Works by Duchêne, David A.

Results: 33

Road to Extinction? Past and Present Population Structure and Genomic Diversity in the Koala.

Published in:

Molecular Biology & Evolution, 2025, v. 42, n. 4, p. 1, doi. 10.1093/molbev/msaf057

By:

Cahsan, Binia De;
Velasco, Marcela Sandoval;
Westbury, Michael V;
Duchêne, David A;
Sinding, Mikkel H Strander;
Morales, Hernán E;
Kalthoff, Daniela C;
Barnes, Ian;
Brace, Selina;
Miguez, Roberto Portela;
Roca, Alfred L;
Greenwood, Alex D;
Johnson, Rebecca N;
Lott, Matthew J;
Gilbert, M Thomas P

Publication type:

Article

Bayesian molecular dating: opening up the black box.

Published in:

Biological Reviews, 2018, v. 93, n. 2, p. 1165, doi. 10.1111/brv.12390

By:

Bromham, Lindell;
Hua, Xia;
Duchêne, David A.;
Duchêne, Sebastián;
Ritchie, Andrew M.;
Ho, Simon Y. W.

Publication type:

Article

Bird lineages colonizing urban habitats have diversified at high rates across deep time.

Published in:

Global Ecology & Biogeography, 2022, v. 31, n. 9, p. 1784, doi. 10.1111/geb.13558

By:

Iglesias‐Carrasco, Maider;
Tobias, Joseph A.;
Duchêne, David A.;
Pigot, Alex L

Publication type:

Article

Phylogenetic patterns in the geographic distributions of birds support the tropical conservatism hypothesis.

Published in:

Global Ecology & Biogeography, 2015, v. 24, n. 11, p. 1261, doi. 10.1111/geb.12370

By:

Duchêne, David A.;
Cardillo, Marcel

Publication type:

Article

ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.

Published in:

Genome Biology & Evolution, 2024, v. 16, n. 4, p. 1, doi. 10.1093/gbe/evae064

By:

Duchêne, David A;
Duchêne, Sebastián;
Stiller, Josefin;
Heller, Rasmus;
Ho, Simon Y W

Publication type:

Article

Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees.

Published in:

Genome Biology & Evolution, 2023, v. 15, n. 12, p. 1, doi. 10.1093/gbe/evad213

By:

Penn, Matthew J;
Scheidwasser, Neil;
Penn, Joseph;
Donnelly, Christl A;
Duchêne, David A;
Bhatt, Samir

Publication type:

Article

Differences in Performance among Test Statistics for Assessing Phylogenomic Model Adequacy.

Published in:

Genome Biology & Evolution, 2018, v. 10, n. 6, p. 1375, doi. 10.1093/gbe/evy094

By:

Duchêne, David A.;
Duchêne, Sebastian;
Ho, Simon Y. W.

Publication type:

Article

The Genome as an Evolutionary Timepiece.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 9, p. 3006, doi. 10.1093/gbe/evw220

By:

Ho, Simon Y. W.;
Chen, Amanda X. Y.;
Lins, Luana S. F.;
Duchêne, David A.;
Lo, Nathan

Publication type:

Article

Cross-validation to select Bayesian hierarchical models in phylogenetics.

Published in:

BMC Evolutionary Biology, 2016, v. 16, p. 1, doi. 10.1186/s12862-016-0688-y

By:

Duchêne, Sebastián;
Duchêne, David A.;
Di Giallonardo, Francesca;
Eden, John-Sebastian;
Geoghegan, Jemma L.;
Holt, Kathryn E.;
Ho, Simon Y. W.;
Holmes, Edward C.

Publication type:

Article

Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).

Published in:

Molecular Biology & Evolution, 2022, v. 39, n. 12, p. 1, doi. 10.1093/molbev/msac241

By:

Hempel, Elisabeth;
Bibi, Faysal;
Faith, J Tyler;
Koepfli, Klaus-Peter;
Klittich, Achim M;
Duchêne, David A;
Brink, James S;
Kalthoff, Daniela C;
Dalén, Love;
Hofreiter, Michael;
Westbury, Michael V

Publication type:

Article

Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.

