
Volume 72, Issue 5
September 2023
Cover image
Cover image

Introgression events allow the sharing of genetic information among different species, illustrated here as the cross-linking of branches on the Tree of Life. Zhang and collaborators propose a deep-learning approach to study these evolutionary events, and apply it to different organisms shown in the image (design, Yubo Zhang).
ISSN 1063-5157
EISSN 1076-836X
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Volume 72, Issue 5, September 2023
SPOTLIGHT ARTICLES
Speciation in Coastal Basins Driven by Staggered Headwater Captures: Dispersal of a Species Complex, Leporinus bahiensis, as Revealed by Genome-wide SNP Data
Jorge L Ramirez and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 973–983, https://doi.org/10.1093/sysbio/syad034
Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance
Wade R Roberts and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 984–997, https://doi.org/10.1093/sysbio/syad038
The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands
Adrià Bellvert and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 998–1012, https://doi.org/10.1093/sysbio/syad046
REGULAR MANUSCRIPTS
Inferring Historical Introgression with Deep Learning
Yubo Zhang and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1013–1038, https://doi.org/10.1093/sysbio/syad033
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations
Alexander M Kramer and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1039–1051, https://doi.org/10.1093/sysbio/syad031
PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny
Alexey Markin and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1052–1063, https://doi.org/10.1093/sysbio/syad028
Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation
Lihua Yang and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1064–1083, https://doi.org/10.1093/sysbio/syad029
Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics
Jennifer C Girón and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1084–1100, https://doi.org/10.1093/sysbio/syad025
A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data
Julia Van Etten and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1101–1118, https://doi.org/10.1093/sysbio/syad037
DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies
Paschalia Kapli and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1119–1135, https://doi.org/10.1093/sysbio/syad036
Scalable Bayesian Divergence Time Estimation With Ratio Transformations
Xiang Ji and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1136–1153, https://doi.org/10.1093/sysbio/syad039
Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement Forests
David A Rasmussen and Fangfang Guo
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1154–1170, https://doi.org/10.1093/sysbio/syad040
SOFTWARE FOR SYSTEMATICS AND EVOLUTIONS
PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow
John Fogg and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1171–1179, https://doi.org/10.1093/sysbio/syad030
The ClaDS rate-heterogeneous birth–death prior for full phylogenetic inference in BEAST2
Joëlle Barido-Sottani and Hélène Morlon
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1180–1187, https://doi.org/10.1093/sysbio/syad027
POINT OF VIEWS
The Major Features of Macroevolution
L Francisco Henao-Diaz and Matt Pennell
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1188–1198, https://doi.org/10.1093/sysbio/syad032
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics
Jakub Truszkowski and others
Systematic Biology, Volume 72, Issue 5, September 2023, Pages 1199–1206, https://doi.org/10.1093/sysbio/syad045
CORRECTION
Correction to: Modeling phylogenetic biome shifts on a planet with a past
Systematic Biology, Volume 72, Issue 5, September 2023, Page 1207, https://doi.org/10.1093/sysbio/syad035
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