Article
Multidisciplinary Sciences
Chase Doran Brownstein
Summary: During the Cretaceous period, terrestrial vertebrates experienced diversifications and turnovers due to global geographical change, although the poor fossil record from the early Late Cretaceous has concealed how dinosaurs and other terrestrial vertebrates responded to these events. This study describes two dinosaurs from the North American paleolandmass Appalachia, shedding light on the timing of important anatomical innovations in two widespread dinosaur lineages. The phylogenetic positions of the dinosaurs show similarities between Appalachian and Eurasian dinosaur faunas, indicating a degree of endemism in Appalachian dinosaur assemblages due to episodes of vicariance.
ROYAL SOCIETY OPEN SCIENCE
(2021)
Article
Ecology
Phillip L. Skipwith, Paul M. Oliver
Summary: A key area of interest in evolutionary biology is the role of ecological opportunity in adaptive radiations. This study investigates ecomorphologically diverse radiations of geckos in continental and insular contexts to test two hypotheses. Surprisingly, the results show that speciation rates are homogenous while morphological diversification rates are idiosyncratic and uncorrelated with speciation rates. This study adds to the growing body of evidence that suggests ecologically diverse radiations may not exhibit exceptional shifts in speciation dynamics or morphological diversification.
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
Plant Sciences
Zhen-Chen Qi, Pan Li, Jun-Jie Wu, Alexander Gamisch, Tuo Yang, Yun-Peng Zhao, Wu-Qing Xu, Shi-Chao Chen, Kenneth M. Cameron, Ying-Xiong Qiu, Cheng-Xin Fu
Summary: Geographical variation in species richness in plant groups is determined by the interplay between historical, evolutionary, and ecological processes. However, the processes underlying the disparity in species richness between Asia and the Americas in Smilacaceae remain poorly understood. This study reveals that Smilacaceae originated and diversified in middle to low latitudes in Central America and Eurasia during the Late Eocene, and species diversification rates were positively correlated with niche evolution and divergence. The high plant richness in Asia may be explained by greater diversification in this region, potentially promoted by heterogeneous environments.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Plant Sciences
Han-Yang Lin, Miao Sun, Ya-Jun Hao, Daijiang Li, Matthew A. Gitzendanner, Cheng-Xin Fu, Douglas E. Soltis, Pamela S. Soltis, Yun-Peng Zhao
Summary: This study investigates the patterns of phylogenetic diversity (PD) and phylogenetic beta diversity (PBD) of congeners disjunctly distributed between eastern Asia and eastern North America (EA-ENA disjuncts) and their associated factors. The results show that, despite having fewer disjunct species than EA, ENA disjuncts have higher standardized effect size of PD (SES-PD) at the continental scale. The SES-PD of EA-ENA disjuncts decreases with increasing latitude, with a stronger latitudinal diversity gradient in EA sites.
Article
Evolutionary Biology
Michele Rossini, Vasily Grebennikov, Thomas Merrien, Andreia Miraldo, Heidi Viljanen, Sergei Tarasov
Summary: The phylogenetic relationships of the Paleotropical dung beetle clades (Grebennikovius, Epactoides, and Ochicanthon) were reconstructed using morphology and molecular data. The study reveals the divergence and dispersal patterns of these clades in relation to geological changes and climate conditions between Africa, Madagascar, and Reunion island.
