The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting
Abstract
The extent and evolutionary significance of hybridization is difficult to evaluate because of the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present a novel parametric approach for statistically distinguishing hybridization from incomplete lineage sorting based on minimum genetic distances of a nonrecombining locus. It is based on the idea that the expected minimum genetic distance between sequences from two species is smaller for some hybridization events than for incomplete lineage sorting scenarios. When applied to empirical data sets, distributions can be generated for the minimum interspecies distances expected under incomplete lineage sorting using coalescent simulations. If the observed distance between sequences from two species is smaller than its predicted distribution, incomplete lineage sorting can be rejected and hybridization inferred. We demonstrate the power of the method using simulations and illustrate its application on New Zealand alpine buttercups (Ranunculus). The method is robust and complements existing approaches. Thus it should allow biologists to assess with greater accuracy the importance of hybridization in evolution.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
MODELTEST: testing the model of DNA substitution.
Posada, D., & Crandall, K. A. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.817 · Cited by 19,820
Universal primers for amplification of three non-coding regions of chloroplast DNA
Taberlet, P., Gielly, L., Pautou, G., & Bouvet, J. (1991) · Plant Molecular Biology · doi:10.1007/bf00037152 · Cited by 5,694
Proceedings of the American philosophical society
(1838) · Journal of the Franklin Institute · doi:10.1016/s0016-0032(38)92229-x · Cited by 5,524
Journal of the Royal Statistical Society (B)
Fildes, R. (1993) · International Journal of Forecasting · doi:10.1016/0169-2070(93)90088-5 · Cited by 3,437
Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.523 · Cited by 3,021
Wolfe, K. H., Li, W. H., & Sharp, P. M. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.24.9054 · Cited by 2,317
Funk, D. J., & Omland, K. E. (2003) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.34.011802.132421 · Cited by 2,237
Kingman, J. F. C. (1982) · Stochastic Processes and their Applications · doi:10.1016/0304-4149(82)90011-4 · Cited by 2,155
Ribosomal ITS sequences and plant phylogenetic inference
Álvarez, I., & Wendel, J. F. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00208-2 · Cited by 1,877
Natural Hybridization and Evolution
Arnold, M. L. (1997) · doi:10.1093/oso/9780195099744.001.0001 · Cited by 1,785
On the genealogy of large populations
Kingmán, J. F. C. (1982) · Journal of Applied Probability · doi:10.1017/s0021900200034446 · Cited by 1,628
Hybridization and adaptive radiation
Seehausen, O. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.01.003 · Cited by 1,627
Hybridization as a stimulus for the evolution of invasiveness in plants?
Ellstrand, N. C., & Schierenbeck, K. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.13.7043 · Cited by 1,606
The role of hybridization in evolution
Barton, N. H. (2001) · Molecular Ecology · doi:10.1046/j.1365-294x.2001.01216.x · Cited by 1,603
Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae)
Sang, T., Crawford, D. J., & Stuessy, T. F. (1997) · American Journal of Botany · doi:10.2307/2446155 · Cited by 1,458
Hey, J., & Nielsen, R. (2004) · Genetics · doi:10.1534/genetics.103.024182 · Cited by 1,442
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Bruen, T. C., Philippe, H., & Bryant, D. (2006) · Genetics · doi:10.1534/genetics.105.048975 · Cited by 1,382
Hybrid origins of plant species
Rieseberg, L. H. (1997) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.28.1.359 · Cited by 1,246
Major Ecological Transitions in Wild Sunflowers Facilitated by Hybridization
Rieseberg, L. H., Raymond, O., Rosenthal, D. M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J. L., Schwarzbach, A. E., Donovan, L. A., & Lexer, C. (2003) · Science · doi:10.1126/science.1086949 · Cited by 1,240
Inferring Phylogeny Despite Incomplete Lineage Sorting
Maddison, W. P., & Knowles, L. L. (2006) · Systematic Biology · doi:10.1080/10635150500354928 · Cited by 1,142
Rannala, B., & Yang, Z. (2003) · Genetics · doi:10.1093/genetics/164.4.1645 · Cited by 1,131
Discordance of Species Trees with Their Most Likely Gene Trees
Degnan, J. H., & Rosenberg, N. A. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020068 · Cited by 968
