% This file was created with JabRef 2.10. % Encoding: UTF-8 @article{gibson2020genome, title={Genome-wide genotyping estimates mating system parameters and paternity in the island species Tolpis succulenta}, author={Gibson, Matthew JS and Crawford, Daniel J and Holder, Mark T and Mort, Mark E and Kerbs, Benjamin and de Sequeira, Miguel Menezes and Kelly, John K}, journal={American Journal of Botany}, volume={107}, number={8}, pages={1189--1197}, year={2020} } @Article{McTavishSH2015, Title = {Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - the impact of model mis-specification in distance corrections}, Author = {Emily Jane McTavish and Mike Steel and Mark T.~Holder}, Journal = {Molecular Phylogenetics and Evolution}, Year = {2015}, Volume = {93}, Pages = {289--295}, Url = {http://dx.doi.org/10.1016/j.ympev.2015.07.027} } @Article{AlfaroHolder, Title = {The Posterior and the Prior in {B}ayesian Phylogenetics}, Author = {Michael E.~Alfaro and Mark T.~Holder}, Journal = {Annual Review of Ecology, Evolution, and Systematics}, Year = {2006}, Pages = {19-42}, Volume = {37}, Url = {http://www.annualreviews.org/doi/full/10.1146/annurev.ecolsys.37.091305.110021} } @Article{AllmanHH2010, Title = {Estimating trees from filtered data: Identifiability of models for morphological phylogenetics}, Author = {Elizabeth S.~Allman and Mark T.~Holder and John A.~Rhodes}, Journal = {Journal of Theoretical Biology}, Year = {2010}, Number = {1}, Pages = {108-119}, Volume = {263}, Doi = {10.1016/j.jtbi.2009.12.001}, Keywords = {Mkv model}, Url = {http://www.sciencedirect.com/science/article/B6WMD-4XX160T-2/2/5adf8b8af77dd551890d7cb5b0e62dba} } @Article{AyresEtAl2012, Title = {{BEAGLE}: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics}, Author = {Daniel L. Ayres and Aaron Darling and Derrick J. Zwickl and Peter Beerli and Mark T. Holder and Paul O. Lewis and John P. Huelsenbeck and Fredrik Ronquist and David L. Swofford and Michael P. Cummings and Andrew Rambaut and Marc A. Suchard}, Journal = {Systematic Biology}, Year = {2012}, Number = {1}, Pages = {170-173}, Volume = {61}, Doi = {10.1093/sysbio/syr100}, Url = {http://sysbio.oxfordjournals.org/content/61/1/170.full.pdf+html} } @Article{BrauerEtAl2002, Title = {Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference}, Author = {Matthew J. Brauer and Mark T. Holder and Laurie A. Dries and Derrick J. Zwickl and Paul O. Lewis and David M. Hillis}, Journal = {Molecular Biology and Evolution}, Year = {2002}, Number = {10}, Pages = {1717-1726}, Volume = {19}, Url = {http://mbe.oxfordjournals.org/content/19/10/1717.full} } @Article{BurnsEtAl1995a, Title = {Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN11, TEXAN12, TEXAN13, TEXAN14 and TEXAN15 loci}, Author = {Burns, BM and Taylor, JF and Herring, KL and Herring, AD and Holder, MT and Collins, JS and Guerra, TM and Sanders, JO and Davis, SK}, Journal = {Animal Genetics}, Year = {1995}, Number = {3}, Pages = {201--201}, Volume = {26}, Doi = {10.1111/j.1365-2052.1995.tb03165.x}, Publisher = {Wiley Online Library}, Url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1995.tb03165.x/abstract} } @Article{BurnsEtAl1995c, Title = {Bovine microsatellite mononucleotide and dinucleotide repeat polymorphisms at the TEXAN6, TEXAN7, TEXAN8, TEXAN9 and TEXAN10 loci}, Author = {Burns, BM and Taylor, JF and Herring, KL and Herring, AD and Holder, MT and Collins, JS and Guerra, TM and Sanders, JO and Davis, SK}, Journal = {Animal Genetics}, Year = {1995}, Number = {2}, Pages = {128--129}, Volume = {26}, Doi = {10.1111/j.1365-2052.1995.tb02654.x}, Publisher = {Wiley Online