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1

Estimating species trees using approximate Bayesian computation

Helen Hang Fan, Laura S. Kubatko

Journal:

Molecular Phylogenetics and Evolution

Year:

2011

Language:

english

File:

PDF, 577 KB

english, 2011

2

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

Christian Roos, Dietmar Zinner, Laura S Kubatko, Christiane Schwarz, Mouyu Yang, Dirk Meyer, Stephen D Nash, Jinchuan Xing, Mark A Batzer, Markus Brameier, Fabian H Leendertz, Thomas Ziegler, Dyah Per

Journal:

BMC Evolutionary Biology

Year:

2011

Language:

english

File:

PDF, 993 KB

english, 2011

3

Cassava brown streak virus has a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance

Alicai, Titus, Ndunguru, Joseph, Sseruwagi, Peter, Tairo, Fred, Okao-Okuja, Geoffrey, Nanvubya, Resty, Kiiza, Lilliane, Kubatko, Laura, Kehoe, Monica A., Boykin, Laura M.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 2.30 MB

english, 2016

4

Vitamin D receptor gene polymorphisms and susceptibility M. tuberculosis in Native Paraguayans

Alicia K. Wilbur, Laura Salter Kubatko, Ana M. Hurtado, Kim R. Hill, Anne C. Stone

Journal:

Year:

2007

Language:

english

File:

PDF, 253 KB

english, 2007

5

HyDe: a Python Package for Genome-Scale Hybridization Detection

Blischak, Paul D, Chifman, Julia, Wolfe, Andrea D, Kubatko, Laura S

Journal:

Systematic Biology

Year:

2018

Language:

english

File:

PDF, 851 KB

english, 2018

6

The effects of locus number, genetic divergence, and genotyping error on the utility of dominant markers for hybrid identification

Sovic, Michael G., Kubatko, Laura S., Fuerst, Paul A.

Journal:

Ecology and Evolution

Year:

2014

Language:

english

File:

PDF, 808 KB

english, 2014

7

Tree-based quantitative trait mapping in the presence of external covariates

Thompson, Katherine L., Linnen, Catherine R., Kubatko, Laura

Journal:

Statistical Applications in Genetics and Molecular Biology

Year:

2016

Language:

english

File:

PDF, 4.40 MB

english, 2016

8

The first four million years of human evolution || More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure

Anne C. Stone, Fabia U. Battistuzzi, Laura S. Kubatko, George H. Perry Jr, Evan Trudeau, Hsiuman Lin and Sudhir Kumar

Journal:

Philosophical Transactions Biological Sciences

Year:

2010

Language:

english

File:

PDF, 1.94 MB

english, 2010

9

Modeling the past: a resource for the future

Laura S. Kubatko

Journal:

Trends in Ecology & Evolution

Year:

2009

Language:

english

File:

PDF, 75 KB

english, 2009

10

Species Delimitation and Global Biosecurity

Boykin,, Boykin,, Karen Armstrong,, Laura Kubatko,, Paul De Barro,

Journal:

Evolutionary Bioinformatics

Year:

2011

Language:

english

File:

PDF, 10.37 MB

english, 2011

11

Reduced Susceptibility to Praziquantel among Naturally Occurring Kenyan Isolates of Schistosoma mansoni

Melman, Sandra D., Steinauer, Michelle L., Cunningham, Charles, Kubatko, Laura S., Mwangi, Ibrahim N., Wynn, Nirvana Barker, Mutuku, Martin W., Karanja, Diana M. S., Colley, Daniel G., Black, Carla L.

Journal:

PLoS Neglected Tropical Diseases

Year:

2009

Language:

english

File:

PDF, 1.45 MB

english, 2009

12

Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids

Blischak, Paul D., Kubatko, Laura S., Wolfe, Andrea D.

Journal:

Molecular Ecology Resources

Year:

2016

Language:

english

File:

PDF, 360 KB

english, 2016

13

Distribution of coalescent histories under the coalescent model with gene flow

Tian, Yuan, Kubatko, Laura S.

Journal:

Molecular Phylogenetics and Evolution

Year:

2016

Language:

english

File:

PDF, 5.49 MB

english, 2016

14

Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation

Wascher, Matthew, Kubatko, Laura

Journal:

Systematic Biology

Year:

2020

File:

PDF, 3.16 MB

2020

15

Review and guide to a future naming system of African Bemisia tabaci species

Boykin, Laura M., Kinene, Tonny, Wainaina, James M., Savill, Anders, Seal, Susan, Mugerwa, Habibu, Macfadyen, Sarina, Tay, Wee Tek, De Barro, Paul, Kubatko, Laura, Alicai, Titus, Omongo, Christopher A

Journal:

Systematic Entomology

Year:

2018

Language:

english

File:

PDF, 140 KB

english, 2018

16

Median-joining network analysis of SARS-CoV-2 genomes is neither phylogenetic nor evolutionary

SÃ¡nchez-Pacheco, Santiago J., Kong, Sungsik, Pulido-Santacruz, Paola, Murphy, Robert W., Kubatko, Laura

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 487 KB

2020

17

A codon model of nucleotide substitution with selection on synonymous codon usage

Kubatko, Laura, Shah, Premal, Herbei, Radu, Gilchrist, Michael A.

