaea   Aptenodytes forsteri   Aptenodytes patagonicus   Apteryx haastii   Apteryx australis mantelli   Apteryx owenii   Apteryx rowi   Brachyramphus brevirostris   Brachyramphus marmoratus   Bubo scandiacus   Bubo virginianus   Bucephala clangula   Cerorhinca monocerata   Chlidonias leucopterus   Chlidonias niger   Eudyptes pachyrhynchus   Eudyptes robustus   Eudyptula minor   Euphagus cyanocephalus   Fratercula arctica   Fratercula cirrhata   Fratercula corniculata   Gelochelidon nilotica   Himantopus himantopus   Himantopus himantopus leucocephalus   Himantopus himantopus melanurus   Himantopus mexicanus   Hydroprogne caspia   Icterus galbula   Jacana jacana   Limnodromus griseus   Limnodromus scolopaceus   Morus bassanus   Morus capensis   Morus serrator   Numenius phaeopus   Numenius tahitiensis   Phalaropus fulicaria   Phalaropus lobatus   Pheucticus ludovicianus   Pygoscelis papua   Recurvirostra americana   Recurvirostra andina   Rissa tridactyla   Sialia sialis   Spheniscus demersus   Spheniscus magellanicus   Spizella passerina   Stercorarius longicaudus   Stercorarius parasiticus   Sternula albifrons   Sternula superciliaris   Sturnella neglecta   Sturnus malabaricus   Synthliboramphus antiquus   Synthliboramphus wumizusume   Sturnus pagodarum   Sterna sandvicensis   Tringa brevipes   Tringa flavipes   Tringa glareola   Tringa melanoleuca   Tringa nebularia   Tringa semipalmata   Tringa totanus   Uria aalge   Uria lomvia 

Sequences 309

Sequences cited by this article.

Distribution of object

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Overlapping (3)

Studies in the same area, based on intersecting polygons enclosing all point localities associated with the study. Due to limitations of the underlying database the overlap is calculated using the minimum bounding rectangle, not the actual polygon.
  1. Mitochondrial paraphyly in a polymorphic poison frog species (Dendrobatidae; D. pumilio)
  2. A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences
  3. Multigenic and morphometric differentiation of ground squirrels (Spermophilus, Scuiridae, Rodentia) in Turkey, with a description of a new species