Library}, Url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1995.tb02654.x/abstract} } @Article{BurnsEtAl1995b, Title = {Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN16, TEXAN17, TEXAN18, TEXAN19 and TEXAN20 loci}, Author = {Burns, BM and Taylor, JF and Herring, KL and Herring, AD and Holder, MT and Holder, DA and Collins, JS and Sanders, JO and Davis, SK}, Journal = {Animal Genetics}, Year = {1995}, Number = {3}, Pages = {208--209}, Volume = {26}, Doi = {10.1111/j.1365-2052.1995.tb03174.x}, Publisher = {Wiley Online Library}, Url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1995.tb03174.x/abstract} } @Article{EdgcombEtAl2011, Title = {Protistan Microbial Observatory in the {Cariaco Basin, Caribbean. I}. Species richness and endemicity}, Author = {Virginia Edgcomb and William Orsi and John Bunge and Sunok Jeon and Richard Christen and Chesley Leslin and Mark Holder and Gordon T. Taylor and Paula Suarez and Ramon Varela and Slava Epstein}, Journal = {ISME Journal}, Year = {2011}, Number = {8}, Pages = {1344-1356}, Volume = {5}, Doi = {10.1038/ismej.2011.6}, Url = {http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20116a.html} } @Article{EvansHBOC2010, Title = {The Phylogenetic Position of {Myxozoa}: Exploring Conflicting Signals in Phylogenomic and Ribosomal Data Sets}, Author = {Nathaniel M. Evans and Mark T. Holder and Marcos S. Barbeitos and Beth Okamura and Paulyn Cartwright}, Journal = {Molecular Biology and Evolution}, Year = {2010}, Month = {Dec}, Number = {12}, Pages = {2733--2746}, Volume = {27}, Doi = {10.1093/molbev/msq159}, Url = {http://mbe.oxfordjournals.org/content/27/12/2733.full?sid=3dce9a83-c059-4046-8e05-84be548051d9} } @Article{GelfandEtAl2006, Title = {Explaining Species Distribution Patterns through Hierarchical Modeling}, Author = {Alan E Gelfand and Silander, Jr., John A. and {Shan-shan} Wu and Andrew M. Latimer and Paul O. Lewis and Anthony G. Rebelo and Mark Holder}, Journal = {{B}ayesian Analysis}, Year = {2006}, Pages = {41-92}, Volume = {1}, Url = {http://ba.stat.cmu.edu/journal/2006/vol01/issue01/gelfand.pdf} } @Article{HeathHH2012, Title = {A {D}irichlet Process Prior for Estimating Lineage-Specific Substitution Rates.}, Author = {Tracy A. Heath and Mark T. Holder and John P. Huelsenbeck}, Journal = {Molecular Biology and Evolution}, Year = {2012}, Number = {3}, Pages = {939-955}, Volume = {29}, Doi = {10.1093/molbev/msr255}, Url = {http://mbe.oxfordjournals.org/content/early/2011/11/04/molbev.msr255.abstract} } @InCollection{HillisHolder2000, Title = {Reconstructing the Tree of Life}, Author = {David M. Hillis and Mark T. Holder}, Booktitle = {New Technologies for the Life Sciences: A Trends Guide.}, Publisher = {Elsevier}, Year = {2000}, Pages = {47-50}, Volume = {{\em Supplement to Trends Journals}}, } @Article{HolderEtAl1994, Title = {Bovine microsatellite dinucleotide repeat polymorphisms at the TEXAN-1, TEXAN-2, TEXAN-3, TEXAN-4 and TEXAN-5 loci}, Author = {Holder, DA and Arevalo, E. and Holder, MT and Taylor, JF and Davis, SK}, Journal = {Animal Genetics}, Year = {1994}, Number = {3}, Pages = {201--201}, Volume = {25}, Doi = {10.1111/j.1365-2052.1994.tb00123.x}, Publisher = {Wiley Online Library}, Url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2052.1994.tb00123.x/abstract} } @InCollection{HolderH2007, Title = {Phylogeography and Population Genetics}, Author = {Kristina Kichler Holder and Mark T. Holder}, Booktitle = {Biology and Conservation of {R}idley Sea Turtles}, Publisher = {Johns Hopkins University Press}, Year = {2007}, Editor = {Pamela T. Plotkin}, Pages = {107--118} } @Article{HolderAndersonHolloway2001, Title = {Difficulties in Detecting Hybridization}, Author = {Mark T. Holder and Jennifer A. Anderson and Alisha K. Holloway}, Journal = {Systematic Biology}, Year = {2001}, Number = {6}, Pages = {978-982}, Volume = {50}, Doi = {10.1080/106351501753462911}, Url = {http://sysbio.oxfordjournals.org/cgi/reprint/50/6/978} } @Article{HolderEtAl1999, Title = {Two living species of coelacanths?