Correction
Ornithology
Tyler S. Imfeld, F. Keith Barker, Robb T. Brumfield
Article
Ecology
Christine D. Bacon, Natalia Gutierrez-Pinto, Suzette Flantua, Diego Castellanos Suarez, Carlos Jaramillo, R. Toby Pennington, Alexandre Antonelli
Summary: Utilizing DNA sequence data, this study delves into the evolutionary history of the genus Cavanillesia, with a focus on the endemic C. chicamochae in the Chicamocha Canyon of Colombia. The research reveals marked genetic differentiation within populations of C. chicamochae in the canyon, likely influenced by climate change and local landscape processes. The findings underscore the urgent need for conservation efforts to preserve the unique biodiversity in the region.
Article
Ecology
Glaucia Del-Rio, Marco A. Rego, Bret M. Whitney, Fabio Schunck, Luis F. Silveira, Brant C. Faircloth, Robb T. Brumfield
Summary: The study investigates the formation of hybrid zones between two obligate army-ant-followers, the White-breasted Antbird and the Harlequin Antbird, in the Amazon Basin. Major geographic displacement between mitochondrial and nuclear clines was observed, with potential causes including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. Data indicates expansion and unidirectional introgression of one species into the distribution of the other.
Article
Biology
Catherine M. Ivy, Oliver H. Wearing, Chandrasekhar Natarajan, Rena M. Schweizer, Natalia Gutierrez-Pinto, Jonathan P. Velotta, Shane C. Campbell-Staton, Elin E. Petersen, Angela Fago, Zachary A. Cheviron, Jay F. Storz, Graham R. Scott
Summary: Genetic variants in haemoglobin associated with high-altitude adaptation in deer mice were found to also be linked to breathing phenotypes that enhance oxygen uptake in hypoxia, showing unexpected effects of adaptive variation in Hb on physiology beyond its traditional function in oxygen transport.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Ecology
Nelson Buainain, Mateus Ferreira, Jorge E. Avendano, Carlos D. Cadena, Brant C. Faircloth, Robb T. Brumfield, Joel Cracraft, Camila C. Ribas
Summary: This study compares the diversification dynamics of montane and lowland populations of a songbird genus in the Neotropics and finds overall similarities in their evolutionary processes. The current taxonomic arrangement may underestimate species diversity within the genus.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Multidisciplinary Sciences
Lukas J. Musher, Melina Giakoumis, James Albert, Glaucia Del-Rio, Marco Rego, Gregory Thom, Alexandre Aleixo, Camila C. Ribas, Robb T. Brumfield, Brian Tilston Smith, Joel Cracraft
Summary: The rearrangements of Amazonian river networks play an important role in promoting speciation and diversification of species. They facilitate divergence and secondary contact among populations, leading to the formation of micro-endemic and unrecognized taxa.
Article
Biochemistry & Molecular Biology
Andre E. Moncrieff, Brant C. Faircloth, Robb T. Brumfield
Summary: Recent molecular phylogenetic analysis of Lepidothrix manakins has helped clarify their evolutionary relationships, particularly the placement of L. coronata and the relationships within the L. nattereri + L. vilasboasi + L. iris clade. By using RADcap data, we established the subspecies-level phylogeny of Lepidothrix, confirming the monophyly of L. coronata and the presence of two biological species separated by the Andes. The relationships within the L. nattereri + L. vilasboasi + L. iris clade remained unresolved, indicating extensive allele sharing among these taxa. Additionally, we documented a rare hybridization event between L. coronata and L. suavissima.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Brian Tilston Smith, Jon Merwin, Kaiya L. Provost, Gregory Thom, Robb T. Brumfield, Mateus Ferreira, William M. Mauck, Robert G. Moyle, Timothy Wright, Leo Joseph
Summary: This study investigates the factors influencing gene tree discordance in the parrots. The researchers found that the most common occurrence of discordance in tree topologies was at nodes dating between the late Miocene and Pliocene, often at the taxonomic level of the genus. By quantifying the information content in each tip, they were able to identify instances of topological conflict and nonmonophyletic genera in the species tree. The results also showed that noise played a more important role in supporting alternative topologies when signal favored one of the topologies.
SYSTEMATIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jessie F. Salter, Peter A. Hosner, Whitney L. E. Tsai, John E. McCormack, Edward L. Braun, Rebecca T. Kimball, Robb T. Brumfield, Brant C. Faircloth
Summary: Phylogenomics with historical specimen-driven analysis is becoming increasingly important in filling gaps in evolutionary history of diverse groups. Analyzing subclades can help distinguish artifactual causes of discordance introduced by historical samples.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Min Zhao, Sarah M. Kurtis, Noor D. White, Andre E. Moncrieff, Rafael N. Leite, Robb T. Brumfield, Edward L. Braun, Rebecca T. Kimball
Summary: This study focuses on the phylogenetic relationships between Antilophia and Chiroxiphia genera in manakins. By analyzing more than 11,000 loci from whole genomes and applying different analytical methods, the study reveals the importance of identifying factors that can affect phylogenetic signal when dealing with complex phylogenetic problems.
SYSTEMATIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Oscar Johnson, Camila C. C. Ribas, Alexandre Aleixo, Luciano N. N. Naka, Michael G. G. Harvey, Robb T. T. Brumfield
Summary: Understanding the factors that influence genetic structure across species is essential for studying speciation and population genetics. This study examined population genetic data from bird species specialized in different Amazonian habitat types. The results showed that habitat type significantly affects population genetic structure, with species in more dynamic habitats having higher levels of gene flow. These differences in genetic variation across taxa specialized in distinct habitats could lead to divergent responses to environmental change and habitat-specific diversification dynamics over time.
Article
Biochemistry & Molecular Biology
Jessie F. F. Salter, Robb T. T. Brumfield, Brant C. C. Faircloth
Summary: Humans have significantly affected the distribution of plant and animal species, mainly through the translocation of individuals and the introduction of species to new habitats. This has made it challenging to understand the evolutionary history of populations and their biogeographical patterns. Studies combining genetic data with archaeological, linguistic, and historical evidence have confirmed prehistoric examples of human-mediated dispersal, but it remains uncertain whether these methods can distinguish recent dispersal events.
Article
Ecology
Andre E. Moncrieff, Brant C. Faircloth, Rosalind C. Remsen, Anna E. Hiller, Cristhian Felix, Angelo P. Capparella, Alexandre Aleixo, Thomas Valqui, Robb T. Brumfield
Summary: Rivers often serve as geographic boundaries and genetic barriers for species in the Amazon Basin, but these boundaries can break down in narrower headwater regions. A study on the Blue-capped Manakin in the western Amazon Basin found that rivers, especially the Amazon and Ucayali, act as dispersal barriers for the species. However, headwater regions show increased genetic connectivity, suggesting the importance of headwater gene flow in the diversification of the Amazon rainforest. The Ucayali River headwater region stood out as an exception, with non-admixed populations of the species on opposite sides of a narrow river channel, possibly due to additional prezygotic barriers limiting gene flow.
Review
Ornithology
Eamon C. Corbett, Robb T. Brumfield, Brant C. Faircloth
Summary: This article summarizes the causes of avian eye colour variation at three levels: mechanistic, genetic, and evolutionary. Mechanistically, avian iris pigments include melanin and carotenoids. Genetically, potential eye colour genes have been identified through breeding studies and genomic research. Evolutionarily, several hypotheses have been proposed to explain the adaptive significance of eye colour variation.
Article
Genetics & Heredity
Elisa C. Elizondo, Brant C. Faircloth, Robb T. Brumfield, Subir B. Shakya, Vincenzo A. Ellis, Carl J. Schmidt, Adrienne Kovach, W. Gregory Shriver
Summary: This article introduces a secretive marsh bird species called the clapper rail, which is adapted to high salinity habitats. The clapper rail and its closely related species, the king rail, have similar appearances but different habitat preferences. The author assembled the clapper rail's genome to investigate the mechanisms behind its salt tolerance and the maintenance of the species boundary between the two rail species.
G3-GENES GENOMES GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)