SYSTEMATIC ENTOMOLOGY
(2022)
Article
Multidisciplinary Sciences
Michael J. Landis, Ignacio Quintero, Martha M. Munoz, Felipe Zapata, Michael J. Donoghue
Summary: Geographical features have an impact on species dispersal, extinction, and speciation. This study uses a Bayesian hierarchical modeling framework to transform regional features into evolutionary rates. The results show that distance between regions affects dispersal rates and speciation rates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Zoology
Parin Jirapatrasilp, Piyoros Tongkerd, Ekgachai Jeratthitikul, Thor-Seng Liew, Arthit Pholyotha, Chirasak Sutcharit, Somsak Panha
Summary: Members of the terrestrial snail family Dyakiidae from Southeast Asia exhibit distinct geographical distribution patterns and varying degrees of complexity in their amatorial organ gland. A new genus and species, Pseudoquantula lenticularis, was discovered, and mainland Southeast Asia was identified as the ancestral range of Dyakiidae. The study also found that all 14 morphological characters used were homoplastic, and the enigmatic genus Pseudoplecta exhibited secondary loss of the amatorial organ gland.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
Article
Multidisciplinary Sciences
Ignacio Quintero, Michael J. Landis, Walter Jetz, Helene Morlon
Summary: The difference in species abundance between the tropics and the extra tropics is a major pattern in biogeography. Understanding the processes that regulate this diversity gradient is a challenge. By using spatiotemporal phylogenetic and paleontological models, we found that both extinctions in the extra tropics and outflow of tropical species contribute to shaping biodiversity. These dynamics accurately predict present-day levels of species richness across latitudes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Zoology
Pierre-Olivier Antoine, Marian C. Reyes, Noel Amano, Angel P. Bautista, Chun-Hsiang Chang, Julien Claude, John De Vos, Thomas Ingicco
Summary: Rhinos, one of the most endangered mammalian species, have a documented past diversity but their evolutionary history remains unclear. Through a phylogenetic analysis of rhinoceros fossils from the Philippines and Taiwan, we reveal their systematic affinities and dispersal patterns.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biology
Josefin Stiller, Graham Short, Healy Hamilton, Norah Saarman, Sarah Longo, Peter Wainwright, Greg W. Rouse, W. Brian Simison
Summary: By sampling ultraconserved elements and taxon, we reconstructed the phylogeny of syngnathids and discovered previously overlooked species diversity and significant biogeographic patterns. The changes in diversification rates suggest possible links to declining global temperatures, the separation of the Atlantic and Pacific faunas, and associated environmental changes.
Article
Multidisciplinary Sciences
Jamie B. Thompson, Katie E. Davis, Harry O. Dodd, Matthew A. Wills, Nicholas K. Priest
Summary: Although climate change affects diversification, its effects are inconsistent and less widespread than localized climate or species accumulation. This study focuses on highly speciose orchid subfamily and reveals that historic global cooling, not time or other climate factors, drives speciation in terrestrial orchids. With extensive data and analysis, the study demonstrates that global cooling played a significant role in contemporaneous diversification in all major orchid bioregions. This research provides valuable insights into the long-term impacts of global climate change on biodiversity.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Matthew McLean, Rick D. Stuart-Smith, Sebastien Villeger, Arnaud Auber, Graham J. Edgar, M. Aaron MacNeil, Nicolas Loiseau, Fabien Leprieur, David Mouillot
Summary: Research indicates that despite differences in biogeography and evolutionary history, similar environments host reef fish assemblages with similar trait compositions. This suggests that similar trait-based management strategies can be applied across different regions, potentially leading to improved conservation outcomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Nelson Buainain, Marina F. A. Maximiano, Mateus Ferreira, Alexandre Aleixo, Brant C. Faircloth, Robb T. Brumfield, Joel Cracraft, Camila C. Ribas
Summary: This study evaluates the species limits and evolutionary history of Tunchiornis ochraceiceps, a forest songbird, using an integrative approach including plumage coloration, morphometrics, vocalization, and genomic data. The species has a relatively old crown age and comprises several lineages with little evidence of gene flow among them. The research proposes a taxonomic arrangement of four species, including a deeply divergent cryptic species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biology
Rodolfo Salas-Gismondi, Diana Ochoa, Stephane Jouve, Pedro E. Romero, Jorge Cardich, Alexander Perez, Thomas DeVries, Patrice Baby, Mario Urbina, Matthieu Carre
Summary: Fossils from marine deposits in Peru reveal that crocodylians were coastal residents in the southeastern Pacific for approximately 14 million years during the Miocene epoch. The fossil record shows that the evolution of marine crocodylians primarily occurred in gavialids and their stem relatives. Marine gavialoids were shallow sea dwellers and their diversification was influenced by coastal habitats. However, they disappeared from the sea during the Pliocene marine megafauna extinction.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(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
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
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
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)