}, Author = {Mark T. Holder and Mark V. Erdmann and Thomas P. Wilcox and Roy L. Caldwell and David M. Hillis}, Journal = {Proceedings of the National Academy of Sciences}, Year = {1999}, Number = {22}, Pages = {12616-12620}, Volume = {96}, Doi = {10.1073/pnas.96.22.12616}, Url = {http://www.pnas.org/content/96/22/12616.short} } @Article{HolderLewis2003, Title = {Phylogeny Estimation: Traditional and {B}ayesian Approaches}, Author = {Mark T. Holder and Paul O. Lewis}, Journal = {Nature Reviews Genetics}, Year = {2003}, Pages = {275-284}, Volume = {43}, Doi = {10.1038/nrg1044}, Url = {http://www.nature.com/nrg/journal/v4/n4/full/nrg1044.html} } @Article{HolderLS2010, Title = {The {Akaike} Information Criterion Will Not Choose the No Common Mechanism Model}, Author = {Mark T. Holder and Paul O. Lewis and David L. Swofford}, Journal = {Systematic Biology}, Year = {2010}, Month = {Jul}, Number = {4}, Pages = {477-485}, Volume = {59}, Doi = {10.1093/sysbio/syq028}, Url = {http://sysbio.oxfordjournals.org/cgi/content/full/59/4/477} } @InCollection{HolderLSB2014, Title = {Variable tree topology stepping-stone marginal likelihood estimation}, Author = {Mark T. Holder and Paul O. Lewis and David L. Swofford and David Bryant}, Booktitle = {Bayesian Phylogenetics: Methods, Algorithms, and Applications}, Publisher = {CRC}, Year = {2014}, Address = {Boca Raton, FL, USA}, Editor = {Ming-Hui Chen and Lynn Kuo and Paul O. Lewis}, Pages = {95--112}, Owner = {mholder}, Timestamp = {2014.05.31} } @Article{HolderLewisSwoffordLarget2005, Title = {Hastings Ratio of the LOCAL Proposal Used in {B}ayesian Phylogenetics}, Author = {Mark T. Holder and Paul O. Lewis and David L. Swofford and Bret Larget}, Journal = {Systematic Biology}, Year = {2005}, Pages = {961-965}, Volume = {54}, Doi = {10.1080/10635150500354670}, Issue = {6}, Url = {http://sysbio.oxfordjournals.org/cgi/content/full/54/6/961} } @Article{HolderS2011, Title = {Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts}, Author = {Mark T. Holder and Mike Steel}, Journal = {Journal of Theoretical Biology}, Year = {2011}, Month = {July}, Number = {1}, Pages = {159--166}, Volume = {280}, Doi = {10.1016/j.jtbi.2011.04.005}, Url = {http://www.sciencedirect.com/science/article/B6WMD-52MY688-1/2/8e287b6af19b84e35bdf3d9e7e0d1a3f} } @InCollection{HolderSB2010, Title = {Recent Developments in {B}ayesian Phylogenetics}, Author = {Mark T. Holder and Jeet Sukumaran and Rafe M. Brown}, Booktitle = {Bayesian Modeling in Bioinformatics}, Publisher = {Chapman \& Hall/CRC}, Year = {2010}, Editor = {Dipak K. Dey and Samiran Ghosh and Bani K. Mallick}, Pages = {193-232}, } @Article{HolderSL2008, Title = {A justification for reporting majority-rule consensus tree in {B}ayesian phylogenetics}, Author = {Mark T. Holder and Jeet Sukumaran and Paul O. Lewis}, Journal = {Systematic Biology}, Year = {2008}, Number = {5}, Pages = {814-821}, Volume = {57}, Doi = {10.1080/10635150802422308}, Url = {http://sysbio.oxfordjournals.org/cgi/content/full/57/5/814} } @Article{HolderZD2008, Title = {Evaluating the Robustness of Phylogenetic Methods to Among-Site Variability in Substitution Processes}, Author = {Mark T. Holder and Derrick J. Zwickl and Christophe Dessimoz}, Journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, Year = {2008}, Pages = {4013-4012}, Volume = {363}, Doi = {10.1098/rstb.2008.0162}, Url = {http://rstb.royalsocietypublishing.org/content/363/1512/4013} } @Article{KichlerEtAl1999, Title = {Detection of multiple paternity in the {K}emp's ridley sea turtle with limited sampling}, Author = {Kristina L. Kichler and Mark T. Holder and Scott K. Davis and Rene Marquez and David Owens}, Journal = {Molecular Ecology}, Year = {1999}, Pages = {819-830}, Volume = {8}, Doi = {10.1046/j.1365-294X.1999.00635.x}, Url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-294X.1999.00635.x/abstract} } @Article{KochH2012, Title = {An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy}, Author = {Jordan M. Koch and Mark T. Holder}, Journal = {PLOS Currents Tree of Life}, Year = {2012}, Number = {1}, Volume = {Dec 14 [last modified: 2012 Dec 14]}, Doi = {10.1371/4fd1286980c08}, Url = {http://currents.plos.org/treeoflife/article/an-algorithm-for-calculating-the-probability-of-classes-of-data-patterns-on-a-genealogy} } @Article{LaknerHGN2011, Title = {What's in a Likelihood? Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood}, Author = {Clemens Lakner and Mark T. Holder and Nick Goldman and Gavin J. P. Naylor}, Journal = {Systematic Biology}, Year = {2011}, Number = {2}, Pages = {161-174.}, Volume = {60}, Doi = {10.1093/sysbio/syq088}, Url = {http://sysbio.oxfordjournals.org/content/60/2/161} } @Article{LappEtAl2007, Title = {The 2006 {NESCent} Phyloinformatics Hackathon: A Field Report}, Author = {Hilmar Lapp and Sendu Bala and James P. Balhoff and Amy Bouck and Naohisa Goto and Mark Holder and Richard Holland and Alisha Holloway and Toshiaki Katayama and Paul O. Lewis and Aaron Mackey and Brian I. Osborne and William H. Piel and Sergei L. Kosakovsky Pond and Art Poon and Wei-Gang Qiu and Jason E. Stajich and Arlin Stoltzfus and Tobias Thierer and Albert J. Vilella and Rutger A. Vos and Christian M. Zmasek and Derrick Zwickl and Todd J. Vision}, Journal = {Evolutionary Bioinformatics}, Year = {2007}, Pages = {357--366}, Volume = {3}, Url = {http://la-press.com/article.php?article\_id=480} } @Article{LewisHolderHolsinger2005, Title = {Polytomies and {B}ayesian phylogenetic inference}, Author = {Paul O. Lewis and Mark T. Holder and Kent E. Holsinger}, Journal = {Systematic Biology}, Year = {2005}, Pages = {241--253}, Volume = {54}, Doi = {10.1080/10635150590924208}, Issue = {2}, Url = {http://sysbio.oxfordjournals.org/cgi/content/full/54/2/241} } @Article{LewisHS2015, Title = {Phycas: Software for {B}ayesian Phylogenetic Analysis}, Author = {Lewis, Paul O and Holder, Mark T and Swofford, David L}, Journal = {Systematic Biology}, Year = {2015}, Number = {3}, Pages = {525-531}, Volume = {64}, Doi = {10.1093/sysbio/syu132}, Owner = {mholder}, Publisher = {Oxford University Press}, Timestamp = {2015.01.19}, Url = {https://doi.org/10.1093/sysbio/syu132} } @Article{LiberlesEtAl2012, Title = {The interface of protein structure, protein biophysics, and molecular evolution}, Author = {David A. Liberles and Sarah A. Teichmann and Ivet Bahar and Ugo Bastolla and Jesse Bloom and Erich Bornberg-Bauer and Lucy J. Colwell and A. P. Jason de Koning and Nikolay V. Dokholyan and Julian Echave and Arne Elofsson and Dietlind L. Gerloff and Richard A. Goldstein and Johan A. Grahnen and Mark T. Holder and Clemens Lakner and Nicholas Lartillot and Simon C. Lovell and Gavin Naylor and Tina Perica and David D. Pollock and Tal Pupko and Lynne Regan and Andrew Roger and Nimrod Rubinstein and Eugene Shakhnovich and Kimmen Sj\"olander and Shamil Sunyaev and Ashley I. Teufel and Jeffrey L. Thorne and Joseph