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.

Download Full-text

Faculty Opinions recommendation of A likelihood ratio test of speciation with gene flow using genomic sequence data.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.3540959.3240060 ◽

2010 ◽

Author(s):

Nicolas Galtier ◽

Julien Dutheil

Keyword(s):

Gene Flow ◽

Likelihood Ratio ◽

Likelihood Ratio Test ◽

Genomic Sequence ◽

Sequence Data ◽

Ratio Test

Download Full-text

A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

Genome Biology and Evolution ◽

10.1093/gbe/evq011 ◽

2010 ◽

Vol 2 ◽

pp. 200-211 ◽

Cited By ~ 39

Author(s):

Ziheng Yang

Keyword(s):

Gene Flow ◽

Likelihood Ratio ◽

Likelihood Ratio Test ◽

Genomic Sequence ◽

Sequence Data ◽

Ratio Test

Download Full-text

Comparing Groups of Life-Course Sequences Using the Bayesian Information Criterion and the Likelihood-Ratio Test

Sociological Methodology ◽

10.1177/0081175020959401 ◽

2020 ◽

pp. 008117502095940

Author(s):

Tim Futing Liao ◽

Anette Eva Fasang

Keyword(s):

Life Course ◽

Likelihood Ratio ◽

Likelihood Ratio Test ◽

Simulation Study ◽

Bayesian Information Criterion ◽

Sequence Data ◽

Information Criterion ◽

West Germany ◽

Ratio Test ◽

Life Courses

How can we statistically assess differences in groups of life-course trajectories? The authors address a long-standing inadequacy of social sequence analysis by proposing an adaption of the Bayesian information criterion (BIC) and the likelihood-ratio test (LRT) for assessing differences in groups of sequence data. Unlike previous methods, this adaption provides a useful measure for degrees of difference, that is, the substantive significance, and the statistical significance of differences between predefined groups of life-course trajectories. The authors present a simulation study and an empirical application on whether employment life-courses converged after reunification in the former East Germany and West Germany, using data for six birth-cohort groups ages 15 to 40 years from the German National Education Panel Study. The new methods allow the authors to show that convergence of employment life-courses around reunification was stronger for men than for women and that it was most pronounced in terms of the duration of employment states but weaker for their order and timing in the life-course. Convergence of East German and West German women’s employment lives set in earlier and reflects a secular trend toward a more gender-egalitarian division of labor in West Germany that is unrelated to reunification. The simulation study and the substantive application demonstrate the usefulness of the proposed BIC and LRT methods for assessing group differences in sequence data.

Download Full-text

Which Statistic Should Be Used to Detect Item Preknowledge When the Set of Compromised Items Is Known?

Applied Psychological Measurement ◽

10.1177/0146621617698453 ◽

2017 ◽

Vol 41 (6) ◽

pp. 403-421 ◽

Cited By ~ 5

Author(s):

Sandip Sinharay

Keyword(s):

Likelihood Ratio ◽

Likelihood Ratio Test ◽

Type I Error ◽

Null Distribution ◽

Real Data ◽

Major Type ◽

Ratio Test ◽

Type I ◽

Posterior Shift ◽

Item Preknowledge

Benefiting from item preknowledge is a major type of fraudulent behavior during educational assessments. Belov suggested the posterior shift statistic for detection of item preknowledge and showed its performance to be better on average than that of seven other statistics for detection of item preknowledge for a known set of compromised items. Sinharay suggested a statistic based on the likelihood ratio test for detection of item preknowledge; the advantage of the statistic is that its null distribution is known. Results from simulated and real data and adaptive and nonadaptive tests are used to demonstrate that the Type I error rate and power of the statistic based on the likelihood ratio test are very similar to those of the posterior shift statistic. Thus, the statistic based on the likelihood ratio test appears promising in detecting item preknowledge when the set of compromised items is known.

Download Full-text