Article
Evolutionary Biology
Xin-Yu Du, Jin-Mei Lu, Li-Bing Zhang, Jun Wen, Li-Yaung Kuo, Claudine M. Mynssen, Harald Schneider, De-Zhu Li
Summary: Comprising the majority of extant fern species diversity, Polypodiales are believed to have originated in the Late Cretaceous. Divergence time estimates utilizing plastome data and fossil constraints support the origin of Polypodiales and its closest relatives in the Triassic, major lineages established in the Jurassic.
Article
Plant Sciences
Pirada Sumanon, Henrik Balslev, Timothy M. A. Utteridge, Wolf L. Eiserhardt
Summary: This study reconstructed a species-level phylogenetic tree of the genus Maesa, dividing it into African and Asian-Pacific clades, each further divided into two or three subclades. Five subgenera of Maesa were proposed based on this phylogenetic analysis. However, resolving species boundaries within some species complexes was challenging due to a lack of phylogenetic signal at shallow levels.
Article
Evolutionary Biology
Ran Wei, Jie Yang, Li-Juan He, Hong-Mei Liu, Jia-Yu Hu, Si-Qi Liang, Xue-Ping Wei, Cun-Feng Zhao, Xian-Chun Zhang
Summary: This study investigated the deep phylogenetic relationships within Polypodiaceae by utilizing 81 plastid genomes, improving the resolution of backbone phylogeny. The research identified potential phylogenetic artefacts affecting the incongruence of phylogenetic inferences and provided a robust framework for future subfamilial taxonomy within Polypodiaceae.
Article
Plant Sciences
Alessandro Oliveira de Souza, Gwilym P. Lewis, Marcos Jose da Silva
Summary: Chamaecrista, a genus with over 330 species, has a complex taxonomic history. Molecular phylogenetic analyses and morphology support the recognition of four main clades, while revealing the non-monophyly of traditional taxonomic units.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Anatomy & Morphology
Alexey V. Vaganov
Summary: The study utilized SEM to characterize spore morphology of 24 taxa in the subfamily Pteridoideae and projected standardized data onto the phylogenetic tree, exploring the evolution of characteristics and relationships within the Pteridaceae family.
MICROSCOPY RESEARCH AND TECHNIQUE
(2022)
Article
Fisheries
Chien-Hui Yang, Ka Yan Ma, Ka Hou Chu, Tin-Yam Chan
Summary: This study reconstructed a robust molecular phylogeny for Penaeus s.l. shrimps using the largest dataset to date. The findings revealed some paraphyletic genera within Penaeus s.l. Furthermore, the traditional morphological characters used for species differentiation are not synapomorphic or evolutionarily informative. Therefore, retaining these shrimps in a single genus is appropriate to reflect their evolutionary relationships.
Article
Plant Sciences
Jean-Yves Dubuisson, Timothee Le Pechon, Sabine Hennequin, Germinal Rouhan, Alexandre Salino, Vincent Deblauwe, Vincent Droissart, Hanna Tuomisto, Samuli Lehtonen, Atsushi Ebihara
Summary: This study revealed a greater morphological diversity in the filmy fern genus Trichomanes than traditionally recognized, proposing a new subgenus Afrotrichomanes for the Afro-Malagasy taxa. The origins of Palaeotropical species in the genus are suggested to have occurred through both recent colonization from the Neotropics and a possible Mesozoic vicariance event. The low species diversity of the genus in the Afro-Malagasy region was discussed.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Plant Sciences
Tao Fujiwara, Phyo Kay Khine, Kiyotaka Hori, Thant Shin, Noriaki Murakami, Harald Schneider
Summary: A new species of the fern genus Lepisorus, Lepisorus medioximus, has been discovered in Shan state, Myanmar. This new species is distinct from phylogenetically related species in terms of its morphological characters, such as the rhizome scales, size and shape of the lamina, position of sori, and paraphyses.
Article
Agriculture, Dairy & Animal Science
Mohammed Ahmed, Oleksandr Holovachov
Summary: Advancements in DNA sequencing and molecular phylogenetics have greatly impacted our understanding of nematode evolution, leading to significant changes in classification. While the current classification of Nematoda does not always accurately reflect their evolutionary relationships, further research and improvements are needed to better understand the phylogeny of this diverse group of animals.
Article
Chemistry, Physical
Jeffrey B. Schriber, Daniel R. Nascimento, Alexios Koutsoukas, Steven A. Spronk, Daniel L. Cheney, C. David Sherrill
Summary: CLIFF is a machine-learned intermolecular force field that combines accurate physics equations with automatic parameterization, achieving high precision in drug discovery and protein models. It demonstrates excellent performance in both test sets and applications by accurately ranking ligand binding strengths and producing low errors compared to reference values.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Plant Sciences
Eugeny V. Boltenkov, Elena V. Artyukova
Summary: This study conducted molecular and morphological analyses to investigate the taxonomic composition and relationships within I. sect. Psammiris. The results supported the monophyly of the section and proposed a novel classification, as well as providing updated information on the species and a new identification key.
Article
Evolutionary Biology
Junxia Zhang, Zhaoyi Li, Jiaxing Lai, Zhisheng Zhang, Feng Zhang
Summary: Studies have found that traditional UCE probe sets have relatively low capture efficiency for the RTA clade of spiders. This study successfully developed a new UCE probe set, which showed high capture efficiency and resolved the phylogeny of the RTA clade of spiders.
Article
Entomology
Dominik Kusy, Michal Motyka, Ladislav Bocak
Summary: We analyze the relationships between two click beetles Paulusiella Lobl, 2007 and Analestesa Leach, 1824 (=Cebriognathus Chobaut, 1899) that cannot jump. By using mitochondrial genomes and nuclear genes, we find that Paulusiella is closely related to Hemiops Laporte, 1838 (Hemiopinae) and Analestesa belongs to the Cardiophorinae subfamily. This study provides new molecular evidence for the evolutionary relationships of click beetles. Rating: 7 out of 10.
INSECT SYSTEMATICS AND DIVERSITY
(2023)
Article
Biochemistry & Molecular Biology
Sven Gippner, Scott L. Travers, Mark D. Scherz, Timothy J. Colston, Mariana L. Lyra, Ashwini Mohan, Malte Multzsch, Stuart Nielsen, Lois Rancilhac, Frank Glaw, Aaron M. Bauer, Miguel Vences
Summary: The dwarf geckos of the genus Lygodactylus are found in continental Africa, Madagascar, and South America. This study confirmed the monophyly of 14 Lygodactylus species groups and estimated the crown diversification of Lygodactylus to have started at 46 mya. Further research on related genera and phylogenomic approaches may help provide better biogeographic insights into the evolutionary history of these geckos.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Ana Rita G. Simoes, Lauren A. Eserman, Alexandre R. Zuntini, Lars W. Chatrou, Timothy M. A. Utteridge, Olivier Maurin, Saba Rokni, Shyamali Roy, Felix Forest, William J. Baker, Sasa Stefanovic
Summary: This study uses a large dataset of nuclear genes to provide support for resolving phylogenetic uncertainties within the Convolvulaceae family. It confirms that Cuscuta belongs within the family, but challenges the monophyly of Merremieae and provides novel relationships within Dicranostyloideae. The exact placements of Erycibe and Cuscuta remain uncertain and require further investigation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Si-Qi Liang, Ronald L. L. Viane, Xian-Chun Zhang, Ran Wei
Summary: The Asplenium pekinense complex includes multiple ploidy species, with A. sarelii and A. pekinense being more common, while A. anogrammoides and A. altajense are rare species often misidentified. The A. varians complex is composed of the widespread A. tenuicaule, rare A. semivarians, and three other tetraploid species. Both species complexes are known for their taxonomic difficulty due to their history of reticulate evolution.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2021)
Article
Plant Sciences
Cun-Feng Zhao, Ran Wei, Qiao-Ping Xiang, Xian-Chun Zhang
Article
Biochemistry & Molecular Biology
Hong-Rui Zhang, Ran Wei, Qiao-Ping Xiang, Xian-Chun Zhang
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2020)
Article
Plant Sciences
Jong-Soo Kang, Hong-Rui Zhang, Ya-Rong Wang, Si-Qi Liang, Zhi-Yuan Mao, Xian-Chun Zhang, Qiao-Ping Xiang
Article
Evolutionary Biology
Ran Wei, Jie Yang, Li-Juan He, Hong-Mei Liu, Jia-Yu Hu, Si-Qi Liang, Xue-Ping Wei, Cun-Feng Zhao, Xian-Chun Zhang
Summary: This study investigated the deep phylogenetic relationships within Polypodiaceae by utilizing 81 plastid genomes, improving the resolution of backbone phylogeny. The research identified potential phylogenetic artefacts affecting the incongruence of phylogenetic inferences and provided a robust framework for future subfamilial taxonomy within Polypodiaceae.
