Article
Zoology
Laura C. Breitkreuz, Ivonne J. Garzon-Orduna, Shaun L. Winterton, Michael S. Engel
Summary: We present a phylogeny of Chrysopidae based on combined molecular and morphological data. Apochrysinae was found to be sister to the rest of the family (Nothochrysinae and Chrysopinae), and the monogeneric tribe Nothancylini is confirmed as sister to the remaining Chrysopinae. The other four tribes are grouped into two clades, Belonopterygini + Leucochrysini and Ankylopterygini + Chrysopini. The Nineta-group is transferred from Chrysopini to Ankylopterygini. Within the diverse and species-rich Chrysopini, five genus-group clades are recognized: Chrysopa, Chrysoperla, Chrysopodes, Eremochrysa, and Meleoma. Mapping of characters on the phylogeny provides insights into their evolution in the family. Taxonomic changes proposed include the inclusion of Chrysopidia, Nineta, and Tumeochrysa in the tribe Ankylopterygini, and the synonymization of Furcochrysa with Chrysopa.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Jacob A. Gorneau, Cristina A. Rheims, Corrie S. Moreau, Linda S. Rayor
Summary: This study provides a comprehensive phylogenetic inference of Huntsman spiders, incorporating extensive biology and life history data. It reveals the correlation between sociality and life history traits in these spiders, as well as the need for further revision of certain clades. Morphological scoring of an endemic Australian subfamily contextualizes existing molecular data.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh
Summary: Sequence simulators are important in phylogenetics for evaluating methods, hypothesis testing, and generating data. AliSim is a new tool that efficiently simulates biologically realistic alignments, outperforming popular software in terms of speed and efficiency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Nicolas Gutierrez Morales, Antonio L. Toscano De Brito, Anna Victoria Silverio Righetto Mauad, Eric De Camargo Smidt
Summary: This study provides a phylogenetic analysis of Pabstiella based on molecular data, revealing its origin in the Andes and the Atlantic Rainforest and suggesting the important role of the Atlantic Rainforest in the origin of subtribe Pleurothallidinae. Reconstruction of morphological characters showed high levels of homoplasy, indicating complex evolutionary history of the genus.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Han Yan, Zhirui Hu, Gregg W. C. Thomas, Scott Edwards, Timothy B. Sackton, Jun S. Liu
Summary: The paper introduces PhyloAcc-GT, a method that extends PhyloAcc by modeling gene tree heterogeneity, to effectively identify lineage-specific accelerations in substitution rate while accounting for incomplete lineage sorting. The method outperforms other methods in detecting complex patterns of rate shifts and is robust to population size parameter specification.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Ian G. Brennan, Alan R. Lemmon, Emily Moriarty Lemmon, Daniel M. Portik, Valter Weijola, Luke Welton, Stephen C. Donnellan, J. Scott Keogh
Summary: The study investigates the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). The results suggest that Australian Varanus communities exhibit high functional diversity as a result of interspecific competition among monitors on a continental scale, rather than with faunivorous marsupials. The patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data, highlighting macroevolutionary patterns that may develop in parallel across widely distributed sympatric groups.
SYSTEMATIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sudhir Kumar
Summary: Molecular evolutionary analysis requires computationally intensive steps that have a significant environmental impact. However, innovative methods and heuristics can reduce the carbon footprint, lower environmental costs, and promote green evolutionary computing.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Yuqi Huang, Minghao Sun, Lenan Zhuang, Jin He
Summary: This study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, revealing loss or gain of AIG members in different species during evolution. The findings can be used for future functional characterization of AIGs.
Article
Oncology
Antonia Chroni, Sayaka Miura, Lauren Hamilton, Tracy Vu, Stephen G. Gaffney, Vivian Aly, Sajjad Karim, Maxwell Sanderford, Jeffrey P. Townsend, Sudhir Kumar
Summary: By analyzing the genetic heterogeneity of tumors in cancer patients, we found that the migration histories of metastasis are often best described by a hybrid model of metastatic tumor evolution. We discovered that new tumor seedings arise from clones of pre-existing metastases as frequently as they do from clones from primary tumors. Additionally, there were many clone exchanges between the source and recipient tumors.