Published in:

Molecular Biology & Evolution, 2021, v. 38, n. 9, p. 3884, doi. 10.1093/molbev/msab055

By:

Westbury, Michael V;
Duc, Diana Le;
Duchêne, David A;
Krishnan, Arunkumar;
Prost, Stefan;
Rutschmann, Sereina;
Grau, Jose H;
Dalén, Love;
Weyrich, Alexandra;
Norén, Karin;
Werdelin, Lars;
Dalerum, Fredrik;
Schöneberg, Torsten;
Hofreiter, Michael

Publication type:

Article

Linking Branch Lengths across Sets of Loci Provides the Highest Statistical Support for Phylogenetic Inference.

Published in:

Molecular Biology & Evolution, 2020, v. 37, n. 4, p. 1202, doi. 10.1093/molbev/msz291

By:

Duchêne, David A;
Tong, K Jun;
Foster, Charles S P;
Duchêne, Sebastián;
Lanfear, Robert;
Ho, Simon Y W

Publication type:

Article

New Statistical Criteria Detect Phylogenetic Bias Caused by Compositional Heterogeneity.

Published in:

Molecular Biology & Evolution, 2017, v. 34, n. 6, p. 1529, doi. 10.1093/molbev/msx092

By:

Duchêne, David A.;
Duchêne, Sebastian;
Ho, Simon Y. W.

Publication type:

Article

Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations.

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 11, p. 2986, doi. 10.1093/molbev/msv154

By:

Duchêne, David A.;
Duchêne, Sebastian;
Holmes, Edward C.;
Ho, Simon Y. W.

Publication type:

Article

The Performance of the Date-Randomization Test in Phylogenetic Analyses of Time-Structured Virus Data.

Published in:

Molecular Biology & Evolution, 2015, v. 32, n. 7, p. 1895, doi. 10.1093/molbev/msv056

By:

Duchêne, Sebastián;
Duchêne, David;
Holmes, Edward C.;
Ho, Simon Y.W.

Publication type:

Article

Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach: Bayesian Inference of Phylogenetic Distances...: M. J. Penn et al.

Published in:

Bulletin of Mathematical Biology, 2025, v. 87, n. 2, p. 1, doi. 10.1007/s11538-024-01403-z

By:

Penn, Matthew J.;
Scheidwasser, Neil;
Donnelly, Christl A.;
Duchêne, David A.;
Bhatt, Samir

Publication type:

Article

Distinct evolutionary regimes across domains of the Plasmodium falciparum CSP gene.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-98456-4

By:

Al-Kaisy, Rusul;
Bhatt, Samir;
Duchêne, David A.

Publication type:

Article

A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea.

Published in:

Molecular Ecology, 2023, v. 32, n. 17, p. 4829, doi. 10.1111/mec.17069

By:

Westbury, Michael V.;
Cabrera, Andrea A.;
Rey‐Iglesia, Alba;
De Cahsan, Binia;
Duchêne, David A.;
Hartmann, Stefanie;
Lorenzen, Eline D.

Publication type:

Article

Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.

Published in:

Molecular Ecology, 2022, v. 31, n. 10, p. 2898, doi. 10.1111/mec.16443

By:

Derežanin, Lorena;
Blažytė, Asta;
Dobrynin, Pavel;
Duchêne, David A.;
Grau, José Horacio;
Jeon, Sungwon;
Kliver, Sergei;
Koepfli, Klaus‐Peter;
Meneghini, Dorina;
Preick, Michaela;
Tomarovsky, Andrey;
Totikov, Azamat;
Fickel, Jörns;
Förster, Daniel W.

Publication type:

Article

Evidence for Concerted and Mosaic Brain Evolution in Dragon Lizards.

Published in:

Brain, Behavior & Evolution, 2017, v. 90, n. 3, p. 211, doi. 10.1159/000478738

By:

Hoops, Daniel;
Vidal-García, Marta;
Ullmann, Jeremy F.P.;
Janke, andrew L.;
Stait-Gardner, Timothy;
Duchêne, David a.;
Price, William S.;
Whiting, Martin J.;
Keogh, J. Scott

Publication type:

Article

Simulating and detecting autocorrelation of molecular evolutionary rates among lineages.

Published in:

Molecular Ecology Resources, 2015, v. 15, n. 4, p. 688, doi. 10.1111/1755-0998.12320

By:

Ho, Simon Y. W.;
Duchêne, Sebastián;
Duchêne, David

Publication type:

Article

Tree imbalance causes a bias in phylogenetic estimation of evolutionary timescales using heterochronous sequences.