Article
Biochemistry & Molecular Biology
Ran Wei, Cun-Feng Zhao, Qiao-Ping Xiang, Xian-Chun Zhang
Summary: The establishment of Ellipinema was to accommodate Lepisorus jakonensis in the plastid gene tree. However, new nuclear data revealed that Ellipinema and allied genera are deeply nested within Lepisorus. The incongruent phylogenetic placement between nuclear and plastid results may suggest ancient hybridization events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Meng-Hua Zhang, Ran Wei, Qiao-Ping Xiang, Atsushi Ebihara, Xian-Chun Zhang
Summary: The Eurasian and Mediterranean Selaginella helvetica group is taxonomically challenging, with 10 taxa identified through phylogenetic analyses. Nuclear DNA markers are more informative than chloroplast DNA markers in delineating closely related species within Selaginella.
Article
Plant Sciences
Ran Wei, Xian-Chun Zhang
Summary: The study explored the phylogenetic relationships within the Polypodiaceae family using plastid and nuclear genome data, revealing incongruences between some clades and along the backbone of the phylogeny. This discrepancy may be attributed to complex evolutionary histories within these clades, such as rapid radiation, incomplete lineage sorting, ancient hybridization, and recent introgression. Despite these challenges, the study identified nine major clades in Polypodiaceae that can be recognized as subfamilies, with support from both molecular and non-molecular features.
Article
Biochemistry & Molecular Biology
Si-Qi Liang, Xian-Chun Zhang, Ran Wei
Summary: This study investigates the spatial genetic structure of the Athyrium sinense complex and identifies geographical distance, environment, climatic history, and external dispersal constraints as driving forces. The findings reveal a clear north-south divergence in East Asia, with climate fluctuations playing a crucial role in the formation of this divergence. The present genetic structure is attributed to adaptation to heterogeneous environments and the effects of gene flow are constrained by factors such as canopy density, wind direction, and habitat continuity.
Article
Plant Sciences
Qiao-Ping Xiang, Jun-Yong Tang, Ji-Gao Yu, David Roy Smith, Yan-Mei Zhu, Ya-Rong Wang, Jong-Soo Kang, Jie Yang, Xian-Chun Zhang
Summary: This study discovered that the plastome of Selaginella sinensis has accelerated substitution rates, a low GC content, pervasive repeat elements, and a dynamic network structure. It also lacks certain related recombinases. The study suggests that the interplay between a deficient DNA-RRR system and high repeat content has led to the unique divergence of the S. sinensis plastome.
Article
Biochemistry & Molecular Biology
Meng-Hua Zhang, Qiao-Ping Xiang, Xian-Chun Zhang
Summary: This study provides a comprehensive analysis of the plastomes of Selaginellaceae, revealing conflicts and uncertainties in their phylogenetic relationships and exploring the underlying causes. The results demonstrate that the coalescent method is more effective in overcoming issues caused by outlier genes and extreme RNA editing events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Plant Sciences
Jong-Soo Kang, Jigao Yu, Xian-Chun Zhang, Qiao-Ping Xiang
Summary: The study reports extensive C-to-U editing in the plastomes and mitogenomes of Selaginella plants, and explores the association between RNA editing, genomic features, and the PPR protein family. The findings suggest a potential link between aberrant DNA repair systems and the evolution of post-transcriptional modifications in organelle genomes.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Plant Sciences
Jie Yang, Qiao-Ping Xiang, Xian-Chun Zhang
Summary: By integrating chloroplast genome data and morphological evidence, this study identifies five species within the Selaginella tamariscina group, including two new species and one new subspecies.
Article
Biochemistry & Molecular Biology
Ji-Gao Yu, Jun-Yong Tang, Ran Wei, Mei-Fang Lan, Rui-Chen Xiang, Xian-Chun Zhang, Qiao-Ping Xiang
Summary: The genome size of the homosporous lycophyte Lycopodium clavatum is 2.30 Gb, with over 85% repetitive elements, of which 62% are long terminal repeat (LTR). The study reveals a high birth rate and low death rate of LTR-RTs in homosporous lycophytes, contrasting the situation in heterosporous lycophytes. Additionally, the study identifies two whole genome duplications and the presence of key enzymes for the HupA biosynthetic pathway in L. clavatum, which are absent in other major land plant lineages. This research is crucial for the medicinal utilization of lycophytes and provides important insights into the evolution and biology of early vascular land plants.
PLANT MOLECULAR BIOLOGY
(2023)