James H Degnan

Summary

Affiliation: University of Canterbury
Country: New Zealand

Publications

  1. pmc A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
    Tanja Stadler
    Institute of Integrative Biology, Universitatsstrasse 16, 8092, Zurich, Switzerland
    Algorithms Mol Biol 7:7. 2012
  2. doi Anomalous unrooted gene trees
    James H Degnan
    Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
    Syst Biol 62:574-90. 2013
  3. doi The probability distribution of ranked gene trees on a species tree
    James H Degnan
    Department of Mathematics and Statistics, Private Bag 4800, University of Canterbury, Christchurch 8140, New Zealand
    Math Biosci 235:45-55. 2012
  4. doi Gene tree discordance, phylogenetic inference and the multispecies coalescent
    James H Degnan
    Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Trends Ecol Evol 24:332-40. 2009
  5. pmc Properties of consensus methods for inferring species trees from gene trees
    James H Degnan
    Department of Human Genetics, 1241 East Catherine Street, University of Michigan, Ann Arbor, MI 48109 0618, USA
    Syst Biol 58:35-54. 2009
  6. doi Species tree inference by the STAR method and its generalizations
    Elizabeth S Allman
    Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK, USA
    J Comput Biol 20:50-61. 2013
  7. pmc Comparing spatial maps of human population-genetic variation using Procrustes analysis
    Chaolong Wang
    University of Michigan, USA
    Stat Appl Genet Mol Biol 9:Article 13. 2010
  8. pmc Fast and consistent estimation of species trees using supermatrix rooted triples
    Michael DeGiorgio
    Center for Computational Medicine and Bioinformatics, University of Michigan, USA
    Mol Biol Evol 27:552-69. 2010
  9. ncbi A characterization of the set of species trees that produce anomalous ranked gene trees
    James H Degnan
    Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch 8013, New Zealand
    IEEE/ACM Trans Comput Biol Bioinform 9:1558-68. 2012
  10. pmc Coalescence-time distributions in a serial founder model of human evolutionary history
    Michael DeGiorgio
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 189:579-93. 2011

Detail Information

Publications18

  1. pmc A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
    Tanja Stadler
    Institute of Integrative Biology, Universitatsstrasse 16, 8092, Zurich, Switzerland
    Algorithms Mol Biol 7:7. 2012
    ..Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime...
  2. doi Anomalous unrooted gene trees
    James H Degnan
    Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
    Syst Biol 62:574-90. 2013
    ..The results could be useful for understanding gene tree discordance and designing simulations studies for inferring challenging species trees...
  3. doi The probability distribution of ranked gene trees on a species tree
    James H Degnan
    Department of Mathematics and Statistics, Private Bag 4800, University of Canterbury, Christchurch 8140, New Zealand
    Math Biosci 235:45-55. 2012
    ..We then show that similar to the unranked case, ranked gene trees that do not match either the ranking or the topology of the species tree can have greater probability than the matching ranked gene tree...
  4. doi Gene tree discordance, phylogenetic inference and the multispecies coalescent
    James H Degnan
    Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Trends Ecol Evol 24:332-40. 2009
    ....
  5. pmc Properties of consensus methods for inferring species trees from gene trees
    James H Degnan
    Department of Human Genetics, 1241 East Catherine Street, University of Michigan, Ann Arbor, MI 48109 0618, USA
    Syst Biol 58:35-54. 2009
    ..Our results therefore suggest a method for using multiple loci to infer the species-tree topology, even when it is discordant with the most likely gene tree...
  6. doi Species tree inference by the STAR method and its generalizations
    Elizabeth S Allman
    Department of Mathematics and Statistics, University of Alaska Fairbanks, Fairbanks, AK, USA
    J Comput Biol 20:50-61. 2013
    ..We discuss the impact of gene tree sampling schemes for species tree inference using generalized STAR methods and reinterpret the original STAR as a consensus method based on clades...
  7. pmc Comparing spatial maps of human population-genetic variation using Procrustes analysis
    Chaolong Wang
    University of Michigan, USA
    Stat Appl Genet Mol Biol 9:Article 13. 2010
    ....
  8. pmc Fast and consistent estimation of species trees using supermatrix rooted triples
    Michael DeGiorgio
    Center for Computational Medicine and Bioinformatics, University of Michigan, USA
    Mol Biol Evol 27:552-69. 2010
    ..SMRT-ML is therefore a computationally efficient and statistically consistent estimator of the species tree when gene trees are distributed according to the multispecies coalescent model...
  9. ncbi A characterization of the set of species trees that produce anomalous ranked gene trees
    James H Degnan
    Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch 8013, New Zealand
    IEEE/ACM Trans Comput Biol Bioinform 9:1558-68. 2012
    ..The results have implications for the use of ranked gene trees in phylogenetic inference...
  10. pmc Coalescence-time distributions in a serial founder model of human evolutionary history
    Michael DeGiorgio
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
    Genetics 189:579-93. 2011
    ..We interpret the theoretical results in relation to their implications for human population genetics...
  11. doi Determining species tree topologies from clade probabilities under the coalescent
    Elizabeth S Allman
    Department of Mathematics and Statistics, University of Alaska Fairbanks, PO Box 756660, Fairbanks, AK 99775, USA
    J Theor Biol 289:96-106. 2011
    ....
  12. pmc Genomics and genome-wide association studies: an integrative approach to expression QTL mapping
    James H Degnan
    Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
    Genomics 92:129-33. 2008
    ..We demonstrate that our family-based screening approach performs well in the analysis of integrative genomic datasets and that screening using either heritability or conditional power produces similar, though not identical, results...
  13. ncbi Gene tree distributions under the coalescent process
    James H Degnan
    Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico 87131, USA
    Evolution 59:24-37. 2005
    ..The method for computing gene tree distributions is implemented in the computer program COAL...
  14. doi Coalescent histories for discordant gene trees and species trees
    Noah A Rosenberg
    Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, United States
    Theor Popul Biol 77:145-51. 2010
    ....
  15. pmc EFBAT: exact family-based association tests
    Kady Schneiter
    Department of Mathematics and Statistics, Utah State University, 3900 Old Main Hill, Logan, UT 84322 3900, USA
    BMC Genet 8:86. 2007
    ..These tests are especially valuable for being robust to population structure. We introduce a tool, EFBAT, which performs exact family-based tests of association for X-chromosome and autosomal biallelic markers...
  16. doi Clades, clans, and reciprocal monophyly under neutral evolutionary models
    Sha Zhu
    Biomathematics Research Centre, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
    Theor Popul Biol 79:220-7. 2011
    ..Our findings are relevant for calculating the statistical significance of observed monophyly and reciprocal monophyly in phylogenetics...
  17. doi Genotype, haplotype and copy-number variation in worldwide human populations
    Mattias Jakobsson
    Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    Nature 451:998-1003. 2008
    ..Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations...
  18. doi Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
    Elizabeth S Allman
    Department of Mathematics and Statistics, University of Alaska Fairbanks, PO Box 756660, Fairbanks, AX 99775, USA
    J Math Biol 62:833-62. 2011
    ..The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled...