Article
Multidisciplinary Sciences
Mark S. Hibbins, Lara C. Breithaupt, Matthew W. Hahn
Summary: Phylogenetic comparative methods are crucial in evolutionary biology, but they often fail to account for discordant gene trees that do not align with the species tree. We introduce two new methods that incorporate gene tree histories into comparative analysis and show that they provide more accurate estimates of trait evolution than traditional methods. Applying these methods to floral traits in the Solanum genus, we demonstrate the impact of gene tree discordance on trait variation. Our approaches have broad applications in phylogenetics, including ancestral state reconstruction and lineage-specific rate shifts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Yusaku Ohkubo, Nobuyuki Kutsukake, Itsuro Koizumi
Summary: Phylogenetic comparative methods have been important in studying the evolution of phenotypic traits. However, previous methods faced limitations in dealing with directional selection. This paper proposes a novel Gaussian process macroevolutionary model, called BSDS, which combines mathematical tractability and flexibility. The proposed method yields more reliable inferences and is much faster than previous simulation-based methods.
Article
Biology
Michael L. Yuan, Erin P. Westeen, Guinevere O. U. Wogan, Ian J. Wang
Summary: This study investigates the evolution of female ornamentation in Anolis lizards. The results show that female dewlaps are evolutionarily labile and species with larger females and reduced sexual size dimorphism are more likely to possess female dewlaps. Furthermore, the presence of female dewlaps influences diversification rates in anoles, but only as a secondary effect to a hidden state.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Fisheries
James T. Thorson
Summary: Phylogenetic comparative methods (PCM) and phylogenetic structural equation models (PSEM) can replace linear models and improve performance in fisheries meta-analyses, but they are rarely applied in fisheries science.
FISH AND FISHERIES
(2023)
Article
Ecology
James T. T. Thorson, Aurore A. A. Maureaud, Romain Frelat, Bastien Merigot, Jennifer S. S. Bigman, Sarah T. T. Friedman, Maria Lourdes D. Palomares, Malin L. L. Pinsky, Samantha A. A. Price, Peter Wainwright
Summary: This study extends previous methods by using structural equation models and associations among categorical traits to achieve mixed-trait imputation. Results show that a one-degree increase in habitat temperature is associated with an average 3.5% increase in natural mortality and a 3.0% decrease in fecundity.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Behavioral Sciences
Jeffrey Podos
Summary: This essay explores the roles of costs and constraints in the evolution of sexual traits. The author suggests that the relative influence of costs and constraints shifts over different stages of sexual trait elaboration, with constraints ultimately becoming the dominant factor.
Article
Ecology
Dean C. Adams, Michael L. Collyer
Summary: Simulation-based and permutation-based inferential methods are commonly used in phylogenetic comparative methods. However, the results from the analysis of variance based on these methods can be quite different. The differences may arise from the null-model process or data permutations, as well as different estimation methods for coefficients and statistics.
Article
Ecology
Joseph A. Tobias, Catherine Sheard, Alex L. Pigot, Adam J. M. Devenish, Jingyi Yang, Ferran Sayol, Montague H. C. Neate-Clegg, Nico Alioravainen, Thomas L. Weeks, Robert A. Barber, Patrick A. Walkden, Hannah E. A. MacGregor, Samuel E. I. Jones, Claire Vincent, Anna G. Phillips, Nicola M. Marples, Flavia A. Montano-Centellas, Victor Leandro-Silva, Santiago Claramunt, Bianca Darski, Benjamin G. Freeman, Tom P. Bregman, Christopher R. Cooney, Emma C. Hughes, Elliot J. R. Capp, Zoe K. Varley, Nicholas R. Friedman, Heiko Korntheuer, Andrea Corrales-Vargas, Christopher H. Trisos, Brian C. Weeks, Dagmar M. Hanz, Till Topfer, Gustavo A. Bravo, Vladimir Remes, Larissa Nowak, Lincoln S. Carneiro, Amilkar J. Moncada R., Beata Matysiokova, Daniel T. Baldassarre, Alejandra Martinez-Salinas, Jared D. Wolfe, Philip M. Chapman, Benjamin G. Daly, Marjorie C. Sorensen, Alexander Neu, Michael A. Ford, Rebekah J. Mayhew, Luis Fabio Silveira, David J. Kelly, Nathaniel N. D. Annorbah, Henry S. Pollock, Ada M. Grabowska-Zhang, Jay P. McEntee, Juan Carlos T. Gonzalez, Camila G. Meneses, Marcia C. Munoz, Luke L. Powell, Gabriel A. Jamie, Thomas J. Matthews, Oscar Johnson, Guilherme R. R. Brito, Kristof Zyskowski, Ross Crates, Michael G. Harvey, Maura Jurado Zevallos, Peter A. Hosner, Tom Bradfer-Lawrence, James M. Maley, F. Gary Stiles, Hevana S. Lima, Kaiya L. Provost, Moses Chibesa, Mmatjie Mashao, Jeffrey T. Howard, Edson Mlamba, Marcus A. H. Chua, Bicheng Li, M. Isabel Gomez, Natalia C. Garcia, Martin Packert, Jerome Fuchs, Jarome R. Ali, Elizabeth P. Derryberry, Monica L. Carlson, Rolly C. Urriza, Kristin E. Brzeski, Dewi M. Prawiradilaga, Matt J. Rayner, Eliot T. Miller, Rauri C. K. Bowie, Rene-Marie Lafontaine, R. Paul Scofield, Yingqiang Lou, Lankani Somarathna, Denis Lepage, Marshall Illif, Eike Lena Neuschulz, Mathias Templin, D. Matthias Dehling, Jacob C. Cooper, Olivier S. G. Pauwels, Kangkuso Analuddin, Jon Fjeldsa, Nathalie Seddon, Paul R. Sweet, Fabrice A. J. DeClerck, Luciano N. Naka, Jeffrey D. Brawn, Alexandre Aleixo, Katrin Bohning-Gaese, Carsten Rahbek, Susanne A. Fritz, Gavin H. Thomas, Matthias Schleuning
Summary: Functional traits provide a quantitative framework for theories in evolutionary biology, ecology, and ecosystem science. The AVONET dataset contains comprehensive functional trait data for all bird species, allowing integration with other datasets and providing a global template for testing hypotheses and exploring the origins, structure, and functioning of biodiversity.