Article
Plant Sciences
Juliane Kretschmann, Anze Zerdoner Calasan, Johanna Knechtel, Pawel M. Owsianny, Eva Facher, Marc Gottschling
Summary: The evolution of the epitheca in calcareous dinophytes and their relatives is poorly understood. This study investigated the taxonomic identity of Chimonodinium lomnickii var. wierzejskii and studied the morphology and molecular phylogeny of eight monoclonal strains. The findings suggest an evolutionary transformation of the epitheca and the presence of atavism in these microorganisms.
EUROPEAN JOURNAL OF PHYCOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Matthew A. Spence, Matthew D. Mortimer, Ashley M. Buckle, Bui Quang Minh, Colin J. Jackson
Summary: This study used a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny, showing extensive diversification of the superfamily into many novel functional clades. Analysis indicated that the hub proteins are ancient and similar due to convergent evolution, rather than horizontal gene transfer as previously speculated. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Leticia Chiara Baldassio de Paula, Rodrigo de Vilhena Perez Dios, Filipe Macedo Gudin, Marcelo Domingos de Santis, Deivys Moises Alvarez-Garcia, Manuel Antunes Junior, Beatriz Vieira Freire, Fernando Portella de Luna Marques, Daniel Jose Galafasse Lahr, Silvio Shigueo Nihei
Summary: Tachinidae is the second largest and species-rich family in Diptera, with all members being parasitoids. This study presents the first phylogenomic analysis of Tachinidae using transcriptomic data, revealing the subfamilial relationships and the existence of a fifth lineage.
Article
Biodiversity Conservation
Emma K. Roberts, Emily A. Wright, Asha E. Worsham, Daniel M. Hardy, Robert D. Bradley
Summary: The extraordinary morphological diversity among extant mammals poses challenges for studies of speciation, adaptation, molecular evolution, and reproductive isolation. Despite molecular studies, uncertainties remain regarding divergence events. A phylogenetic tool based on a single reproductive molecular marker provides a solution to this longstanding issue.
Article
Biology
Edmund R. R. Moody, Tara A. Mahendrarajah, Nina Dombrowski, James W. Clark, Celine Petitjean, Pierre Offre, Gergely J. Szollosi, Anja Spang, Tom A. Williams, George H. Perry
Summary: Core gene phylogenies are important for understanding early evolution, but different gene sets and methods have led to different views of the tree of life. Recent analyses suggest that Archaea may be less divergent from Bacteria than previously thought, and estimates of inter-domain distance are inflated due to rapid evolution of ribosomal proteins. Resolving this debate is crucial for understanding the diversity of archaeal and bacterial domains and the early course of cellular evolution.
Article
Evolutionary Biology
Isabella Garcia-Gomez, Martin O. Pereyra, Jimmy Cabra-Garcia, Jhon Jairo Ospina-Sarria
Summary: This study investigated the variation and ancestral states of secondary sexual characters in the genus Pristimantis using ancestral character-state reconstruction. The results showed that sexual dichromatism exhibited at least five independent transformation series in Pristimantis, while vocal slits and nuptial pads were inferred to be ancestral conditions. Additionally, morphological synapomorphies were identified for specific groups within Pristimantis.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Plant Sciences
Lei Zhao, Ying-Ying Yang, Xiao-Jian Qu, Hong Ma, Yi Hu, Hong-Tao Li, Ting-Shuang Yi, De-Zhu Li
Summary: This study improves our understanding of aroid phylogeny by using a large number of nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade's adaptation to aquatic environments, the results suggest that whole-genome duplication may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade.
