Article
Evolutionary Biology
Benjamin J. Cooper, Michael J. Moore, Norman A. Douglas, Warren L. Wagner, Matthew G. Johnson, Rick P. Overson, Sylvia P. Kinosian, Angela J. McDonnell, Rachel A. Levin, Robert A. Raguso, Hilda Flores Olvera, Helga Ochoterena, Jeremie B. Fant, Krissa A. Skogen, Norman J. Wickett
Summary: This study used target enrichment, gene tree/species tree methods, and morphological analysis to reconstruct the phylogenetic history and evaluate taxon circumscriptions of Oenothera sect. Calylophus. The study found improved support for species relationships by combining exons and flanking noncoding regions. It also discovered evidence for multiple evolutionary origins of bee pollination, edaphic specialization on gypsum, and permanent translocation heterozygosity in the group. The study applied newly emerging techniques and dense infraspecific sampling to effectively reconstruct the complex history of the rapid radiation.
SYSTEMATIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Naoko P. Kurata, Michael J. Hickerson, Sandra L. Hoffberg, Ned Gardiner, Melanie L. J. Stiassny, S. Elizabeth Alter
Summary: Freshwater fishes exhibit notable diversity despite occupying a small fraction of the earth's surface. Research suggests that high-energy rapids can act as physical barriers affecting gene flow direction, but also provide multidirectional dispersal opportunities for riverine fishes in certain temporal and spatial scales.
Article
Multidisciplinary Sciences
Sonal Singhal, Guarino R. Colli, Maggie R. Grundler, Gabriel C. Costa, Ivan Prates, Daniel L. Rabosky
Summary: The rates of species formation vary across different taxa and are affected by both microevolutionary processes and macroevolutionary patterns. This study demonstrates that population isolation has little influence on speciation rates in lizards and snakes, suggesting that other stages of speciation may play larger roles.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Valentin Rineau, Jan Smycka, David Storch
Summary: Biodiversity on Earth is influenced by abiotic perturbations and rapid diversifications, as well as biotic interactions. Analysis of the fossil record reveals that diversity has a universal impact on origination and extinction rates, although the precise mechanisms are complex. The global regulation of diversity through negative diversity dependence seems to be a common feature in the biosphere, with significant implications for understanding the current biodiversity crisis.
Article
Biodiversity Conservation
R. Alexander Pyron, Matt Pennell
Summary: Macroevolutionary research on extinction has primarily focused on large-scale processes, while recent conservation studies concentrate on population-level dynamics in the Anthropocene. Combining these perspectives can reveal hidden assumptions of value and highlight promising research agendas in conservation biology.
BIOLOGICAL CONSERVATION
(2022)
Article
Biology
Thomas A. Neubauer, Torsten Hauffe, Daniele Silvestro, Christopher R. Scotese, Bjorn Stelbrink, Christian Albrecht, Diana Delicado, Mathias Harzhauser, Thomas Wilke
Summary: Understanding the drivers of species diversification over geological time is crucial for our knowledge of long-term evolutionary processes. This study used a large fossil dataset, a multivariate birth-death model, and a comprehensive set of biotic and abiotic predictors to estimate the drivers of diversification for European freshwater gastropods over the past 100 million years. The results showed temporal heterogeneity in the factors influencing diversification rates, with diversity-dependence and topography consistently playing important roles.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Fern Spaulding, Jessica F. McLaughlin, Rebecca G. Cheek, Kevin G. McCracken, Travis C. Glenn, Kevin Winker
Summary: This study examines the divergence and speciation processes in a clade of ducks and reveals the uncertain relationships and species limits within the green-winged teal complex. By analyzing mitochondrial and genome-wide nuclear DNA, the researchers determined the phylogenetic relationships and gene flow among different lineages. The results showed that while nuclear DNA suggests three subspecies and a close relative from South America, the mitochondrial genomes revealed a different phylogeny. The study highlights the power of ultraconserved elements in studying systematics and population genomics in cases with uncertain relationships and species limits.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Ecology
Joaquin Ortego, Jorge Gutierrez-Rodriguez, Victor Noguerales
Summary: The study used genomic data to infer the consequences of dispersal-related trait variation in short-winged and long-winged Corsican grasshoppers, revealing that reduced dispersal has fueled geographical diversification in the short-winged taxon and increased the opportunity for allopatric speciation in topographically complex landscapes.