Article
Biochemistry & Molecular Biology
Gustavo Sanchez, Oleg Simakov, Daniel Rokhsar
Summary: In recent years, cephalopods have become a focus of research due to the increasing availability of sequenced genomes, molecular tools, and laboratory culture. The limited information on the Nautilus, a survivor of a cephalopod lineage that diverged from the coleoid clade, has hindered our understanding of genetic changes and contributions to cephalopod evolution. The publication of Nautilus genomes in Molecular Ecology will provide insights into the timing and impact of genetic changes in cephalopod evolution.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Masanori Tatani, Takeshi Yamasaki, Hiroto Tanaka, Toshiyuki Nakata, Satoshi Chiba
Summary: Studies on avian flight evolution have found weak correlation between wing shape and flight styles, as well as phylogenetic constraints. However, changes in localized wing parts, such as the alula, have enabled birds to achieve diverse flight styles despite a conserved wing outline. The morphology of the alula is influenced by body mass and flight style. The study highlights the importance of variations in localized wing parts in the evolution of avian flight.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Ecology
Josef C. Uyeda, Nicholas Bone, Sean McHugh, Jonathan Rolland, Matthew W. Pennell
Summary: Phylogenetic comparative methods are used to test functional relationships between traits, but cannot definitively prove causal links. Different phylogenetic approaches imply different causal assumptions. It is important for statistical methods to make biologically reasonable assumptions.
Article
Ecology
Stilianos Louca, L. Francisco Henao-Diaz, Matt Pennell
Summary: Numerous phylogenetic studies have reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates, known as age-rate-scaling (ARS). This study explores the potential causes of ARS, including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and sampling bias. The authors find that only sampling biases are likely to contribute to the observed ARS and develop methods to correct for this bias. They also confirm through simulations that sampling biases favoring higher diversification rates may explain the residual ARS. Overall, sampling biases appear to be a parsimonious and plausible explanation for the widely observed pattern of ARS.
Article
Biology
Ignacio Quintero, Marc A. Suchard, Walter Jetz
Summary: This study characterizes the evolution of bird species' temperature and precipitation niche spaces and finds that extant birds evolved from warm, mesic climatic niches to colder and drier environments. The overall rates of niche evolution have steadily increased, with some lineages experiencing exceptionally high rates due to the colonization of new niche spaces. The findings highlight the importance of integrating comprehensive environmental and phylogenetic information in ecological and conservation studies.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biology
Claire A. McLean, Jane Melville, Joseph Schubert, Rebecca Rose, Iliana Medina
Summary: Changes in fire regimes due to human activities have an impact on spider populations, with shorter fire intervals posing a threat to certain species. Fire also affects the abundance and composition of spider species in forests compared to other vegetation types. Functional traits may influence how spiders respond to fire, with orb and sheet web weavers being more likely to be absent after fire.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Ecology
Andrew J. Helmstetter, Rosana Zenil-Ferguson, Herve Sauquet, Sarah P. Otto, Marcos Mendez, Mario Vallejo-Marin, Juerg Schoenenberger, Concetta Burgarella, Bruce Anderson, Hugo de Boer, Sylvain Glemin, Jos Kafer
Summary: This study synthesized data from 152 studies on angiosperm clades using state-dependent speciation and extinction models, and found that intrinsic traits related to reproduction and morphology are often linked to species diversification. However, a set of universal drivers did not emerge as these traits had inconsistent effects across clades. Additionally, the study found that data set properties such as tree size, age, and sampling quality were correlated to SSE model results, and provided best practices for study design and reporting.