A likelihood ratio test for species membership based on DNA sequence data

DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability.

[1]  S. Ball,et al.  DNA barcodes for biosecurity: invasive species identification , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[2]  N. Platnick,et al.  The intellectual content of taxonomy: a comment on DNA taxonomy , 2003 .

[3]  C..  Simulating Probability Distributions in the Coalescent * , 2022 .

[4]  S Lek,et al.  Classifying individuals among infra-specific taxa using microsatellite data and neural networks. , 1996, Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie.

[5]  Tim Hesterberg,et al.  Monte Carlo Strategies in Scientific Computing , 2002, Technometrics.

[6]  Jon A Yamato,et al.  Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. , 1995, Genetics.

[7]  Robert Hanner,et al.  The problems and promise of DNA barcodes for species diagnosis of primate biomaterials , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[8]  B. Rannala,et al.  Detecting immigration by using multilocus genotypes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Jody Hey,et al.  Divergence population genetics of chimpanzees. , 2004, Molecular biology and evolution.

[10]  I. Stirling,et al.  Microsatellite analysis of population structure in Canadian polar bears , 1995, Molecular ecology.

[11]  K. Liang,et al.  Asymptotic Properties of Maximum Likelihood Estimators and Likelihood Ratio Tests under Nonstandard Conditions , 1987 .

[12]  P. J. Green,et al.  Density Estimation for Statistics and Data Analysis , 1987 .

[13]  R. Nielsen,et al.  Distinguishing migration from isolation: a Markov chain Monte Carlo approach. , 2001, Genetics.

[14]  M. Vences,et al.  Deciphering amphibian diversity through DNA barcoding: chances and challenges , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[15]  Nicolas Salamin,et al.  Land plants and DNA barcodes: short-term and long-term goals , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[16]  Jeremy R. deWaard,et al.  Biological identifications through DNA barcodes , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[17]  Arie van der Meijden,et al.  Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians , 2005, Frontiers in Zoology.

[18]  R. Nielsen,et al.  Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species , 2004, Molecular ecology.

[19]  Mark Blaxter,et al.  Molecular barcodes for soil nematode identification , 2002, Molecular ecology.

[20]  R. Nielsen,et al.  Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis , 2004, Genetics.

[21]  D. Tautz,et al.  A plea for DNA taxonomy , 2003 .

[22]  P. Donnelly,et al.  Inference in molecular population genetics , 2000 .

[23]  Alessandro Minelli,et al.  DNA points the way ahead in taxonomy , 2002, Nature.

[24]  P. Hebert,et al.  Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species , 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[25]  J. Hey.  On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas , 2005, PLoS biology.

[26]  C. Humphries,et al.  Shortcuts in systematics? A commentary on DNA-based taxonomy , 2003 .

[27]  D. Tautz,et al.  Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[28]  P. Hebert,et al.  Identification of Birds through DNA Barcodes , 2004, PLoS biology.

[29]  G Luikart,et al.  New methods employing multilocus genotypes to select or exclude populations as origins of individuals. , 1999, Genetics.

[30]  C. Moritz,et al.  Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia , 1998 .

[31]  D. Janzen,et al.  Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[32]  G. S. de Hoog,et al.  Microcoding: the second step in DNA barcoding , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.