W. Thornton and Daniel M. Weinreich and Simon Whelan}, Journal = {Protein Science}, Year = {2012}, Number = {6}, Pages = {769-785}, Volume = {21}, Doi = {10.1002/pro.2071}, Url = {http://onlinelibrary.wiley.com/doi/10.1002/pro.2071/abstract} } @Article{LiuWHNYSL2011, Title = {{SAT{\'e}-II}: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees}, Author = {Kevin Liu and Tandy J. Warnow and Mark T. Holder and Serita Nelesen and Jiaye Yu and Alexandros Stamatakis and C. Randal Linder}, Journal = {Systematic Biology}, Year = {2012}, Number = {1}, Pages = {90-106}, Volume = {61}, Doi = {10.1093/sysbio/syr095}, Url = {http://sysbio.oxfordjournals.org/content/61/1/90.full} } @Article{mctavish2015phylesystem, Title = {Phylesystem: a git-based data store for community curated phylogenetic estimates}, Author = {McTavish, Emily Jane B and Hinchliff, Cody E and Allman, James F and Brown, Joseph W and Cranston, Karen A and Holder, Mark T and Rees, Jonathan A and Smith, Stephen A}, Journal = {Bioinfomatics}, Year = {2015}, Volume = {31}, Number = {17}, Pages = {2794-2800}, Doi = {10.1093/bioinformatics/btv276}, Publisher = {Cold Spring Harbor Labs Journals}, Url = {https://doi.org/10.1093/bioinformatics/btv276} } @Article{OaksEtAl2012, Title = {Evidence for climate-driven diversification? A caution for interpreting {ABC} inferences of simultaneous historical events}, Author = {Jamie R. Oaks and Jeet Sukumaran and Jacob A. Esselstyn and Charles W. Linkem and Cameron D. Siler and Mark T. Holder and Rafe M. Brown}, Journal = {Evolution}, Year = {2013}, Pages = {991-1010}, Volume = {67}, Doi = {10.1111/j.1558-5646.2012.01840.x}, Url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01840.x/full} } @Article{PetersonH2012, Title = {Phylogenetic Assessment of {Filoviruses}: How Many Lineages of {Marburg virus}?}, Author = {A. Townsend Peterson and Mark T. Holder}, Journal = {Ecology and Evolution}, Year = {2012}, Number = {8}, Pages = {1826-1833}, Volume = {2}, Doi = {10.1002/ece3.297}, Url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.297/full} } @Article{PetersonKGSH2010, Title = {The big questions for biodiversity informatics}, Author = {A. Townsend Peterson and Sandra Knapp and Robert Guralnick and Jorge Sober{\'o}n and Mark T. Holder}, Journal = {Systematics and Biodiversity}, Year = {2010}, Number = {2}, Pages = {159--168}, Volume = {8}, Doi = {10.1080/14772001003739369}, Keywords = {analysis, biodiversity data capture, data integration, ecology, evolutionary biology, informatics, interpretation, phylogeny}, Url = {http://dx.doi.org/10.1080/14772001003739369} } @Article{SukumaranH2011, Title = {{Ginkgo}: spatially-explicit simulator of complex phylogeographic histories}, Author = {Jeet Sukumaran and Mark T. Holder}, Journal = {Molecular Ecology Resources}, Year = {2011}, Number = {2}, Pages = {364-369}, Volume = {11}, Doi = {10.1111/j.1755-0998.2010.02926.x}, Url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1755-0998.2010.02926.x/abstract} } @Article{SukumaranH2010, Title = {{DendroPy}: a {Python} library for phylogenetic computing}, Author = {J Sukumaran and Mark T. Holder}, Journal = {Bioinformatics}, Year = {2010}, Number = {12}, Pages = {1569--1571}, Volume = {26}, Doi = {10.1093/bioinformatics/btq228}, Url = {http://bioinformatics.oxfordjournals.org/content/26/12/1569.abstract} } @Article{NEXML, Title = {{NeXML:} rich, extensible, and verifiable representation of comparative data and metadata}, Author = {Rutger A. Vos and James P. Balhoff and Jason Caravas and Mark T. Holder and Hilmar Lapp and Wayne~P. Maddison and Peter~E. Midford and Anurag Priyam and Jeet Sukumaran and Xuhua