Systematic biology

Keyphrases

Publications

2024

Daniele Silvestro, Thibault Latrille, Nicolas Salamin
Toward a semi-supervised learning approach to phylogenetic estimation. Systematic biology (2024)
Giorgio Bianchini, Martin Hagemann, Patricia Sánchez-Baracaldo
Stochastic Character Mapping, Bayesian Model Selection, and Biosynthetic Pathways Shed New Light on the Evolution of Habitat Preference in Cyanobacteria. Systematic biology (2024)
Thore Koppetsch, Milan Malinsky, Michael Matschiner
Towards reliable detection of introgression in the presence of among-species rate variation. Systematic biology (2024)
Alexander E Fedosov, Paul Zaharias, Thomas Lemarcis, Maria Vittoria Modica, Mandë Holford, Marco Oliverio, Yuri I Kantor, Nicolas Puillandre
Phylogenomics of Neogastropoda: the backbone hidden in the bush. Systematic biology (2024)
Chao Liu, Xiao-Fan Zhou, Yuanning Li, Chris Todd Hittinger, Ronghui Pan, Jinyan Huang, Xue-Xin Chen, Antonis Rokas, Yun Chen, Xing-Xing Shen
The influence of the number of tree searches on maximum likelihood inference in phylogenomics. Systematic biology (2024)
Matthew J Penn, Neil Scheidwasser, Mark P Khurana, David A Duchêne, Christl A Donnelly, Samir Bhatt
Phylo2Vec: a vector representation for binary trees. Systematic biology (2024)
Mathilde Barthe, Loïs Rancilhac, Maria C Arteaga, Anderson Feijó, Marie-Ka Tilak, Fabienne Justy, W J Loughry, Colleen M McDonough, Benoit de Thoisy, François Catzeflis, Guillaume Billet, Lionel Hautier, Benoit Nabholz, Frédéric Delsuc
Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield. Systematic biology (2024)
Carlos A Maya-Lastra, Patrick W Sweeney, Deren A R Eaton, Vania Torrez, Carla Maldonado, Malu I Ore-Rengifo, Mónica Arakaki, Michael J Donoghue, Erika J Edwards
Caught in the Act: Incipient Speciation at the Southern limit of Viburnum in the Central Andes. Systematic biology (2024)
Sebastian Höhna, Allison Y Hsiang
Sequential Bayesian Phylogenetic Inference. Systematic biology (2024)
Andrew F Magee, Andrew J Holbrook, Jonathan E Pekar, Itzue W Caviedes-Solis, Fredrick A Matsen Iv, Guy Baele, Joel O Wertheim, Xiang Ji, Philippe Lemey, Marc A Suchard
Random-effects substitution models for phylogenetics via scalable gradient approximations. Systematic biology (2024)
Avery Kruger, Vaishaal Shankar, T Jonathan Davies
Inferring the Evolutionary Model of Community-Structuring Traits with Convolutional Kitchen Sinks. Systematic biology (2024)

volume 73, number 1, 2024

James Rosindell, Kerry Manson, Rikki Gumbs, William D Pearse, Mike Steel
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage. Systematic biology 73 (1) (2024)
Mark P Khurana, Neil Scheidwasser-Clow, Matthew J Penn, Samir Bhatt, David A Duchêne
The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference. Systematic biology 73 (1) (2024)
Xiao-Xu Pang, Da-Yong Zhang
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information. Systematic biology 73 (1) (2024)
James Rosindell, Kerry Manson, Rikki Gumbs, William D Pearse, Mike Steel
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage. Systematic biology 73 (1) (2024)
Mark P Khurana, Neil Scheidwasser-Clow, Matthew J Penn, Samir Bhatt, David A Duchêne
The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference. Systematic biology 73 (1) (2024)
Xiao-Xu Pang, Da-Yong Zhang
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information. Systematic biology 73 (1) (2024)
Mark P Khurana, Neil Scheidwasser-Clow, Matthew J Penn, Samir Bhatt, David A Duchêne
The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference. Systematic biology 73 (1) (2024)
James Rosindell, Kerry Manson, Rikki Gumbs, William D Pearse, Mike Steel
Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage. Systematic biology 73 (1) (2024)
Mark P Khurana, Neil Scheidwasser-Clow, Matthew J Penn, Samir Bhatt, David A Duchêne
The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference. Systematic biology 73 (1) (2024)
Ammon Thompson, Benjamin J Liebeskind, Erik J Scully, Michael J Landis
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong. Systematic biology 73 (1) (2024)
Xiao-Xu Pang, Da-Yong Zhang
Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information. Systematic biology 73 (1) (2024)
Ammon Thompson, Benjamin J Liebeskind, Erik J Scully, Michael J Landis
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong. Systematic biology 73 (1) (2024)
Ammon Thompson, Benjamin J Liebeskind, Erik J Scully, Michael J Landis
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong. Systematic biology 73 (1) (2024)

