Article
Biochemistry & Molecular Biology
Chao Zhang, Siavash Mirarab
Summary: This paper introduces a threshold-free weighting scheme for quartet-based species tree inference, which improves the utility of summary methods and reduces incongruence with gene concatenation.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Ishrat Tanzila Farah, Muktadirul Islam, Kazi Tasnim Zinat, Atif Hasan Rahman, Shamsuzzoha Bayzid
Summary: Estimating species trees from multilocus data sets is challenging due to gene tree heterogeneity caused by incomplete lineage sorting. Summary methods combine gene trees to estimate a species tree by optimizing various scores. This study explores the presence and impacts of equally optimal trees in species tree estimation using methods that consider incomplete lineage sorting. The experiment indicates that one method, MDC, may result in competitive quartet consistency scores but worse tree accuracy compared to another method, MQC, demonstrating the importance of considering equally optimal species trees in phylogenomic inference using summary methods.
SYSTEMATIC BIOLOGY
(2021)
Article
Evolutionary Biology
Xing-Xing Shen, Jacob L. Steenwyk, Antonis Rokas
Summary: Topological conflict is common in phylogenomic data with concatenation and coalescent methods. This study found that around 30-36% of genes in animal and plant phylogenomic studies exhibit inconsistency between likelihood-based and quartet-based signals, leading to a higher likelihood score but lower quartet score in one topology compared to another. Inconsistent genes are more likely to show high levels of gene tree discordance and may not accurately recover either of the conflicting topologies. Removing inconsistent genes can improve accuracy in data sets with low levels of incomlete lineage sorting and gene tree estimation error, but may not always lead to topologically identical species phylogenies in data sets with higher levels of incomlete lineage sorting and gene tree estimation error.
SYSTEMATIC BIOLOGY
(2021)
Article
Biology
Kristina Wicke, Mareike Fischer, Laura Kubatko
Summary: Phylogenetic diversity indices such as the FP index are commonly used in biodiversity conservation to prioritize species. However, due to discordance between gene trees and species trees, these indices may result in different rankings.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman, Md. Shamsuzzoha Bayzid
Summary: The study introduces a new method, QT-GILD, which utilizes deep learning and natural language processing to impute missing quartets in gene trees. This approach greatly improves the accuracy of species tree estimation. Experimental results demonstrate the effectiveness of QT-GILD in imputing quartet distribution and accounting for gene tree estimation error.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Phillip Shults, Matthew Hopken, Pierre-Andre Eyer, Alexander Blumenfeld, Mariana Mateos, Lee W. Cohnstaedt, Edward L. Vargo
Summary: This study used genomic data to investigate population structure and genetic differentiation within the C. variipennis species complex. Two cryptic species were found, and all five species showed significant differentiation in both sympatry and allopatry. Evidence of hybridization was detected in three different species pairings, indicating incomplete reproductive isolation.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Qiong Zhang, Ryan A. Folk, Zhi-Qiong Mo, Hang Ye, Zhao-Yuan Zhang, Hua Peng, Jian-Li Zhao, Shi-Xiong Yang, Xiang-Qin Yu
Summary: Gene tree discordance is an important legacy of biological evolution, with rapid diversification being a major cause of gene tree discordance in the Camellia genus. This study investigated the phylogeny of Camellia and the possible causes of gene tree discordance using transcriptome data from 55 species. The results revealed varying levels of gene tree discordance in the backbone of Camellia and confirmed that none of the proposed sections of Camellia are monophyletic. Integrating all orthologous genes provided the best resolution for the species tree of Camellia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Paul M. Hime, Alan R. Lemmon, Emily C. Moriarty Lemmon, Elizabeth Prendini, Jeremy M. Brown, Robert C. Thomson, Justin D. Kratovil, Brice P. Noonan, R. Alexander Pyron, Pedro L. Peloso, Michelle L. Kortyna, J. Scott Keogh, Stephen C. Donnellan, Rachel Lockridge Mueller, Christopher J. Raxworthy, Krushnamegh Kunte, Santiago R. Ron, Sandeep Das, Nikhil Gaitonde, David M. Green, Jim Labisko, Jing Che, David W. Weisrock
Summary: This study provides a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting conserved exons. It clarifies relationships among amphibians and identifies gene tree-species tree conflict. The results strongly support amphibian monophyly and a sister relationship between frogs and salamanders, with a surprisingly younger timescale for crown and ordinal amphibian diversification.
SYSTEMATIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Max Hill, Sebastien Roch
Summary: This study investigates the impact of intralocus recombination on species tree estimation from multiple loci, revealing that intralocus recombination can create an inconsistency zone which may amplify the effects of incomplete lineage sorting and lead to inconsistency in inference.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Rebeca Hernandez-Gutierrez, Cassio van den Berg, Carolina Granados Mendoza, Marcia Penafiel Cevallos, M. Efrain Freire, Emily Moriarty Lemmon, Alan R. Lemmon, Susana Magallon
Summary: This study aims to generate a phylogenetic hypothesis of the cotton and cacao family using nuclear genes, and analyzes the discordance among different methods and gene histories.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Jian Liu, Anders J. Lindstrom, Xun Gong
Summary: Our study explores the plastome characteristics and deep phylogenetic relationships within the Cycas genus. We find that all Cycas plastomes have consistent gene content and structure, with only one gene loss detected in a Philippine species. We identify three plastome regions with high nucleotide variability. Molecular evolutionary analysis reveals purifying selection in most plastid protein-coding genes, except ndhB. Phylogenomic analyses using concatenated and coalescent methods show conflicting topologies at shallow nodes.
Article
Biochemical Research Methods
Alexey Markin, Oliver Eulenstein
Summary: Research proves that ASTRAL is statistically consistent under the DLCoal model, supporting empirical evidence from simulation-based studies, and also demonstrates that the quartet-based inference approach is statistically consistent under DLCoal.
Article
Evolutionary Biology
Diego F. Morales-Briones, Gudrun Kadereit, Delphine T. Tefarikis, Michael J. Moore, Stephen A. Smith, Samuel F. Brockington, Alfonso Timoneda, Won C. Yim, John C. Cushman, Ya Yang
Summary: This study investigates gene tree discordance in the plant family Amaranthaceae s.l. using a combination of methods, revealing potential ancient and rapid lineage diversification in the family leading to unresolved conflicts. The research highlights the challenges of identifying sources of gene tree discordance, particularly with phylogenetic network methods, and underscores the importance of thoroughly testing for multiple sources of conflict in phylogenomic analyses.
SYSTEMATIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Benoit Morel, Paul Schade, Sarah Lutteropp, Tom A. Williams, Gergely J. Szollosi, Alexandros Stamatakis
Summary: SpeciesRax is a maximum likelihood method that can infer a rooted species tree from a set of gene family trees and can account for gene duplication, loss, and transfer events. It leverages the phylogenetic rooting signal in gene trees and infers species tree branch lengths and support values through paralogy-aware quartets extracted from the gene family trees. It is faster and at least as accurate as the best competing methods.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Roman Ufimov, Juan Manuel Gorospe, Tomas Fer, Martha Kandziora, Luciana Salomon, Marcela van Loo, Roswitha Schmickl
Summary: This study developed a novel approach to detect and utilize paralogues for phylogenetic tree inference and validated it in plant groups. The results demonstrate that distinguishing between orthologues and paralogues can improve the accuracy of phylogenetic trees and the support of species trees in certain cases.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Evolutionary Biology
Christopher Blair, Cecile Ane
SYSTEMATIC BIOLOGY
(2020)
Article
Evolutionary Biology
Nisa Karimi, Corrinne E. Grover, Joseph P. Gallagher, Jonathan F. Wendel, Cecile Ane, David A. Baum
SYSTEMATIC BIOLOGY
(2020)
Article
Ecology
Alexander Zizka, Jefferson G. Carvalho-Sobrinho, R. Toby Pennington, Luciano P. Queiroz, Suzana Alcantara, David A. Baum, Christine D. Bacon, Alexandre Antonelli
JOURNAL OF BIOGEOGRAPHY
(2020)
Article
Biology
Zhen Peng, Alex M. Plum, Praful Gagrani, David A. Baum
JOURNAL OF THEORETICAL BIOLOGY
(2020)
Article
Biochemical Research Methods
Ruoyi Cai, Cecile Ane
Summary: This study proposes a goodness-of-fit test for assessing the fit of phylogenetic networks, validates the performance of the test through simulations on real-world networks, and provides a rigorous tool for model selection and identifying poorly inferred areas on a network.
Article
Ecology
Nisa Karimi, Samuel Saghafi, Ken Keefover-Ring, Sarah M. Venter, Cecile Ane, David A. Baum
Summary: The study reveals that despite possessing typical floral traits associated with bat pollination, African baobabs are mainly pollinated by hawkmoths. This suggests that the pollination system in baobabs may be more flexible than previously thought.