Xia and Arlin Stoltzfus}, Journal = {Systematic Biology}, Year = {2012}, Number = {4}, Pages = {675--689}, Volume = {61}, Doi = {10.1093/sysbio/sys025}, Url = {http://sysbio.oxfordjournals.org/content/61/4/675} } @Article{ZwicklHolder2005, Title = {Model Parameterization, Prior Distributions and the General Time-Reversible Model in {B}ayesian Phylogenetics}, Author = {Derrick J. Zwickl and Mark T. Holder}, Journal = {Systematic Biology}, Year = {2004}, Pages = {877-888}, Volume = {53}, Doi = {10.1080/10635150490522584}, Issue = {6}, Url = {http://sysbio.oxfordjournals.org/cgi/content/full/53/6/877} } @article{10.7717/peerj.3058, title = {A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species}, author = {Redelings, Benjamin D. and Holder, Mark T.}, year = 2017, month = mar, keywords = {Supertree, Phylogenetics, Taxonomy, Software, Tree of life}, abstract = { We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree. We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies. This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project’s “synthetic tree” starting at version 5. This software pipeline is called “\textit{propinquity}”. It relies heavily on “\textit{otcetera}”—a set of C++ tools to perform most of the steps of the pipeline. All of the components are free software and are available on GitHub. }, volume = 5, pages = {e3058}, journal = {PeerJ}, issn = {2167-8359}, url = {https://doi.org/10.7717/peerj.3058}, doi = {10.7717/peerj.3058} } @InCollection{RedelingsH2019, Title = {Taxonomic supertree construction with \emph{incertae sedis} taxa}, Author = {Benjamin D.~Redelings and Mark T. Holder}, Booktitle = {Bioinformatics and Phylogenetics}, Editor = {Tandy Warnow}, Publisher = {Springer}, Year = {2019}, Pages = {151--173}, Volume = {}, } @InCollection{GhoshSHLRBR2020, Title = {Copulas and their potential for ecology}, Author = {Shyamolina Ghosh and Lawrence W.~Sheppard and Mark T.~Holder and Terrance E.~Loecke and Philip C. Reid and James D.~Bever and Daniel C.~Reuman}, Booktitle = {Advances in Ecological Research}, Editor = {}, Publisher = {Elsevier}, Year = {2020}, Pages = {{\em in press}}, Volume = {}, } @InCollection{HolderM2016, Title = {Phylogenetic Tree Comparison}, Author = {Mark T. Holder and Emily Jane B.~McTavish}, Booktitle = {Encyclopedia of Evolutionary Biology}, Editor = {}, Publisher = {Elsevier}, Year = {2016}, Pages = {277-284}, Volume = {}, } @article{10.1093/sysbio/syab033, author = {McTavish, Emily Jane and Sanchez Reyes, Luna Luisa and Holder, Mark T}, title = "{OpenTree: A Python package for Accessing and Analyzing data from the Open Tree of Life}", journal = {Systematic Biology}, year = {2021}, month = {05}, abstract = "{The Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the Python package opentree, which provides a user friendly Python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.}", issn = {1063-5157}, doi = {10.1093/sysbio/syab033}, url = {https://doi.org/10.1093/sysbio/syab033}, note = {syab033}, eprint = {https://academic.oup.com/sysbio/advance-article-pdf/doi/10.1093/sysbio/syab033/37904001/syab033.pdf}, } @article{10.1371/journal.pcbi.1008924, doi = {10.1371/journal.pcbi.1008924}, author = {Sukumaran, Jeet AND Holder, Mark T. AND Knowles, L. Lacey}, journal = {PLOS Computational Biology}, publisher = {Public Library of Science}, title = {Incorporating the speciation process into species delimitation}, year = {2021}, month = {05}, volume = {17}, url = {https://doi.org/10.1371/journal.pcbi.1008924}, pages = {1-19}, abstract = {The “multispecies” coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.}, number = {5}, }