Article
Genetics & Heredity
Thomas H. Q. Powell, Glen Ray Hood, Meredith M. Doellman, Pheobe M. Deneen, James J. Smith, Stewart H. Berlocher, Jeffrey L. Feder
Summary: This study investigates the genetic variation and divergence in the Rhagoletis pomonella species group (RPSG) and finds that different taxa within the group are currently diverging under gene flow. The derived species are nested within the genetic variation of hawthorn-infesting populations of R. pomonella and show marked differences in genotype clustering and differentiation among sympatric populations.
Article
Ecology
Michael Foote
Summary: Through comparing detrended estimates of diversity and rates of origination, extinction, and net diversification, the study shows that at the global scale, there is a negative correlation between rates of diversification and origination and diversity. However, the correlation between extinction rates and diversity is weak. This diversity-dependent diversification is a pervasive factor in the macroevolution of marine animal life.
AMERICAN NATURALIST
(2023)
Article
Biochemistry & Molecular Biology
Matthew J. Christmas, Julia C. Jones, Anna Olsson, Ola Wallerman, Ignas Bunikis, Marcin Kierczak, Valentina Peona, Kaitlyn M. Whitley, Tuuli Larva, Alexander Suh, Nicole E. Miller-Struttmann, Jennifer C. Geib, Matthew T. Webster
Summary: Evidence suggests that gene flow commonly occurs between recently diverged species, despite barriers to gene flow. Genetic barriers to gene flow often accumulate in regions of low recombination and near centromeres.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Behavioral Sciences
Maria J. A. Creighton, Dan A. Greenberg, Simon M. Reader, Arne O. Mooers
Summary: Behavioral innovation and social learning are positively correlated with diversification rates among primate genera, but not at shallower phylogenetic depths. Stronger associations are found when examining older diversification events, suggesting that extinction resistance may play a key role. Dispersal-mediated explanations may account for conflicting patterns observed across clades.
Article
Biochemistry & Molecular Biology
Swapnil Tichkule, Simone M. Caccio, Guy Robinson, Rachel M. Chalmers, Ivo Mueller, Samantha J. Emery-Corbin, Daniel Eibach, Kevin M. Tyler, Cock van Oosterhout, Aaron R. Jex
Summary: This study presents a whole-genome study of Cryptosporidium hominis, a major cause of diarrhea in low- and middle-income countries. The study identifies two distinct lineages of C. hominis, with one lineage predominantly found in low-income countries in Africa and Asia, and another lineage found in high-income countries in Europe, North America, and Oceania. The study also detects genomic regions of introgression between the lineages, leading to high diversity and divergence in potential virulence genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Daniel L. Rabosky, Roger B. J. Benson
Summary: Estimates of evolutionary diversification rates based on the age-richness rate (ARR) estimator are problematic for comparative studies due to theoretical and empirical shortcomings, as well as a lack of predictive ability for real datasets.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kyle A. O'Connell, Ivan Prates, Lauren A. Scheinberg, Kevin P. Mulder, Rayna C. Bell
Summary: A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically-relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity.
Article
Plant Sciences
Osazee O. Oyanoghafo, Corey O' Brien, Brendan Choat, David Tissue, Paul D. Rymer
Summary: This study found that climate, specifically rainfall and aridity, is the key predictor of variation in cavitation resistance among diverse flora. Drought avoidance strategies such as terete leaf form and greater Huber value are important for species to colonize and persist in arid biomes. Stem P-50, an adaptive trait genetically determined, is a reliable and robust predictor of species vulnerability to climate change.