volume 73, number 2, 2024

Michaël P J Nicolaï, Bert Van Hecke, Svana Rogalla, Gerben Debruyn, Rauri C K Bowie, Nicholas J Matzke, Shannon J Hackett, Liliana D'Alba, Matthew D Shawkey
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae). Systematic biology 73 (2) (2024)
Carlos J Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Mimi Zeng, Jeevanie Liliah, Daniel Mulcahy, Alfredo Ascanio, Tereza Jezkova, Adam D Leaché, Tomas Flouri, Ziheng Yang, Christopher Blair
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Systematic biology 73 (2) (2024)
Qiuyi Li, Yao-Ban Chan, Nicolas Galtier, Céline Scornavacca
The Effect of Copy Number Hemiplasy on Gene Family Evolution. Systematic biology 73 (2) (2024)
Luna L Sánchez Reyes, Emily Jane McTavish, Brian O'Meara
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life. Systematic biology 73 (2) (2024)
Killian Smith, Daniel Ayres, René Neumaier, Gert Wörheide, Sebastian Höhna
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI. Systematic biology 73 (2) (2024)
Beatriz Willink, Jessica L Ware, Erik I Svensson
Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny. Systematic biology 73 (2) (2024)
Konstantinos Giannakis, Luke Richards, Iain G Johnston
Ecological Predictors of Organelle Genome Evolution: Phylogenetic Correlations with Taxonomically Broad, Sparse, Unsystematized Data. Systematic biology 73 (2) (2024)
Killian Smith, Daniel Ayres, René Neumaier, Gert Wörheide, Sebastian Höhna
Bayesian Phylogenetic Analysis on Multi-Core Compute Architectures: Implementation and Evaluation of BEAGLE in RevBayes With MPI. Systematic biology 73 (2) (2024)
Thomas K F Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn, Bui Quang Minh, Robert Lanfear
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees. Systematic biology 73 (2) (2024)
Qiuyi Li, Yao-Ban Chan, Nicolas Galtier, Céline Scornavacca
The Effect of Copy Number Hemiplasy on Gene Family Evolution. Systematic biology 73 (2) (2024)
Laura A Frost, Ana M Bedoya, Laura P Lagomarsino
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora. Systematic biology 73 (2) (2024)
Dezhi Zhang, Huishang She, Shangyu Wang, Haitao Wang, Shi Li, Yalin Cheng, Gang Song, Chenxi Jia, Yanhua Qu, Frank E Rheindt, Urban Olsson, Per Alström, Fumin Lei
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae). Systematic biology 73 (2) (2024)
J Luis Leal, Pascal Milesi, Eva Hodková, Qiujie Zhou, Jennifer E James, D Magnus Eklund, Tanja Pyhäjärvi, Jarkko Salojärvi, Martin Lascoux
Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles. Systematic biology 73 (2) (2024)
Thomas K F Wong, Caitlin Cherryh, Allen G Rodrigo, Matthew W Hahn, Bui Quang Minh, Robert Lanfear
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees. Systematic biology 73 (2) (2024)
Carlos J Pavón-Vázquez, Qaantah Rana, Keaka Farleigh, Erika Crispo, Mimi Zeng, Jeevanie Liliah, Daniel Mulcahy, Alfredo Ascanio, Tereza Jezkova, Adam D Leaché, Tomas Flouri, Ziheng Yang, Christopher Blair
Gene Flow and Isolation in the Arid Nearctic Revealed by Genomic Analyses of Desert Spiny Lizards. Systematic biology 73 (2) (2024)
Luna L Sánchez Reyes, Emily Jane McTavish, Brian O'Meara
DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life. Systematic biology 73 (2) (2024)
Alex Dornburg, Katerina L Zapfe, Rachel Williams, Michael E Alfaro, Richard Morris, Haruka Adachi, Joseph Flores, Francesco Santini, Thomas J Near, Bruno Frédérich
Considering Decoupled Phenotypic Diversification Between Ontogenetic Phases in Macroevolution: An Example Using Triggerfishes (Balistidae). Systematic biology 73 (2) (2024)
Beatriz Willink, Jessica L Ware, Erik I Svensson
Tropical Origin, Global Diversification, and Dispersal in the Pond Damselflies (Coenagrionoidea) Revealed by a New Molecular Phylogeny. Systematic biology 73 (2) (2024)
Laura A Frost, Ana M Bedoya, Laura P Lagomarsino
Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora. Systematic biology 73 (2) (2024)
Konstantinos Giannakis, Luke Richards, Iain G Johnston
Ecological Predictors of Organelle Genome Evolution: Phylogenetic Correlations with Taxonomically Broad, Sparse, Unsystematized Data. Systematic biology 73 (2) (2024)
J Luis Leal, Pascal Milesi, Eva Hodková, Qiujie Zhou, Jennifer E James, D Magnus Eklund, Tanja Pyhäjärvi, Jarkko Salojärvi, Martin Lascoux
Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles. Systematic biology 73 (2) (2024)
Michaël P J Nicolaï, Bert Van Hecke, Svana Rogalla, Gerben Debruyn, Rauri C K Bowie, Nicholas J Matzke, Shannon J Hackett, Liliana D'Alba, Matthew D Shawkey
The Evolution of Multiple Color Mechanisms Is Correlated with Diversification in Sunbirds (Nectariniidae). Systematic biology 73 (2) (2024)
Anna Wróbel, Ewelina Klichowska, Arkadiusz Nowak, Marcin Nobis
Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot. Systematic biology 73 (2) (2024)
Alex Dornburg, Katerina L Zapfe, Rachel Williams, Michael E Alfaro, Richard Morris, Haruka Adachi, Joseph Flores, Francesco Santini, Thomas J Near, Bruno Frédérich
Considering Decoupled Phenotypic Diversification Between Ontogenetic Phases in Macroevolution: An Example Using Triggerfishes (Balistidae). Systematic biology 73 (2) (2024)
Dezhi Zhang, Huishang She, Shangyu Wang, Haitao Wang, Shi Li, Yalin Cheng, Gang Song, Chenxi Jia, Yanhua Qu, Frank E Rheindt, Urban Olsson, Per Alström, Fumin Lei
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae). Systematic biology 73 (2) (2024)
Anna Wróbel, Ewelina Klichowska, Arkadiusz Nowak, Marcin Nobis
Alpine Extremophytes in Evolutionary Turmoil: Complex Diversification Patterns and Demographic Responses of a Halophilic Grass in a Central Asian Biodiversity Hotspot. Systematic biology 73 (2) (2024)