Article
Zoology
M. Julieta Perez, Guillermo H. Cassini, M. Monica Diaz
Summary: The research found that in octodontids, variations in forelimb features were not primarily associated with phylogeny, but were highly explanatory in terms of function, effectively distinguishing between animals living in epigean and subterranean habitats. Specific features observed in the humerus and ulna indicated adaptive trends in octodontids similar to those found in other mammals.
Article
Biochemistry & Molecular Biology
Richard Cadenillas, Guillermo D'Elia
Summary: The genus Octodon contains five species, but genetic analysis suggests the diversity is underestimated, with different methods delimiting different numbers of candidate species. Some species show genetic and morphological differentiation, while others are considered cryptic species. Phylogenetic incongruence indicates processes like incomplete lineage sorting and introgression during the radiation of the genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Magdalena Bohutinska, Mark Alston, Patrick Monnahan, Terezie Mandakova, Sian Bray, Pirita Paajanen, Filip Kolar, Levi Yant
Summary: Two plant species exhibit different genomic responses to whole genome duplication, suggesting the presence of multiple evolutionary trajectories when adapting to the challenges of whole genome duplication.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Donald Davesne, Matt Friedman, Armin D. Schmitt, Vincent Fernandez, Giorgio Carnevale, Per E. Ahlberg, Sophie Sanchez, Roger B. J. Benson
Summary: Teleost fishes, which make up half of all vertebrate species, underwent a whole-genome duplication early in their evolutionary history, likely contributing to their exceptional radiation. By analyzing bone cell volumes, researchers have concluded that this duplication occurred in the stem lineage of teleosts, with all known extinct stem-group teleosts possessing duplicated genomes. This early event allowed for significant postduplication reorganization before the emergence of the teleost crown group, indicating a potentially indirect link between WGD and evolutionary success.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Kevin J. Peterson, Alan Beavan, Peter J. Chabot, Mark A. McPeek, Davide Pisani, Bastian Fromm, Oleg Simakov
Summary: WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Zhong-Shuai Zhang, Qing-Yin Zeng, Yan-Jing Liu
Summary: The variation of chromosome number and genome size within the Salicaceae family demonstrates frequent ploidy changes and widespread sharing of the salicoid whole genome duplication event among relatives of Populus and Salix. Genome size reduction after whole genome duplication suggests substantial loss of genomic components. The phylogenetic asymmetry in the clade of Populus, Salix, and their close relatives indicates a delayed subsequent radiation post the salicoid whole genome duplication event.
Article
Biology
Tamar Gera, Felix Jonas, Roye More, Naama Barkai
Summary: The study found that about 60% of retained paralogs evolved differential binding preferences, primarily from variations outside the DNA-binding domains. Ancestral preferences were unevenly split between duplicates, with the least conserved paralog preferentially acquiring new targets.
Article
Biochemistry & Molecular Biology
Sarah Farhat, Maria Vittoria Modica, Nicolas Puillandre
Summary: The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Jessie A. Pelosi, Emily H. Kim, W. Brad Barbazuk, Emily B. Sessa
Summary: In this study, we assembled the largest nuclear dataset for ferns and investigated the fern phylogeny, whole genome duplications (WGDs), and gene retention patterns following WGDs. Our results revealed high levels of gene tree-species tree conflict in the fern phylogeny and identified multiple WGDs events. We also found that functions of retained genes following WGDs were largely convergent.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer
Summary: This study introduces a genome alignment method called AnchorWave, which shows significant improvement when applied to species with complex genomes. It can accurately identify multikilobase indels and improve the recall rate of transcription factor-binding sites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Ewa W. Piskorz, Linhao Xu, Yingrui Ma, Hua Jiang
Summary: Our study found that haploid induction and genome doubling in Arabidopsis can result in differential DNA methylation, offering a novel approach to induce epialleles.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Alberto Gatto, Audrey Forest, Jean-Pierre Quivy, Genevieve Almouzni
Summary: This study reveals the dual deposition mode of histone variants H3.1 and H3.3 in human cells during S phase, which ensures a stable marking with H3.3 flanked on both sides by H3.1. The H3.1/H3.3 boundaries correspond to the initiation zones of early origins, and the HIRA-dependent deposition of H3.3 plays a crucial role in preserving these boundaries and contributing to the chromatin-based definition of early replication zones.