Article
Biochemistry & Molecular Biology
Collin W. Ahrens, Rebecca Jordan, Jason Bragg, Peter A. Harrison, Tara Hopley, Helen Bothwell, Kevin Murray, Dorothy A. Steane, John W. Whale, Margaret Byrne, Rose Andrew, Paul D. Rymer
Summary: Genotype-environment association (GEA) methods are widely used in landscape genomics, but the impact of filtering genotyping data on environmental adaptation inferences remains unclear. This study demonstrates that filtering thresholds for missing data and minor allele frequency significantly affect the identification of true positives in GEA results. Recommendations are made regarding filtering strategies for GEA methods, emphasizing the importance of choosing appropriate filters based on study objectives and genomic resources.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Toral Shah, Fandey H. Mashimba, Haji O. Suleiman, Yahya S. Mbailwa, Julio Schneider, Georg Zizka, Vincent Savolainen, Isabel Larridon, Iain Darbyshire
Summary: Advances in high-throughput DNA sequencing have made the generation of molecular phylogenetic trees faster and more affordable, but resolving relationships at species level remains challenging. A comprehensive phylogenomic study for Ochna genus was conducted using a custom probe kit, revealing a new section consisting of species from Madagascar and the Mascarene Islands.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Joao Carlos Filipe, Paul D. Rymer, Margaret Byrne, Giles Hardy, Richard Mazanec, Collin W. Ahrens
Summary: Temperature and precipitation changes are causing forest dieback and extinction events. This study investigates the adaptation of Eucalyptus marginata populations to climate variables in South-west Western Australia using SNP markers. The results show that temperature and precipitation have different patterns of adaptation and suggest the presence of standing genomic variation adapted to current climate gradients.
Article
Zoology
Nicholas Dunn, Vincent Savolainen, Sam Weber, Samantha Andrzejaczek, Chris Carbone, David Curnick
Summary: As elasmobranchs are increasingly threatened, efficient monitoring methods are needed. This study used eDNA metabarcoding to survey fish communities and assess the diversity and distribution of elasmobranch species. The results showed that eDNA metabarcoding can detect and differentiate elasmobranch species based on read abundance. However, further research and development are needed before it can be integrated into conservation tools.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Ecology
Samantha E. Andres, Jeff R. Powell, Paul D. Rymer, Nathan J. Emery
Summary: Climate change and land management decisions have altered fire regimes globally, increasing the risks of extreme fire seasons. In this study, the impact of the 2019-2020 Black Summer fires on the Endangered Persoonia hirsuta shrub was examined. It was found that high fire severity led to increased dieback and mortality of seedlings, and the post-fire soil environment played a role in seedling responses.
Article
Agronomy
Samantha E. Andres, Nathan J. Emery, Paul D. Rymer, Jeff R. Powell
Summary: This study identified candidate fungi and soil physiochemical properties associated with observed dieback and dieback resistance in an Endangered shrub and provides groundwork for further exploring what drives dieback and how it can be managed to promote the conservation of wild populations.
Article
Environmental Sciences
Manuel Esperon-Rodriguez, Mark G. Tjoelker, Jonathan Lenoir, John B. Baumgartner, Linda J. Beaumont, David A. Nipperess, Sally A. Power, Benoit Richard, Paul D. Rymer, Rachael Gallagher
Summary: This research found that over half of urban tree species currently experience non-ideal climate conditions, and the risk is projected to increase by 2050 due to climate change. The study also highlights cities where all tree species are at risk.