Published in:

Molecular Ecology Resources, 2015, v. 15, n. 4, p. 785, doi. 10.1111/1755-0998.12352

By:

Duchêne, David;
Duchêne, Sebastian;
Ho, Simon Y. W.

Publication type:

Article

Phylo2Vec: A Vector Representation for Binary Trees.

Published in:

Systematic Biology, 2025, v. 74, n. 2, p. 250, doi. 10.1093/sysbio/syae030

By:

Penn, Matthew J;
Scheidwasser, Neil;
Khurana, Mark P;
Duchêne, David A;
Donnelly, Christl A;
Bhatt, Samir

Publication type:

Article

The Limits of the Constant-rate Birth–Death Prior for Phylogenetic Tree Topology Inference.

Published in:

Systematic Biology, 2024, v. 73, n. 1, p. 235, doi. 10.1093/sysbio/syad075

By:

Khurana, Mark P;
Scheidwasser-Clow, Neil;
Penn, Matthew J;
Bhatt, Samir;
Duchêne, David A

Publication type:

Article

Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.

Published in:

Systematic Biology, 2022, v. 71, n. 3, p. 676, doi. 10.1093/sysbio/syab075

By:

Duchêne, David A;
Mather, Niklas;
Wal, Cara Van Der;
Ho, Simon Y W

Publication type:

Article

Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference.

Published in:

Systematic Biology, 2022, v. 71, n. 2, p. 490, doi. 10.1093/sysbio/syab051

By:

Vankan, Mezzalina;
Ho, Simon Y W;
Duchêne, David A

Publication type:

Article

A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth–Death Process.

Published in:

Systematic Biology, 2020, v. 69, n. 2, p. 325, doi. 10.1093/sysbio/syz038

By:

Luo, Arong;
Duchêne, David A;
Zhang, Chi;
Zhu, Chao-Dong;
Ho, Simon Y W

Publication type:

Article

Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies.

Published in:

Systematic Biology, 2020, v. 69, n. 1, p. 1, doi. 10.1093/sysbio/syz032

By:

Nie, Yuan;
Foster, Charles S P;
Zhu, Tianqi;
Yao, Ru;
Duchêne, David A;
Ho, Simon Y W;
Zhong, Bojian

Publication type:

Article

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families.

Published in:

Systematic Biology, 2018, v. 67, n. 3, p. 400, doi. 10.1093/sysbio/syx076

By:

DUCHÊNE, DAVID A.;
BRAGG, JASON G.;
DUCHÊNE, SEBASTIÁN;
NEAVES, LINDA E.;
POTTER, SALLY;
MORITZ, CRAIG;
JOHNSON, REBECCA N.;
HO, SIMON Y. W.;
ELDRIDGE, MARK D. B.

Publication type:

Article

A comparison of methods for estimating substitution rates from ancient DNA sequence data.

Published in:

BMC Evolutionary Biology, 2018, v. 18, n. 1, p. N.PAG, doi. 10.1186/s12862-018-1192-3

By:

Tong, K. Jun;
Duchêne, David A.;
Duchêne, Sebastián;
Geoghegan, Jemma L.;
Ho, Simon Y. W.

Publication type:

Article

PhyloMAd: efficient assessment of phylogenomic model adequacy.

Published in:

Bioinformatics, 2018, v. 34, n. 13, p. 2300, doi. 10.1093/bioinformatics/bty103

By:

Duchêne, David A;
Duchêne, Sebastian;
Ho, Simon Y W

Publication type:

Article

Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation.

Published in:

BMC Ecology & Evolution, 2022, v. 22, n. 1, p. 1, doi. 10.1186/s12862-022-02047-0

By:

Montoya, Paola;
Cadena, Carlos Daniel;
Claramunt, Santiago;
Duchêne, David Alejandro

Publication type:

Article

Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts.

Published in:

Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02105-1

By:

Rasmussen, Jacob A.;
Villumsen, Kasper R.;
Duchêne, David A.;
Puetz, Lara C.;
Delmont, Tom O.;
Sveier, Harald;
Jørgensen, Louise von Gersdorff;
Præbel, Kim;
Martin, Michael D.;
Bojesen, Anders M.;
Gilbert, M. Thomas P.;
Kristiansen, Karsten;
Limborg, Morten T.

Publication type:

Article