Article
Multidisciplinary Sciences
Yi-Tian Fu, Renfu Shao, Guo-Hua Suleman, Wei Wang, Hui-Mei Wang, Guo-Hua Liu
Summary: We sequenced the mt genomes of two lice species and found that they share seven minichromosomes with the same gene content and arrangement. Our analysis revealed numerous inter-minichromosomal recombination events, as well as gene duplication, degeneration, deletion, and translocation. The hotspots for inter-minichromosomal recombination were identified as upstream regions of cox3 and nad2 genes. These findings provide important insights into mt genome evolution in metazoans.
Article
Cell Biology
Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides
Summary: This study used a large-scale comparative genomics approach to discover that small genes are more prevalent in phage genomes than in host prokaryotic genomes. These small genes may have important functions, such as encoding anti-CRISPR proteins and antimicrobial proteins.
Article
Biochemistry & Molecular Biology
Sebastian G. Gornik, Victor Flores, Franziska Reinhardt, Lieselotte Erber, Dayana E. Salas-Leiva, Olga Douvropoulou, Imen Lassadi, Elin Einarsson, Mario Moerl, Anna Git, Peter F. Stadler, Arnab Pain, Ross F. Waller
Summary: This study sequenced and assembled mitochondrial genomes of four Perkinsus species and revealed a simple ancestral genome with reduced coding capacity and a tendency for rearrangement. The study identified 75 frameshifts across the four species, which are highly conserved in gene location and likely regulate protein folding. Furthermore, the mitochondrion-encoded rRNA fragments in Perkinsus spp. are incomplete, suggesting import from nuclear DNA.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Ying Zhang, Shaojuan Wang, Haixia Li, Chunli Liu, Fei Mi, Ruirui Wang, Meizi Mo, Jianping Xu
Summary: The study suggests that mitochondrial heteroplasmy and recombination in Cantharellus cibarius may not be limited to a specific population and may not be transient. This indicates that there may have been repeated events of heteroplasmy and recombination during the evolution of the yellow chanterelles.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Rauf Ahmad Shah, Muzafar Riyaz, Savarimuthu Ignacimuthu, Kuppusamy Sivasankaran
Summary: The present study annotated and reconstructed the phylogenetic relationships of the mitogenomes of three Noctuoid and one Hyblaeoid species. The results showed that the phylogenetic relationships of the Noctuoid families were (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). Additionally, one species from the superfamily Hyblaeoidea was found to be clustered separately from the Noctuoidea member groups.
SCIENTIFIC REPORTS
(2022)
Review
Plant Sciences
Yazhong Wang, Willem M. J. van Rengs, Mohd Waznul Adly Mohd Zaidan, Charles J. Underwood
Summary: This review summarizes current knowledge on meiosis in diverse monocot and dicot crop species and provides a comprehensive resource of cloned meiotic mutants in six crop species. Functional roles of meiotic proteins are generally conserved between plant species, despite significant differences in physical lengths of plant chromosomes. Research on meiosis in crops will complement that in Arabidopsis and facilitate a better understanding of how the different stages of meiosis are controlled in plant species, potentially benefiting plant breeding applications.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biotechnology & Applied Microbiology
Benjamin M. Anderson, Kirsten Krause, Gitte Petersen
Summary: The study analyzed the mitochondrial genomes of two parasitic plant species in the genus Cuscuta, revealing typical mitochondrial gene sets and a structurally unusual ccmF(C) gene. Despite examples of HGT in nuclear genomes, there is little to no indication of HGT in the Cuscuta mitochondrial genomes.
Article
Biotechnology & Applied Microbiology
Derek M. Bickhart, Mikhail Kolmogorov, Elizabeth Tseng, Daniel M. Portik, Anton Korobeynikov, Ivan Tolstoganov, Gherman Uritskiy, Ivan Liachko, Shawn T. Sullivan, Sung Bong Shin, Alvah Zorea, Victoria Pascal Andreu, Kevin Panke-Buisse, Marnix H. Medema, Itzhak Mizrahi, Pavel A. Pevzner, Timothy P. L. Smith
Summary: This study demonstrates that deep sequencing combined with haplotype phasing can address the challenge of identifying closely related organisms in microbial communities. The resolution of closely related microbes improves the identification of biosynthetic gene clusters and the assignment of mobile genetic elements to host genomes.