Article
Biochemistry & Molecular Biology
Le Zhang, Yi-Wei Huang, Jia-Lin Huang, Ji-Dong Ya, Meng-Qing Zhe, Chun-Xia Zeng, Zhi-Rong Zhang, Shi-Bao Zhang, De-Zhu Li, Hong-Tao Li, Jun-Bo Yang
Summary: In this study, DNA barcoding was conducted for species identification of Cymbidium using plastomes. A comprehensive DNA barcode reference library for Cymbidium species identification was established. The plastome showed improved species identification rates compared to standard DNA barcodes, but still had limitations. Nuclear genome data were also explored for species identification and showed potential as next-generation nuclear barcodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Ecology
Ya-Huang Luo, Liang-Liang Ma, Sebastian Seibold, Marc W. W. Cadotte, Kevin S. S. Burgess, Shao-Lin Tan, Lin-Jiang Ye, Wei Zheng, Jia-Yun Zou, Zhi-Fa Chen, De-Tuan Liu, Guang-Fu Zhu, Xiao-Chun Shi, Wei Zhao, De-Zhu Li, Jie Liu, Lian-Ming Gao
Summary: This study assessed the effects of different mycorrhizal types on forest carbon storage and the biodiversity-ecosystem functioning (BEF) relationships in the Gaoligong Mountains, Southwest China. It was found that different mycorrhizal types have significant impacts on forest carbon storage and species diversity. Furthermore, future global changes could potentially alter the mycorrhizal-mediated BEF relationships in mountain forests.
JOURNAL OF BIOGEOGRAPHY
(2023)
Review
Biochemistry & Molecular Biology
Cen Guo, Yang Luo, Lian-Ming Gao, Ting-Shuang Yi, Hong-Tao Li, Jun-Bo Yang, De-Zhu Li
Summary: The advancement of next-generation sequencing and long-read sequencing technologies has greatly influenced plant phylogenetic studies. Numerous phylogenetic studies using hundreds to thousands of genes across various clades have emerged in the past decade, bringing plant phylogenetics and evolution into a new era. This review focuses on the application of genomic data in phylogenetic and evolutionary investigations, describes the methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at different taxonomic levels. Challenges, such as systematic errors and underlying biological factors, are discussed, suggesting that a bifurcating tree may not be the most suitable model for the tree of life. Finally, promising avenues for future plant phylogenomic studies are discussed.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Plant Sciences
Sheng-Yuan Qin, Kai Chen, Wen-Ju Zhang, Xiao-Guo Xiang, Zheng-Yu Zuo, Cen Guo, Yao Zhao, Lin-Feng Li, Yu-Guo Wang, Zhi-Ping Song, Ji Yang, Xiao-Qiang Yang, Jian Zhang, Wei-Tao Jin, Qiang Wen, Song-Zi Zhao, Jia-Kuan Chen, De-Zhu Li, Jun Rong
Summary: This study sequenced and assembled the transcriptomes and plastomes of various species in the Camellia genus, providing a comprehensive taxonomic sampling for Camellia sect. Oleifera and C. sect. Paracamellia. Phylogenetic analyses showed that C. sect. Oleifera should be merged with C. sect. Paracamellia. Hybridization was found among polyploid species and their relatives. The divergence of major clades in C. sect. Paracamellia occurred during the middle to late Miocene, and the Quaternary period witnessed rapid diversification likely due to hybridization and polyploidization. This study also suggested that the hexaploid Camellia oleifera may have originated from hybridization between closely related diploid and tetraploid species.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Plant Sciences
Zhi-Hua Zeng, Qian Yu, Qing-Hong Feng, Xin-Jia Wang, Li Zhong, Hua-Ying Sun, Hong Wang, De-Zhu Li, Spencer C. H. Barrett, Wei Zhou
Summary: This study demonstrates the functional consequences of height dimorphism reversal in dioecious plants, shedding light on the reproductive strategies of males and females in terms of pollen and seed dispersal.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Sheng-Yuan Qin, Zheng-Yu Zuo, Cen Guo, Xin-Yu Du, Shui-Yin Liu, Xiang-Qin Yu, Xiao-Guo Xiang, Jun Rong, Bing Liu, Zhi-Fang Liu, Peng-Fei Ma, De-Zhu Li
Summary: This study focuses on the Litsea complex, which is a key lineage of evergreen broadleaved forests (EBLFs) in East Asia, aiming to explore the shift of evergreen versus deciduous trait and understand the origin and historical dynamics of EBLFs under Cenozoic climate change. The results show that the prototype of EBLFs in East Asia probably appeared in the Early Eocene period (about 55-50 million years ago) facilitated by greenhouse warming. With the cooling and drying climate in the Middle to Late Eocene period (48-38 million years ago), deciduous habits evolved. The development of East Asian monsoon in the Early Miocene period (23 million years ago) increased the extreme seasonal precipitation and promoted the emergence of evergreen habits.