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
Beerli, P. (2006) · Bioinformatics · doi:10.1093/bioinformatics/bti803 · Cited by 934
Anderson, E. (1949) · Wiley eBooks · doi:10.5962/bhl.title.4553 · Cited by 838
Properties of a neutral allele model with intragenic recombination
Hudson, R. R. (1983) · Theoretical Population Biology · doi:10.1016/0040-5809(83)90013-8 · Cited by 816
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
Rosenberg, N. A., & Nordborg, M. (2002) · Nature Reviews Genetics · doi:10.1038/nrg795 · Cited by 750
Small, R. L., Ryburn, J. A., Cronn, R. C., Seelanan, T., & Wendel, J. F. (1998) · American Journal of Botany · doi:10.2307/2446640 · Cited by 464
Use of nuclear genes for phylogeny reconstruction in plants
Small, R. L., Cronn, R. C., & Wendel, J. F. (2004) · Australian Systematic Botany · doi:10.1071/sb03015 · Cited by 452
Reconstructing patterns of reticulate evolution in plants
Linder, C. R., & Rieseberg, L. H. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1700 · Cited by 434
Machado, C. A., Kliman, R. M., Markert, J. A., & Hey, J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004103 · Cited by 319
Gene Flow and Natural Selection in the Origin of Drosophila pseudoobscura and Close Relatives
Wang, R. L., Wakeley, J., & Hey, J. (1997) · Genetics · doi:10.1093/genetics/147.3.1091 · Cited by 237
High Survival of Darwin's Finch Hybrids: Effects of Beak Morphology and Diets
Grant, B. R., & Grant, P. R. (1996) · Ecology · doi:10.2307/2265625 · Cited by 231
Testing Hybridization Hypotheses Based on Incongruent Gene Trees
Sang, T., & Zhong, Y. (2000) · Systematic Biology · doi:10.1080/10635159950127321 · Cited by 218
Transfer and Origin of Adaptations through Natural Hybridization: Were Anderson and Stebbins Right?
Arnold, M. L. (2004) · The Plant Cell · doi:10.1105/tpc.160370 · Cited by 202
Buckley, T. R., Cordeiro, M., Marshall, D. C., & Simon, C. (2006) · Systematic Biology · doi:10.1080/10635150600697283 · Cited by 190
Burgess, R., & Yang, Z. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn148 · Cited by 184
Difficulties in Detecting Hybridization
Holder, M. T., Anderson, J. A., & Holloway, A. K. (2001) · Systematic Biology · doi:10.1080/106351501753462911 · Cited by 165
Joly, S., & Bruneau, A. (2006) · Systematic Biology · doi:10.1080/10635150600863109 · Cited by 164
Self-citationLockhart, P. J., McLenachan, P. A., Havell, D., Glenny, D. S., Huson, D. H., & Jensen, U. (2001) · Annals of the Missouri Botanical Garden · doi:10.2307/3298586 · Cited by 151
Self-citationNoor, M. A. F., Grams, K. L., Bertucci, L. A., Almendarez, Y. M., Reiland, J., & Smith, K. R. (2001) · Evolution · doi:10.1554/0014-3820(2001)055[0512:tgoria]2.0.co;2 · Cited by 130
Paun, O., Lehnebach, C. A., Johansson, J. T., Lockhart, P. J., & Hörandl, E. (2005) · Taxon · doi:10.2307/25065478 · Cited by 114
Self-citationPolyploid and hybrid evolution in roses east of the Rocky Mountains
Joly, S., Starr, J. R., Lewis, W. H., & Bruneau, A. (2006) · American Journal of Botany · doi:10.3732/ajb.93.3.412 · Cited by 114
Self-citationUsing supernetworks to distinguish hybridization from lineage-sorting
Holland, B. R., Benthin, S., Lockhart, P. J., Moulton, V., & Huber, K. T. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-202 · Cited by 112
Self-citationSpeciation through homoploid hybridization between allotetraploids in peonies ( Paeonia )
Ferguson, D., & Sang, T. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061288698 · Cited by 93
Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study
Jin, G., Nakhleh, L. K., Snir, S., & Tuller, T. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl163 · Cited by 86
Cited by
Noor, M. A. F., & Bennett, S. M. (2009) · Heredity · doi:10.1038/hdy.2009.151 · Cited by 370
HyDe: A Python Package for Genome-Scale Hybridization Detection
Blischak, P. D., Chifman, J., Wolfe, A. D., & Kubatko, L. S. (2018) · Systematic Biology · doi:10.1093/sysbio/syy023 · Cited by 285
Detection and Polarization of Introgression in a Five-Taxon Phylogeny
Pease, J. B., & Hahn, M. W. (2015) · Systematic Biology · doi:10.1093/sysbio/syv023 · Cited by 268
Metadata
- Authors
- Joly, S., McLenachan, P. A., & Lockhart, P. J.
- Venue
- The American Naturalist
- Publisher
- University of Chicago Press
- Published
- 2009-08
- Volume
- 174
- Issue
- 2
- Pages
- E54-E70
- ISSN
- 0003-0147 (ISSN-L)
- 1537-5323
- OpenAlex
- W1993231286
- Cited by
- 425
- References
- 46
- FWCI
- 11.94
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