NATURE BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Haitao Ma, Dongmei Yu, Jun Li, Yanping Qin, Yang Zhang, Zhiming Xiang, Yuehuan Zhang, Ziniu Yu
Summary: This study analyzed the complete mitochondrial genome of Hippopus porcellanus and determined its evolutionary relationships with other giant clam species. The results showed high similarity between certain species and confirmed the divergence time consistent with the fossil record. This molecular phylogeny provides valuable information for ecological research and conservation efforts.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yanli Che, Wenbo Deng, Weijun Li, Jiawei Zhang, Yukihiro Kinjo, Gaku Tokuda, Thomas Bourguignon, Nathan Lo, Zongqing Wang
Summary: This study investigated the phylogenetic relationships and geographical distribution of Cryptocercus, demonstrating the significant roles of both vicariance and dispersal in shaping the distribution and diversity of these woodroaches. The findings supported six major lineages of Cryptocercus with clear geographical patterns, providing evidence for multiple dispersal and vicariance events that occurred over various time periods in the evolutionary history of the genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Yingfeng Niu, Chengwen Gao, Jin Liu
Summary: Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. This study sequenced and compared the mitochondrial genomes of three Mangifera species, and found that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome was also identified.
Article
Evolutionary Biology
Xue Dong, Wenbo Yi, Chenguang Zheng, Xiuxiu Zhu, Shujing Wang, Huaijun Xue, Zhen Ye, Wenjun Bu
Summary: This study focused on species delimitation of five Leptocorisa species in China, especially the rice seed bugs complex. Genetic markers were used to distinguish between morphologically similar species, with nuclear SNP data proving to be effective in identifying separate species. Mitochondrial introgression resulting from hybridization was suggested as a likely explanation for mito-nuclear discordance between two taxa in the complex. This molecular evidence is crucial for further studies on the ecology and pest management of these important rice pests.
Article
Zoology
Ran Xu, Mariangela Iannello, Justin C. Havird, Liliana Milani, Fabrizio Ghiselli
Summary: This study compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum. The results showed different transcription profiles between mitochondrial and nuclear OXPHOS genes, suggesting that the coordination between the two may involve post-transcriptional/translational regulation.
ZOOLOGICAL RESEARCH
(2022)
Article
Multidisciplinary Sciences
Alexandre Hassanin, Geraldine Veron, Anne Ropiquet, Bettine Jansen van Vuuren, Alexis Lecu, Steven M. Goodman, Jibran Haider, Trung Thanh Nguyen
Summary: This study analyzed the complete mitochondrial genomes of various species within the order Carnivora to reconstruct phylogenetic relationships and estimate divergence times. The findings provide insights into the evolutionary history of different species within the order, revealing that the emergence and diversification of crown carnivorans occurred millions of years ago, with differences in evolution times between the Caniformia and Feliformia groups.
Article
Biochemistry & Molecular Biology
Yanan Sun, Guillemine Daffe, Yanjie Zhang, Joan Pons, Jian-Wen Qiu, Elena K. Kupriyanova
Summary: Mitochondrial genomes from the annelid genus Hydroides exhibit unique characteristics in gene order and sequence evolution compared to other annelids, showing a fast rate of evolution. Phylogenetic analysis suggests that mitochondrial genomes alone may not be sufficient to accurately determine the phylogenetic relationships within Serpulidae due to high base substitution rates. Further research is needed to better understand the variability and evolution of mitochondrial genomes in annelids.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Evolutionary Biology
Daemin Kim, Bruce H. Bauer, Thomas J. Near, Danielle Edwards
Summary: Evolutionary genomics studies the genetic diversity of the sunfish genus Lepomis and finds that it consists of six relatively ancient evolutionary lineages instead of two recognized species. The study also highlights the importance of genetic flow and hybridization in species delimitation and the role of segregating hybrid populations in revealing species characteristics.