Editorial Material
Plant Sciences
Dechang Cao, Jerry M. Baskin, Carol C. Baskin, De-Zhu Li
Summary: Smoke cues released from decaying leaves after drying are crucial for seed germination.
TRENDS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lin-Jiang Ye, Michael Moller, Ya-Huang Luo, Jia-Yun Zou, Wei Zheng, Jie Liu, De-Zhu Li, Lian-Ming Gao
Summary: Selection along environmental gradients in alpine ecosystems can drive adaptive evolution in plants. However, the genetic variation and adaptation in plants along environmental gradients remain poorly understood. To address this gap, we studied the transcriptomic profiles of Rhododendron sanguineum var. haemaleum at different elevations in the Gaoligong Mountains. We found that gene expression patterns in flower and leaf organs showed parallel shifts but with different functionality, indicating flexibility in response strategies to the heterogeneous environments.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Weishu Fan, Zheng-Shan He, Mengqing Zhe, Jing-Qiu Feng, Le Zhang, Yiwei Huang, Fang Liu, Jia-Lin Huang, Ji-Dong Ya, Shi-Bao Zhang, Jun-Bo Yang, Andan Zhu, De-Zhu Li
Summary: This study reports a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii, and provides insights into the molecular regulation of CAM photosynthesis in epiphytes. The study also reveals the rhythmic changes in metabolism and gene expression during the CAM diel cycle. The findings of this study are valuable for investigating post-transcription and translation scenarios in epiphytes.
PLANT COMMUNICATIONS
(2023)
Article
Plant Sciences
Bing Han, Yelan Li, Di Wu, De-Zhu Li, Aizhong Liu, Wei Xu
Summary: Genomic imprinting plays a significant role in the endosperm development, storage compound accumulation, and seed germination in castor bean. The study reveals that DNA methylation has a limited role in controlling genomic imprinting, while histone modifications play a more significant role in regulating the expression of most imprinted genes.
Article
Plant Sciences
Jiu-Xia Zhao, Shu Wang, Jiazhi Liu, Xiao-Dong Jiang, Jing Wen, Zhi-Quan Suo, Jie Liu, Mi-Cai Zhong, Qin Wang, Zhirong Gu, Changning Liu, Yunfei Deng, Jin-Yong Hu, De-Zhu Li
Summary: This study generated a transcriptome resource for two Strobilanthes species, providing valuable information for understanding the molecular mechanisms of perennial monocarpic mass flowering. The differential expression of transcription factors potentially involved in the photoperiod and circadian-clock pathway suggests their role in regulating flowering time diversity.
Article
Plant Sciences
Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li
Summary: Fargesia, the largest genus in the temperate bamboo tribe Arundinarieae, is mainly found in the mountains of Southwest China with over 90 species. These bamboos are essential for subalpine forest ecosystems and provide food and habitat for endangered animals like the giant panda. However, identifying Fargesia species is challenging due to rapid radiation and slow molecular evolutionary rate. In this study, the discriminatory power of complete plastomes and nrDNA sequences were evaluated and found to be more effective than standard barcodes. Despite this, additional nuclear markers are needed for accurate species discrimination.
Article
Plant Sciences
Jing-Xia Liu, Zu-Chang Xu, Yu-Xiao Zhang, Meng-Yuan Zhou, De-Zhu Li
Summary: Three woody bamboo species collected in Hainan, China in 1940, previously described as Dinochloa, are found to be closely related to Melocalamus through molecular phylogenetic analysis and morphological comparison. Therefore, it is suggested to transfer these three species to the genus Melocalamus.
Article
Biochemistry & Molecular Biology
Han-Tao Qin, Michael Moller, Richard Milne, Ya-Huang Luo, Guang-Fu Zhu, De-Zhu Li, Jie Liu, Lian-Ming Gao
Summary: Mountainous regions provide diverse habitats for speciation. In the Hengduan Mountains of southwest China, four Taxus lineages were studied. Conflicting phylogenetic relationships were found between nuclear and chloroplast sequences. Limited gene flow was observed between species. Based on the data, it was determined that two Taxus species originated through hybridization and chloroplast capture events.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