Review
Biology
Lena Vincent, Stephanie Colon-Santos, H. James Cleaves II, David A. Baum, Sarah E. Maurer
Summary: This paper discusses principles for selecting chemical mixtures for prebiotic chemistry experiments, reviews natural environmental conditions that may have created such mixtures, and suggests reasonable guidelines for designing recipes. It explores assembled and synthesized mixtures, and addresses practical concerns such as balancing prebiotically realistic mixtures with experimental tractability. The development of standardized prebiotic recipes and a public prebiotic chemistry database are advocated to facilitate coordination among researchers and identify promising mechanisms in the origin of life.
Article
Biochemical Research Methods
Yen-Wen Wang, Cecile Ane
Summary: In this study, the authors present a kinship estimator called KIMGENS, which is capable of estimating kinship among individuals with various ploidies and is robust to population structure. The results show that KIMGENS outperforms previous estimators in accurately estimating kinship in simulated panmictic, structured, and admixed populations.
Article
Biochemical Research Methods
Zhen Peng, Jeff Linderoth, David A. Baum
Summary: Prior research on the origin of life suggests that the emergence of life requires chemical reaction networks that contain self-amplifying motifs. However, the role of multiple self-amplifying motifs in the gradual accretion of complexity towards life is not well understood. To explore this problem, the concept of a seed-dependent autocatalytic system (SDAS) is developed. Researchers demonstrate that a food-driven system can increase complexity in a contingent manner depending on the topological relationship of SDASs in a chemical reaction network. The analysis provides computational tools for studying abiogenesis and suggests new approaches in the lab.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Evolutionary Biology
Prakash Raj Timilsena, Craig F. Barrett, Alma Pineyro-Nelson, Eric K. Wafula, Saravanaraj Ayyampalayam, Joel R. McNeal, Tomohisa Yukawa, Thomas J. Givnish, Sean W. Graham, J. Chris Pires, Jerrold Davis, Cecile Ane, Dennis W. Stevenson, Jim Leebens-Mack, Esteban Martinez-Salas, Elena R. alvarez-Buylla, Claude W. dePamphilis
Summary: Mycoheterotrophy is a nutritional strategy in plants where they obtain nutrients from soil fungi. The evolution of mycoheterotrophy and loss of photosynthesis has occurred multiple times in plants, especially in monocots. While the reduction of plastomes in mycoheterotrophs is well documented, the evolution of nuclear genomes remains largely unknown.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Jingcheng Xu, Cecile Ane
Summary: Phylogenetic networks are used to model non-vertical inheritance, and we investigate the information contained in average pairwise distances for these networks. We introduce the concept of a distance split tree and prove its relationship to the network's tree of blobs. We also show that the mixed representation of the network is identifiable and discuss the localized information loss around 4-cycles.
JOURNAL OF MATHEMATICAL BIOLOGY
(2023)
Article
Plant Sciences
Prakash Raj Timilsena, Eric K. Wafula, Craig F. Barrett, Saravanaraj Ayyampalayam, Joel R. McNeal, Jeremy D. Rentsch, Michael R. McKain, Karolina Heyduk, Alex Harkess, Matthieu Villegente, John G. Conran, Nicola Illing, Bruno Fogliani, Cecile Ane, J. Chris Pires, Jerrold Davis, Wendy B. Zomlefer, Dennis W. Stevenson, Sean W. Graham, Thomas J. Givnish, James Leebens-Mack, Claude W. DePamphilis
Summary: Our study on monocot relationships utilized a large number of nuclear single-copy genes to provide insights into the phylogenetic inferences, revealing significant differences compared to plastome analysis and highlighting gene tree-species tree discordance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
David A. Baum, Zhen Peng, Emily Dolson, Eric Smith, Alex M. Plum, Praful Gagrani
Summary: Prior research on the origin of life has focused on genetic polymers as the carriers of information. Recent advances in autocatalytic chemical ecology propose a broader framework that allows for adaptive complexification before bounded individuals or genetic encoding emerge. This suggests that the origin of life can be seen as a general and predictable outcome of driven chemical ecosystems, rather than a phenomenon requiring specific, rare conditions.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Multidisciplinary Sciences
Qianshi Lin, Cecile Ane, Thomas J. Givnish, Sean W. Graham
Summary: Triantha occidentalis is a carnivorous plant that captures insects on sticky inflorescences, obtaining significant nitrogen transfer from prey to enhance its growth. It is unique in capturing prey solely with sticky traps adjacent to its flowers, while secreting phosphatase through glandular hairs like other carnivorous plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)