NATURE CLIMATE CHANGE
(2022)
Article
Plant Sciences
Owen G. Osborne, Mariya P. Dobreva, Alexander S. T. Papadopulos, Magna S. B. de Moura, Alexandre T. Brunello, Luciano P. de Queiroz, R. Toby Pennington, Jon Lloyd, Vincent Savolainen
Summary: The architecture of root systems is crucial for plant fitness, competition, and ecosystem processes. However, the difficulty in mapping roots hinders the study of these processes. This study developed a scalable sequencing-based method to map individual tree root systems across multiple species, providing a more efficient and applicable approach for ecological research.
Article
Plant Sciences
Toral Shah, Fandey H. Mashimba, Haji. O. Suleiman, Yahya S. Mbailwa, Vincent Savolainen, Isabel Larridon, Iain Darbyshire
Summary: This study provides a taxonomic revision of the Ochna holstii complex based on genomic and morphological data. It reveals that O. holstii is paraphyletic and identifies a new species, O. mchanga. The study emphasizes the importance of using an integrated approach of molecular and morphological data for resolving difficult species relationships in Ochna.
PLANT ECOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Ewan O. Flintham, Vincent Savolainen, Charles Mullon
Summary: Sexual conflict can arise when males evolve traits that harm females while improving their own mating success. This study shows that conflict is more intense in populations where individuals are in better condition, as condition-dependent expression of sexually selected traits readily evolves. This intensified conflict reduces mean fitness and can lead to a negative association between condition and population size. The coevolution of condition and sexual conflict can make the good genes effect detrimental to populations in the presence of male harm.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Meteorology & Atmospheric Sciences
Elise Pendall, Alison Hewitt, Matthias M. Boer, Yolima Carrillo, Nancy F. Glenn, Anne Griebel, Jason H. Middleton, Peter J. Mumford, Peter Ridgeway, Paul D. Rymer, Greg L. Steenbeeke
Summary: The study found that fire frequency and time since fire have effects on canopy structure, habitat quality, and biodiversity of urban forest fragments. Ecosystems show resilience to different times since fire and fire frequencies, but increasing fire frequency under climate change may impact tree species and community composition.
Article
Biodiversity Conservation
Manuel Esperon-Rodriguez, Paul D. Rymer, Sally A. Power, David N. Barton, Paloma Carinanos, Cynnamon Dobbs, Ana Alice Eleuterio, Francisco J. Escobedo, Richard Hauer, Martin Hermy, Ali Jahani, Jonathan C. Onyekwelu, Johan Ostberg, Diane Pataki, Thomas B. Randrup, Torres Rasmussen, Lara A. Roman, Alessio Russo, Charlie Shackleton, Ingjerd Solfjeld, Natalie S. Doorn, Matthew J. Wells, Bjorn Wistrom, Pengbo Yan, Jun Yang, Mark G. Tjoelker
Summary: Globally, urban greening initiatives are being planned by cities to improve quality of life and mitigate climate change. However, the survival of urban forests and the ecosystem benefits they provide are threatened by climate change. Long-term monitoring studies and adaptive management are needed to identify and prevent climate change-driven failures and mortality.
PLANTS PEOPLE PLANET
(2022)
Article
Forestry
Anthea Challis, Chris Blackman, Collin Ahrens, Belinda Medlyn, Paul Rymer, David Tissue
Summary: The survival of forest trees under climate change-related drought depends on their genetic adaptation and phenotypic plasticity in drought tolerance traits. Trees with enhanced plasticity for drought tolerance, especially those from warm-dry climates, show better survival capabilities. The study highlights the importance of considering intraspecific variation in key drought traits, such as hydraulic and allometric determinants of time to hydraulic failure, to improve predictions of forest die-back under climate change-type drought.
Review
Biology
Thomas M. M. Versluys, Ewan O. Flintham, Alex Mas-Sandoval, Vincent Savolainen
Summary: This paper explores the causes of positive assortative mating in humans, drawing on human and non-human biology, the social sciences, and the humanities. It discusses methods to control for confounders in mate choice studies, as well as ultimate explanations including adaptive and non-adaptive processes. The paper concludes by suggesting a focus on interdisciplinary approaches in future research.