Journal:

Molecular Phylogenetics and Evolution

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

18

Identifiability and Reconstructibility of Species Phylogenies Under a Modified Coalescent

Long, Colby, Kubatko, Laura

Journal:

Bulletin of Mathematical Biology

Year:

2018

Language:

english

File:

PDF, 924 KB

english, 2018

19

Effects of missing data on species tree estimation under the coalescent

Hovmöller, Rasmus, Lacey Knowles, L., Kubatko, Laura S.

Journal:

Molecular Phylogenetics and Evolution

Year:

2013

Language:

english

File:

PDF, 572 KB

english, 2013

20

Inferring Species-Level Phylogenies and Taxonomie Distinctiveness Using Multilocus Data in Sistrurus Rattlesnakes

Laura S. Kubatko, H. Lisle Gibbs and Erik W. Bloomquist

Journal:

Systematic Biology

Year:

2011

Language:

english

File:

PDF, 2.79 MB

english, 2011

21

Conservation genetics and breeding system of Penstemon debilis (Plantaginaceae), a rare beardtongue endemic to oil shale talus in western Colorado, USA

WOLFE, Andrea D., MCMULLEN-SIBUL, Amy, TEPEDINO, V. J., KUBATKO, Laura, NECAMP, Timothy, FASSNACHT, Susan

Journal:

Journal of Systematics and Evolution

Year:

2014

Language:

english

File:

PDF, 433 KB

english, 2014

22

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling

Sarah Hird, Laura Kubatko, Bryan Carstens

Journal:

Molecular Phylogenetics and Evolution

Year:

2010

Language:

english

File:

PDF, 924 KB

english, 2010

23

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

Chen Meng, Laura Salter Kubatko

Journal:

Theoretical Population Biology

Year:

2009

Language:

english

File:

PDF, 2.46 MB

english, 2009

24

Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths

Spade, David A., Herbei, Radu, Kubatko, Laura S.

Journal:

Mathematical Biosciences

Year:

2015

Language:

english

File:

PDF, 705 KB

english, 2015

25

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

Huateng Huang, Qixin He, Laura S. Kubatko, L. Lacey Knowles and Robb Brumfield

Journal:

Systematic Biology

Year:

2010

Language:

english

File:

PDF, 1.79 MB

english, 2010

26

Hypothesis tests for phylogenetic quartets, with applications to coalescent-based species tree inference

Gaither, Jeff, Kubatko, Laura

Journal:

Journal of Theoretical Biology

Year:

2016

Language:

english

File:

PDF, 761 KB

english, 2016

27

DNA barcoding invasive insects: database roadblocks

Boykin, Laura M., Armstrong, Karen, Kubatko, Laura, De Barro, Paul

Journal:

Invertebrate Systematics

Year:

2012

Language:

english

File:

PDF, 162 KB

english, 2012

28

Rooting phylogenetic trees under the coalescent model using site pattern probabilities

Tian, Yuan, Kubatko, Laura

Journal:

BMC Evolutionary Biology

Year:

2017

Language:

english

File:

PDF, 776 KB

english, 2017

29

An invariants-based method for efficient identification of hybrid species from large-scale genomic data

Kubatko, Laura S., Chifman, Julia

Journal:

BMC Evolutionary Biology

Year:

2019

Language:

english

File:

PDF, 813 KB

english, 2019

30

Estimating hybridization in the presence of coalescence using phylogenetic intraspecific sampling

David Gerard, H Lisle Gibbs, Laura Kubatko

Journal:

BMC Evolutionary Biology

Year:

2011

Language:

english

File:

PDF, 953 KB

english, 2011

31

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

Laura Salter Kubatko

Journal:

Systematic Biology

Year:

2009

Language:

english

File:

PDF, 2.02 MB

english, 2009

32

Coalescent methods for estimating phylogenetic trees

Liang Liu, Lili Yu, Laura Kubatko, Dennis K. Pearl, Scott V. Edwards

Journal:

Molecular Phylogenetics and Evolution

Year:

2009

Language:

english

File:

PDF, 346 KB

english, 2009

33

Bayesian inference of selection in the Wright-Fisher diffusion model

Gory, Jeffrey J., Herbei, Radu, Kubatko, Laura S.

