Article
Ecology
Anthony E. Melton, Matthew H. Clinton, Donald N. Wasoff, Limin Lu, Haihua Hu, Zhiduan Chen, Keping Ma, Douglas E. Soltis, Pamela S. Soltis
Summary: Plant species in eastern Asia have larger climatic niche spaces compared to their counterparts in eastern North America. Congeners of eastern Asia-eastern North America disjunct genera tend to occupy similar or equivalent climatic niche spaces within their respective distributions, possibly due to their physiographic contexts.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Biochemistry & Molecular Biology
Wen-Qing Ye, Shan-Shan Zhu, Hans Peter Comes, Tuo Yang, Lian Lian, Wei Wang, Ying-Xiong Qiu
Summary: This study investigates the species richness patterns of Podophylloideae between Eastern Asia and Eastern North America and finds that the higher species richness in Eastern Asia can be explained by a longer period of time available to accumulate species and a greater diversification rate in this region.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Evolutionary Biology
Emmanuel F. A. Toussaint, Emily A. Ellis, Riley J. Gott, Andrew D. Warren, Kelly M. Dexter, Caroline Storer, David J. Lohman, Akito Y. Kawahara
Summary: A study on Heteropterinae skippers found that the group originated in the New World and colonized the eastern Palearctic via the Beringian route, resulting in two independent American clades. A vicariant event between Central and South America predates estimates of the closure of the proto-Caribbean seaway, suggesting active overwater dispersal in the Oligocene. The colonization of Africa from the east Palearctic coincided with the closure of the Tethys Ocean, while the colonization of Madagascar appears to be comparatively recent.
Article
Biochemistry & Molecular Biology
Rudan Lyu, Jiamin Xiao, Mingyang Li, Yike Luo, Jian He, Jin Cheng, Lei Xie
Summary: This study comprehensively reconstructed the evolutionary history of Clematis section Tubulosae, an East Asian endemic lineage, using a phylogenomic approach. Both nuclear datasets were more effective in resolving the phylogeny than the plastome sequence. The origin of the section can be traced back to the Pliocene, and all current species diversified during the Pleistocene. The study also highlighted the importance of climatic oscillation for the spatial-temporal diversification patterns of this lineage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Zoology
Tao Luo, Sha-Sha Yan, Ning Xiao, Jia-Jun Zhou, Xing-Liang Wang, Wei-Cai Chen, Huai-Qing Deng, Bao-Wei Zhang, Jiang Zhou
Summary: Through sequencing mitochondrial genomes and nuclear genes, this study reveals the interspecific phylogenetic relationships and historical biogeography of Asian warty newts in southern China. The study finds that Paramesotriton originated in southwestern China and identifies five hypothetical phylogenetic cryptic species. Ecological analysis and species distribution models indicate different habitat conditions and distribution areas for Paramesotriton species in different regions.
ZOOLOGICAL RESEARCH
(2022)
Article
Plant Sciences
Abdulrokhman Kartonegoro, Sylvia Mota de Oliveira, Peter C. van Welzen
Summary: The study uses 58 plant samples of the Dissochaeteae tribe and molecular dating analysis indicates that the diversity of Dissochaeteae in Southeast Asia originated from a South American ancestor in the late Eocene, possibly migrating from South America to Southeast Asia via North America. The origin and early diversification of Dissochaeteae in Southeast Asia can be traced back to the middle Oligocene, with the majority of genera originating in the Miocene.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Plant Sciences
James C. Lendemer, Jason P. Hollinger
Summary: Schadonia saulskellyana is a newly discovered species in the southern Appalachian Mountains in the eastern United States. It is primarily found on conifer bark and is especially abundant in the endangered high-elevation spruce-fir forests of the region.
Article
Plant Sciences
Zhi-Yuan Du, Jin Cheng, Qiu-Yun (Jenny) Xiang
Summary: The big-bracted dogwood clade Benthamidia of Cornus is a typical example of the floristic disjunction between eastern Asia (EA) and North America (NA), with greater species diversity in EA than in NA. Through phylogenomic and biogeographic analyses, we confirmed the higher phylogenetic diversity and diversification rate of the EA clade. Our results also indicated a trans-Beringian ancestral distribution, dispersal from Mexico to eastern United States, and early diversification in southwest China.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
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
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)
Review
Ecology
Zeng-Yuan Wu, Richard I. Milne, Jie Liu, Ran Nathan, Richard T. Corlett, De-Zhu Li
Summary: Long-distance dispersal (LDD) beyond a species' range is crucial for ecological and evolutionary patterns, but postdispersal establishment has not received enough attention. This review summarizes the current understanding of post-LDD establishment in plant colonization, identifies key determinants of establishment success, develops a general framework for quantifying post-LDD establishment, and outlines future research challenges and opportunities. These include improving LDD detection and understanding using novel approaches, investigating mechanistic modeling and inference to understand establishment success, and comparing establishment between past and present. By addressing knowledge gaps, this review aims to enhance our understanding of the impacts of LDD on plant distributions and long-term consequences.
TRENDS IN ECOLOGY & EVOLUTION
(2023)
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
Plant Sciences
Chun-Jiao Li, Xin-Tong Xie, Hong-Xin Liu, Ruo-Nan Wang, De-Zhu Li
Summary: This study sequenced and assembled the plastomes of East Asian lobelias, revealing variations in plastome gene structure among different taxonomic sections. The study also assessed the variability of several genes and simple sequence repeats, which can be used as important research tools in DNA barcoding and species delineation. The study further identified key genes related to the evolutionary history and adaptive evolution of East Asian lobelias. These findings will contribute to further advancements in taxonomy, evolutionary biology, and the utilization of medicinal plant resources.
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
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
Plant Sciences
Rivontsoa A. Rakotonasolo, Soejatmi Dransfield, Thomas Haevermans, Helene Ralimanana, Maria S. Vorontsova, Meng-Yuan Zhou, De-Zhu Li
Summary: The Hickeliinae is an important subtribe of tropical bamboos, mainly found in Madagascar, Comoros, Reunion Island, and a small part of Tanzania. Molecular phylogenetic analysis of newly sequenced plastid genomes revealed conserved structures and provided informative data for phylogenetic reconstructions. The analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which forms two distant clades. This study provides significant resources for further genetic and phylogenomic research on this under-studied subtribe.
Article
Plant Sciences
Ji-Dong Ya, Wan -Ting Wang, Yun-Long Liu, Hong Jiang, Zhou-Dong Han, Ting Zhang, Hua Huang, Jie Cai, De-Zhu Li
Summary: Five new orchid species from Yunnan Province and Tibet have been described and illustrated. The study sequenced the complete plastomes of these species and their related species to confirm their identities and determine their phylogenetic relationships. The results showed that the N. lihengiae species is closely related to the N. grandiflora and N. pinetorum clade, while N. chawalongensis is sister to N. alternifolia. Additionally, the relationships among species in the genus Gastrochilus were inconsistent, but the two new species, G. lihengiae and G. bernhardtianus, were supported by all datasets.
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)
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)