2 Search Results for "Benedict, Travis"

Document
DOI: 10.4230/LIPIcs.WABI.2018.19
DGEN: A Test Statistic for Detection of General Introgression Scenarios

Authors: Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, and Luay Nakhleh

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
When two species hybridize, one outcome is the integration of genetic material from one species into the genome of the other, a process known as introgression. Detecting introgression in genomic data is a very important question in evolutionary biology. However, given that hybridization occurs between closely related species, a complicating factor for introgression detection is the presence of incomplete lineage sorting, or ILS. The D-statistic, famously referred to as the "ABBA-BABA" test, was proposed for introgression detection in the presence of ILS in data sets that consist of four genomes. More recently, D_FOIL - a set of statistics - was introduced to extend the D-statistic to data sets of five genomes. The major contribution of this paper is demonstrating that the invariants underlying both the D-statistic and D_FOIL can be derived automatically from the probability mass functions of gene tree topologies under the null species tree model and alternative phylogenetic network model. Computational requirements aside, this automatic derivation provides a way to generalize these statistics to data sets of any size and with any scenarios of introgression. We demonstrate the accuracy of the general statistic, which we call D_GEN, on simulated data sets with varying rates of introgression, and apply it to an empirical data set of mosquito genomes. We have implemented D_GEN and made it available, both as a graphical user interface tool and as a command-line tool, as part of the freely available, open-source software package ALPHA (https://github.com/chilleo/ALPHA).
Cite as

Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, and Luay Nakhleh. DGEN: A Test Statistic for Detection of General Introgression Scenarios. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 19:1-19:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{elworth_et_al:LIPIcs.WABI.2018.19,
  author =	{Elworth, Ryan A. Leo and Allen, Chabrielle and Benedict, Travis and Dulworth, Peter and Nakhleh, Luay},
  title =	{{DGEN: A Test Statistic for Detection of General Introgression Scenarios}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{19:1--19:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.19},
  URN =		{urn:nbn:de:0030-drops-93218},
  doi =		{10.4230/LIPIcs.WABI.2018.19},
  annote =	{Keywords: Introgression, genealogies, phylogenetic networks}
}
Document
Keynote Speakers
DOI: 10.4230/LIPIcs.AofA.2018.8
Periods in Subtraction Games (Keynote Speakers)

Authors: Bret Benesh, Jamylle Carter, Deidra A. Coleman, Douglas G. Crabill, Jack H. Good, Michael A. Smith, Jennifer Travis, and Mark Daniel Ward

Published in: LIPIcs, Volume 110, 29th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2018)

Abstract
We discuss the structure of periods in subtraction games. In particular, we discuss ways that a computational approach yields insights to the periods that emerge in the asymptotic structure of these combinatorial games.
Cite as

Bret Benesh, Jamylle Carter, Deidra A. Coleman, Douglas G. Crabill, Jack H. Good, Michael A. Smith, Jennifer Travis, and Mark Daniel Ward. Periods in Subtraction Games (Keynote Speakers). In 29th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 110, pp. 8:1-8:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{benesh_et_al:LIPIcs.AofA.2018.8,
  author =	{Benesh, Bret and Carter, Jamylle and Coleman, Deidra A. and Crabill, Douglas G. and Good, Jack H. and Smith, Michael A. and Travis, Jennifer and Ward, Mark Daniel},
  title =	{{Periods in Subtraction Games}},
  booktitle =	{29th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2018)},
  pages =	{8:1--8:3},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-078-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{110},
  editor =	{Fill, James Allen and Ward, Mark Daniel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.AofA.2018.8},
  URN =		{urn:nbn:de:0030-drops-89015},
  doi =		{10.4230/LIPIcs.AofA.2018.8},
  annote =	{Keywords: combinatorial games, subtraction games, periods, asymptotic structure}
}
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