Article
Biochemistry & Molecular Biology
Chi-Fa Huang, Wen-Yu Liu, Mei-Yeh Jade Lu, Yi-Hua Chen, Maurice S. B. Ku, Wen-Hsiung Li
Summary: Through studying leaf-development transcriptomes, it was found that whole-genome duplication (WGD) facilitated four aspects of C-4 photosynthesis evolution in G. gynandra, including the retention of duplicated genes related to nitrogen recycling and vein development, the evolution of C-4 enzyme genes, and upregulation of genes encoding photosystem I proteins.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Aleksandra Beric, Makenzie E. Mabry, Alex E. Harkess, Julia Brose, M. Eric Schranz, Gavin C. Conant, Patrick P. Edger, Blake C. Meyers, J. Chris Pires
Summary: The mechanisms behind genome size differences in plants, such as expansions of repetitive elements and whole-genome duplications, are still not fully understood. While a correlation between genome size and transposable element content has been confirmed within the plant order Brassicales, no shift in transposable element abundance associated with whole-genome duplications was detected.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Wentao Gong, Xiangchun Pan, Dantong Xu, Guanyu Ji, Yifei Wang, Yuhan Tian, Jiali Cai, Jiaqi Li, Zhe Zhang, Xiaolong Yuan
Summary: Whole genome bisulfite sequencing is crucial for methylome studies. This study evaluated the performance of 14 commonly used alignment algorithms for WGBS in multiple mammals and found that the choice of algorithm significantly impacts CpG site counts, methylation levels, and the calling of differentially methylated regions. BSMAP showed the highest accuracy in detecting CpG coordinates and methylation levels.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Caroline M. S. Cauret, Marie-Theres Gansauge, Andrew S. Tupper, Benjamin L. S. Furman, Martin Knytl, Xue-Ying Song, Eli Greenbaum, Matthias Meyer, Ben J. Evans
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Neurosciences
Darcy B. Kelley, Irene H. Ballagh, Charlotte L. Barkan, Andres Bendesky, Taffeta M. Elliott, Ben J. Evans, Ian C. Hall, Young Mi Kwon, Ursula Kwong-Brown, Elizabeth C. Leininger, Emilie C. Perez, Heather J. Rhodes, Avelyne Villain, Ayako Yamaguchi, Erik Zornik
JOURNAL OF NEUROSCIENCE
(2020)
Article
Anthropology
Ben J. Evans, Marie-Theres Gansauge, Matthew W. Tocheri, Michael A. Schillaci, Thomas Sutikna, Jatmiko, E. Wahyu Saptomo, Amy Klegarth, Anthony J. Tosi, Don J. Melnick, Matthias Meyer
JOURNAL OF HUMAN EVOLUTION
(2020)
Article
Biology
Xue-Ying Song, Benjamin L. S. Furman, Tharindu Premachandra, Martin Knytl, Caroline M. S. Cauret, Domnick Victor Wasonga, John Measey, Ian Dworkin, Ben J. Evans
Summary: Research on the evolution of sex chromosomes in Xenopus species revealed a large region of sex-linked genes with sex-biased expression in X. borealis, suggesting a degenerate ancestral Y-chromosome transitioned into its contemporary Z-chromosome in this species. This study provides insights into how evolutionary transformations of ancestral sex chromosomes affect the function of new sex chromosomes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Review
Biology
Matthias Stoeck, Lukas Kratochvil, Heiner Kuhl, Michail Rovatsos, Ben J. Evans, Alexander Suh, Nicole Valenzuela, Frederic Veyrunes, Qi Zhou, Tony Gamble, Blanche Capel, Manfred Schartl, Yann Guiguen
Summary: The article reviews the evolution of sex in vertebrates, covering sex determination mechanisms, sexual development, and reproductive modes across different clades. With the latest research data, it demonstrates the diversity and complexity of vertebrate sex genomes, as well as the research prospects for the evolution of sex determination.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biology
Ben J. Evans, Benjamin M. Peter, Don J. Melnick, Noviar Andayani, Jatna Supriatna, Jianlong Zhu, Anthony J. Tosi
Summary: In most macaques, females are philopatric while males migrate, leading to divergence of mitochondrial genomes. Analysis revealed evidence of natural selection associated with mitonuclear interactions and gender differences in gene flow shaping genome evolution.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
Laurie S. Stevison, Nick P. Bailey, Zachary A. Szpiech, Taylor E. Novak, Don J. Melnick, Ben J. Evans, Jeffrey D. Wall
Summary: Genital divergence plays an important role in reproductive isolation by establishing a lock-and-key mechanism for reproductive compatibility. The bear macaque, Macaca arctoides, has unique male and female genital morphology compared to its close relatives. Through whole-genome sequence analysis, it was found that M. arctoides shares more genomic regions with the sinica species group than the fascicularis species group. The bear macaque genome also shows evidence of extensive introgression between these two species groups.
ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Shun Hayashi, Kosuke Suda, Fuga Fujimura, Makoto Fujikawa, Kei Tamura, Daisuke Tsukamoto, Ben J. Evans, Nobuhiko Takamatsu, Michihiko Ito
Summary: This study investigated the origin and function of an exon (Ex4) in the sex-determining gene dm-W in African clawed frogs. The researchers found that Ex4 is derived from a noncoding portion of a DNA transposon. Analysis of transposons and Ex4 sequences from other species indicated that Ex4 was generated before the diversification of xenopus species. Further experiments showed that the amino acid sequence of Ex4 increased the DNA-binding ability and transrepression activity of dm-W. These findings provide insights into the origin and functional evolution of chimerical genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Ben J. Evans, Austin B. Mudd, Jessen Bredeson, Benjamin L. S. Furman, Domnick Victor Wasonga, Jessica B. Lyons, Richard M. Harland, Dan S. Rokhsar
Summary: In this study, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog using genomic data. We found that the sex chromosomes of this species have undergone changes between different populations, with a region that is sex-linked in the east population but not in the west population. Our simulations support a model where some sex-linked regions from the east population acquired autosomal segregation in the west population. These findings highlight the complex evolutionary dynamics of the sex chromosomes in the Marsabit clawed frog and provide a foundation for further research on sex-determining genes in this species.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Genetics & Heredity
Tharindu Premachandra, Caroline M. S. Cauret, Werner Conradie, John Measey, Ben J. Evans
Summary: Allotetraploid genomes consist of two subgenomes derived from separate diploid ancestral species. The study found that there is no significant difference in subgenome population structure and gene flow. However, the population structure in both the nuclear genome and the mitochondrial genome roughly correspond with seasonal rainfall variation and the topography of southern Africa.
G3-GENES GENOMES GENETICS
(2023)
Article
Evolutionary Biology
Jianlong Zhu, Ben J. Evans
Summary: In most eukaryotes, aerobic respiration requires interactions between autosomally encoded genes (N-interact genes) and mitochondrial DNA, RNA, and protein. In species where females are philopatric, contrasting distributions of genetic variation in mitochondrial and nuclear genomes create variation in mitonuclear interactions that may be subject to natural selection. Our study on macaque monkeys suggests that natural selection on mitonuclear interactions could have influenced several aspects of macaque societies including species diversity, ecological breadth, female-biased adult sex ratio and demography, sexual dimorphism, and mitonuclear phylogenomics.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Stephen Rong, Christopher R. Neil, Anastasia Welch, Chaorui Duan, Samantha Maguire, Ijeoma C. Meremikwu, Malcolm Meyerson, Ben J. Evans, William G. Fairbrother
Summary: Humans coexisted and interbred with other hominins which later became extinct. By engineering Neanderthal and Denisovan sequences into artificial genes, researchers reconstructed the pre-mRNA processing patterns of these extinct populations. They found genetic differences in exon recognition between extant and extinct hominins and identified splicing variants associated with purifying selection in modern humans and positive selection following introgression. Additionally, they discovered unique alternative splicing variants in genes related to immunity and sperm maturation, as well as variants that may contribute to variation in areas such as bilirubin levels, balding, hemoglobin levels, and lung capacity among modern humans. The findings provide insights into natural selection in human evolution and the role of splicing in gene regulation and phenotype differences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Evolutionary Biology
Jimmy A. Mcguire, Xiaoting Huang, Sean B. Reilly, Djoko T. Iskandar, Cynthia Y. Wang-Claypool, Sarah Werning, Rebecca A. Chong, Shobi Z. S. Lawalata, Alexander L. Stubbs, Jeffrey H. Frederick, Rafe M. Brown, Ben J. Evans, Umilaela Arifin, Awal Riyanto, Amir Hamidy, Evy Arida, Michelle S. Koo, Jatna Supriatna, Noviar Andayani, Robert Hall
Summary: The biota of Sulawesi is known for its unique species and diversification. In this study, the diversification history of Sulawesi flying lizards, an endemic group to Sulawesi, was explored using a geological framework. The analysis revealed that there are more Draco species in Sulawesi than previously thought, with cryptic and arrested speciation events and ancient hybridization affecting the phylogenetic analyses. The colonization of Sulawesi by the common ancestor of the Draco lineatus Group occurred around 11 million years ago, followed by radiations and dynamic species interactions.
SYSTEMATIC BIOLOGY
(2023)
Article
Ecology
Nicola R. Fornaini, Barbora Bergelova, Vaclav Gvozdik, Halina Cernohorska, Vladimir Krylov, Svatava Kubickova, Eric B. Fokam, Gabriel Badjedjea, Ben J. Evans, Martin Knytl
Summary: Using fluorescence in situ hybridization and genomic data, we mapped repetitive elements in six species of African clawed frogs and found that polyploidization and divergence play important roles in the evolution of repetitive elements. We also observed conserved loci number and position in one of the subgenus species, while the number of signals varied in other species derived from different polyploidization events.
EUROPEAN JOURNAL OF WILDLIFE RESEARCH
(2023)
Article
Genetics & Heredity
Benjamin L. S. Furman, Caroline M. S. Cauret, Martin Knytl, Xue-Ying Song, Tharindu Premachandra, Caleb Ofori-Boateng, Danielle C. Jordan, Marko E. Horb, Ben J. Evans