SYSTEMATIC BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Ryo Inaba, Ryouka Kawahara-Miki, Akihisa Shinozawa, Taichi Yasuhara, Takashi Fujii, Keisuke Koyama, Michiko Murata-Okubo, Kousaku Souma, Hiroki Hirayama
Summary: Hormonal induction of parturition in cattle increases the risk of retained fetal membrane. This study revealed the importance of interferon signaling in the immune regulation of placental tissues during parturition.
JOURNAL OF REPRODUCTION AND DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Genta Okude, Minoru Moriyama, Ryouka Kawahara-Miki, Shunsuke Yajima, Takema Fukatsu, Ryo Futahashi
Summary: The functional changes and interactions of transcription factors Kr-h1, broad, and E93 are crucial in the metamorphosis of insects. These findings are significant for understanding the evolution of insect metamorphosis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Ava Ghezelayagh, Richard C. Harrington, Edward D. Burress, Matthew A. Campbell, Janet C. Buckner, Prosanta Chakrabarty, Jessica R. Glass, W. Tyler McCraney, Peter J. Unmack, Christine E. Thacker, Michael E. Alfaro, Sarah T. Friedman, William B. Ludt, Peter F. Cowman, Matt Friedman, Samantha A. Price, Alex Dornburg, Brant C. Faircloth, Peter C. Wainwright, Thomas J. Near
Summary: The study constructs a time-calibrated phylogeny to explore patterns of body shape disparity within spiny-rayed fishes. The authors find a steady accumulation of lineages throughout the Cenozoic, with an increase in morphological disparity after the Cretaceous-Palaeogene event, facilitating the radiation and diversification of spiny-rayed fishes.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Daniel J. MacGuigan, Oliver D. Orr, Thomas J. Near
Summary: The history of riverine fish diversification is largely driven by geographic isolation, where physical barriers and genetic drift lead to speciation. The Johnny Darter (Etheostoma nigrum) species complex, which includes E. olmstedi, E. perlongum, and E. susanae, exhibits gene flow and conflicting species diversity inferences. By using genomic data and population genetic approaches, this study identifies and validates several evolutionary lineages within the complex, emphasizing the need for further research to describe its diversity. The phylogeographic structure within the complex is influenced by major geologic events and river basin rearrangements, making it a hotspot of freshwater biodiversity in eastern North America.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Chase Doran Brownstein, Liandong Yang, Matt Friedman, Thomas J. Near
Summary: This study uses genomic data and fossil records to reveal the evolutionary history and biogeographic patterns of ancient gar clades. The results show that gar clades originated in the eastern part of North America and were influenced by Mesozoic tectonic events. This suggests that the eastern part of North America served as both the origin of extant gar diversity and the refuge for this ancient lineage.
SYSTEMATIC BIOLOGY
(2023)
Article
Cell Biology
Mari Kawaguchi, Wen-Shan Chang, Hazuki Tsuchiya, Nana Kinoshita, Akira Miyaji, Ryouka Kawahara-Miki, Kenji Tomita, Atsushi Sogabe, Makiko Yorifuji, Tomohiro Kono, Toyoji Kaneko, Shigeki Yasumasu
Summary: The seahorse is a unique teleost fish with special morphology, including bony plates and spines, and males possessing a brooding organ called the brood pouch. The flame cone cells, found in the brood pouch and spines, express a gene called pgrich which is not present in related species. This pgrich gene may have originated from the elastin gene with the involvement of transposable elements and obtained its novel function in the flame cone cells during seahorse evolution.