Journal:

Statistical Applications in Genetics and Molecular Biology

Language:

english

File:

PDF, 666 KB

english

34

Monte Carlo estimation of total variation distance of Markov chains on large spaces, with application to phylogenetics

Herbei, Radu, Kubatko, Laura

Journal:

Statistical Applications in Genetics and Molecular Biology

Year:

2013

Language:

english

File:

PDF, 224 KB

english, 2013

35

Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence

Laura Salter Kubatko and James H. Degnan

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 1.85 MB

english, 2007

36

Expected pairwise congruence among gene trees under the coalescent model

Tian, Yuan, Kubatko, Laura S.

Journal:

Molecular Phylogenetics and Evolution

Year:

2017

Language:

english

File:

PDF, 841 KB

english, 2017

37

Fuzzy logic and related methods as a screening tool for detecting gene regulatory networks

Guy N. Brock, William D. Beavis, Laura Salter Kubatko

Journal:

Information Fusion

Year:

2009

Language:

english

File:

PDF, 736 KB

english, 2009

38

SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data

Blischak, Paul D, Kubatko, Laura S, Wolfe, Andrea D

Journal:

Year:

2017

Language:

english

File:

PDF, 354 KB

english, 2017

39

Gene tree rooting methods give distributions that mimic the coalescent process

Tian, Yuan, Kubatko, Laura S.

Journal:

Molecular Phylogenetics and Evolution

Year:

2014

Language:

english

File:

PDF, 757 KB

english, 2014

40

Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence

Kubatko, Laura Salter, Degnan, James H.

Journal:

Systematic Biology

Year:

2007

Language:

english

File:

PDF, 1.29 MB

english, 2007

41

The Effect of Gene Flow on Coalescent-based Species-tree Inference

Long, Colby, Kubatko, Laura

Journal:

Systematic Biology

Year:

2018

Language:

english

File:

PDF, 1.61 MB

english, 2018

42

Letter to the Editor on the article entitled “Estimating species trees using Approximate Bayesian Computation” (Fan and Kubatko, Mol. Phylogenetics Evol. 59, 354–363)

Kubatko, Laura S., Fan, Hang Helen

Journal:

Molecular Phylogenetics and Evolution

Year:

2013

Language:

english

File:

PDF, 149 KB

english, 2013

43

Split scores: a tool to quantify phylogenetic signal in genome-scale data

Allman, Elizabeth S., Kubatko, Laura S., Rhodes, John A.

Journal:

Systematic Biology

Year:

2016

Language:

english

File:

PDF, 2.65 MB

english, 2016

44

Efficacy of Contact Lens Systems Against Recent Clinical and Tap Water Acanthamoeba Isolates

Shoff, Megan E, Joslin, Charlotte E, Tu, Elmer Y, Kubatko, Laura, Fuerst, Paul A

Journal:

Year:

2008

File:

PDF, 93 KB

2008

45

Population genetics ofPenstemon albomarginatus(Plantaginaceae), a rare Mojave Desert species of conservation concern

Wolfe, Andrea D., Necamp, Timothy, Fassnacht, Susan, Blischak, Paul, Kubatko, Laura

Journal:

Conservation Genetics

Year:

2016

Language:

english

File:

PDF, 1.13 MB

english, 2016

46

Coalescent Time Distributions in Trees of Arbitrary Size

Efromovich, Sam, Salter Kubatko, Laura

Journal:

Statistical Applications in Genetics and Molecular Biology

Year:

2008

Language:

english

File:

PDF, 923 KB

english, 2008

47

A note on the relaxation time of two Markov chains on rooted phylogenetic tree spaces

Spade, David A., Herbei, Radu, Kubatko, Laura S.

Journal:

Statistics & Probability Letters

Year:

2014

Language:

english

File:

PDF, 400 KB

english, 2014

48

Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies

Thompson, Katherine L, Kubatko, Laura S

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 866 KB

english, 2013

49

Book Review: A Mathematical Primer of Molecular Phylogenetics, by Xuhua Xia

Journal:

Systematic Biology

Year:

2020

File:

PDF, 235 KB

2020

50

Comparison of methods for rooting phylogenetic trees: A case study using Orcuttieae (Poaceae: Chloridoideae)

Laura M. Boykin, Laura Salter Kubatko, Timothy K. Lowrey

Journal:

Molecular Phylogenetics and Evolution

Year:

2010

Language:

english

File:

PDF, 1.40 MB

english, 2010

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