CELL AND TISSUE RESEARCH
(2023)
Article
Ecology
Daniel J. MacGuigan, Trevor J. Krabbenhoft, Richard C. Harrington, Dylan K. Wainwright, Nathan J. C. Backenstose, Thomas J. Near
Summary: Geographic isolation is a significant factor contributing to speciation in vertebrates. However, the Lake Waccamaw endemic Etheostoma perlongum and its riverine sister species Etheostoma maculaticeps are a rare exception, as there are no physical barriers preventing gene flow between them.
Article
Multidisciplinary Sciences
Maya F. Stokes, Daemin Kim, Sean F. Gallen, Edgar Benavides, Benjamin P. Keck, Julia Wood, Samuel L. Goldberg, Isaac J. Larsen, Jon Michael Mollish, Jeffrey W. Simmons, Thomas J. Near, J. Taylor Perron
Summary: The high levels of biodiversity in mountains suggest a possible connection between geologic processes and biological evolution. The study shows how erosion through different rock types drove allopatric divergence in a fish species. The results suggest a geological mechanism for initiating diversification in mountains long after tectonic activity ceases.
Article
Biology
Jessica R. Glass, Richard C. Harrington, Peter F. Cowman, Brant C. Faircloth, Thomas J. Near
Summary: Inferring patterns of speciation in marine organisms is challenging due to the lack of species-level phylogenies and information on species' distributions, as well as conflicting relationships between species' dispersal, range size, and co-occurrence. However, a recent study on Carangoidei fish species found that there is widespread sympatry among sister species pairs, regardless of node age, and most species pairs coexist across large portions of their ranges.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biodiversity Conservation
Matthew R. Thomas, Rebecca E. Blanton, Ava Ghezelayagh, Thomas J. Near
Summary: The Kentucky Arrow Darter is a distinct species closely related to the E. sagitta and E. nianguae. It differs from E. sagitta in several morphological and genetic traits, and has been supported as a separate species based on meristic, morphometric, and genetic data. The species is threatened due to habitat degradation and water quality issues in the upper Kentucky basin.
BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY
(2023)
Article
Biodiversity Conservation
Julia E. Wood, Richard C. Harrington, Zachariah D. Alley, Matthew R. Thomas, Jeffrey W. Simmons, Thomas J. Near
Summary: Etheostoma xanthovum, also known as the Clarks Darter, is a newly described species found only in the Clarks River drainage in Kentucky and Tennessee, USA. It was previously misidentified as Etheostoma oophylax based on its appearance. However, further molecular and genetic analyses confirm the distinctiveness of E. xanthovum as a separate species.
BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY
(2023)
Article
Zoology
Elyse Parker, Thomas J. Near
Summary: This study used genome-scale DNA data and multispecies coalescent methods to resolve the phylogenetic relationships of the Antarctic notothenioid lineage Artedidraconinae. The results clarified several long-standing challenges in the systematics of Artedidraconinae and enabled the construction of a classification that reflects phylogenetic relationships.
ICHTHYOLOGY AND HERPETOLOGY
(2022)
Article
Zoology
Daniel J. MacGuigan, Genevieve G. Mount, Gregory J. Watkins-Colwell, Thomas J. Near, Max R. Lambert
Summary: This study conducted genomic research on the North American Green Frog, revealing its relationship with the Florida Bog Frog and the pattern of genetic variation within the species, concluding that the Green Frog should be considered as a single species.
ICHTHYOLOGY AND HERPETOLOGY
(2022)
Article
Biology
Chase D. Brownstein, Daemin Kim, Oliver D. Orr, Gabriela M. Hogue, Bryn H. Tracy, M. Worth Pugh, Randal Singer, Chelsea Myles-McBurney, Jon Michael Mollish, Jeffrey W. Simmons, Solomon R. David, Gregory Watkins-Colwell, Eva A. Hoffman, Thomas J. Near
Summary: This article describes an ancient lineage of ray-finned fishes, using DNA sequencing and morphology to confirm the existence of a second species and its origin dating back to the Plio-Pleistocene period. This discovery is significant for vertebrate genomics and developmental research, but the lineage is currently facing conservation threats due to the caviar fishery.
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)
