Article
Entomology
Yihong Qu, Bo Wang, Jianqiang Deng, Yakai Feng, Zhiyun Pi, Lipin Ren, Jifeng Cai
Summary: Forensic entomology plays a unique role in estimating the minimum postmortem interval of decomposed corpses in forensic investigations. This study investigated the community structure of necrophagous flies on Hainan Island and established a GenBank database for species identification. The use of high-resolution melt curve analysis proved to be a fast and cost-effective method for species identification. It enriches the database of forensically important flies in tropical rainforest regions.
Article
Plant Sciences
Ria Cahyaningsih, Lindsey Jane Compton, Sri Rahayu, Joana Magos Brehm, Nigel Maxted
Summary: DNA barcoding has emerged as a scientific breakthrough in plant identification and conservation, especially in the field of medicinal plants. This study focused on analyzing the effectiveness of different DNA barcoding regions for Indonesian medicinal plant identification, with matK being recommended as the main region. Findings from this study have implications for forensic studies and the conservation of medicinal plants on a national and global scale.
Article
Ecology
Rachel Dobson, Andy J. J. Challinor, Robert A. A. Cheke, Stewart Jennings, Stephen G. G. Willis, Martin Dallimer
Summary: Species distribution models (SDM) are widely used to understand species distribution and abundance changes. However, existing SDM tools lack the ability to model species distributions driven by dynamic environmental conditions. dynamicSDM provides novel tools that consider the temporal dimension, allowing for more accurate and detailed modeling. It is flexible, compatible with other SDM tools, and has low computing power and storage needs.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Ecology
Stefan Pinkert, Vijay Barve, Rob Guralnick, Walter Jetz
Summary: This study presents a comprehensive data product of the geographic distributions of extant butterflies, based on literature sources and occurrence records. The database provides insights into the richness and latitudinal gradients of butterfly diversity, highlighting the importance of leveraging multiple distribution information for ecological and conservation analysis.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2022)
Article
Ecology
Santiago Jose Elias Velazco, Miranda Brooke Rose, Andre Felipe Alves de Andrade, Ignacio Minoli, Janet Franklin
Summary: Species distribution models (SDM) have been widely used due to their simplicity and versatility. However, SDM outcomes are sensitive to data input and methodological choices. To address this issue and meet different modeling needs, we present flexsdm, a package that supports flexible species distribution modeling workflows.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Manuele Bazzichetto, Jonathan Lenoir, Daniele Da Re, Enrico Tordoni, Duccio Rocchini, Marco Malavasi, Vojtech Bartak, Marta Gaia Sperandii
Summary: The aim of this study was to assess how different sampling strategies affect the accuracy and precision of species response curves estimated by parametric species distribution models. The researchers simulated the occurrence of virtual plant species in Italy, using various sampling strategies, and compared the results to true coefficients. The study found that uniformly sampling the environmental space provided the best results for generalist species, while sampling occurrence data close to roads had the worst performance. For specialist species, all sampling designs showed comparable outcomes.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Biodiversity Conservation
Tomasz H. Szymura, Henok Kassa, Grzegorz Swacha, Magdalena Szymura, Adam Zajac, Zygmunt Kacki
Summary: This study compared two different data sources and found that the vegetation plot database underestimated species richness but provided additional information. This underestimation could result from limited sampling effort or focusing on particular vegetation types.
ECOLOGICAL INDICATORS
(2023)
Article
Environmental Sciences
Tomasz H. Szymura, Dominika Chmolowska, Magdalena Szymura, Adam Zajqc, Henok Kassa
Summary: One of the challenges in modelling biological invasion is the lack of valid data on the absence of invasive species. The presence of biased squares, which can be determined by environmental factors, can affect the performance of invasion models. By excluding biased squares, the performance of invasion models can be improved.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Food Science & Technology
Kingdow Chanachot, Wanphut Saechua, Jetsada Posom, Panmanas Sirisomboon
Summary: The objective of this research was to classify the geographical origin of durians using near infrared spectroscopy. Effective models were developed by scanning samples from different parts of the fruit and optimizing the classification algorithms. The results demonstrate that near infrared spectroscopy can be used as a rapid and accurate method for geographical identification of durians.
Article
Environmental Sciences
Gang Wang, Xuanjiao Bai, Ying Ren, Yuying Su, Jianping Han
Summary: DNA barcoding is widely used for toxic species identification, but the degradation of DNA in forensic materials limits the use of full-length barcode sequences in food poisoning diagnosis. This study proposes the use of nucleotide signature, a shorter molecular marker derived from DNA barcoding, for the detection of toxic species in deeply processed materials. The nucleotide signatures were developed and validated as specific molecular markers for common poisonous organisms through sequence alignment and screening. High-throughput sequencing (HTS) was used to reveal the poisoning cause in simulated forensic specimens (SFS), demonstrating the successful capture of nucleotide signatures from original HTS data. The method showed a high detection sensitivity and suitability for forensic materials with serious DNA degradation.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Entomology
Nicolai Olenici, Mihai-Leonard Duduman, Ionel Popa, Gabriela Isaia, Marius Paraschiv
Summary: Biological invasions in European forests are increasing, with bark- and wood-boring insects being significant pests. Global trade intensification and climate change contribute to their introduction and spread. This study aimed to investigate the distribution of three invasive beetle species in Romania using different traps. Ips duplicatus was found to be established in most parts of Norway spruce's range, Xylosandrus germanus is spreading with high populations in certain areas, while Neoclytus acuminatus is only present in warmer regions.
Article
Agriculture, Multidisciplinary
Chen Xiao-ling, Ning Dong-dong, Xiao Qian, Jiang Qiu-ying, Lu Yong-yue, Xu Yi-juan
Summary: This study analyzed the distributional trends of invasive species in China and identified the drivers for such trends. The results showed that the abundance of invasive species gradually decreased from south to north and from southeast coast to inland. The value of imports was found to be a strong predictor of the number of invasive species in China.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Multidisciplinary Sciences
Chao Ye, Huiyuan Liu, Haining Qin, Jiangping Shu, Zhihua Zhou, Xiaohua Jin
Summary: National key protected wild plants (NKPWPs) are important for plant diversity conservation in China. Distribution patterns of NKPWPs were examined using data for 1101 species, revealing hotspot areas and conservation gaps. Although a significant percentage of NKPWPs are protected within national nature reserves, many species and their habitats remain outside of these protected areas.
Article
Agronomy
Wei Xu, Yuqi Miao, Shuaimeng Zhu, Jimin Cheng, Jingwei Jin
Summary: This study used three software to simulate the potential distribution and range shifts of apple trees in the near future. The results showed that the distribution range of apple trees may shift to the northwest considering various environmental factors. This study provides important evidence for future policy making.
Article
Ecology
Daniel Lukic, Jonas Eberle, Jana Thormann, Carolus Holzschuh, Dirk Ahrens
Summary: The study investigates the performance of various species delimitation approaches on herbivorous chafer beetles under absence of geographic sampling bias, pointing out the discrepancies between morphospecies and molecular operational taxonomic units (MOTUs) may be explained by historical acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The importance of morphology in correctly interpreting the results of molecular species delimitation is highlighted once again.
ECOLOGY AND EVOLUTION
(2021)
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)
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)
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.
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
Raees Khan, Robert S. S. Hill, Jie Liu, Ed Biffin
Summary: Podocarpaceae is the second largest conifer family with diverse and functional traits, dominating the Southern Hemisphere. However, comprehensive studies on its diversity, distribution, systematics, and ecophysiological aspects are lacking. This study aims to outline and evaluate the current and past diversity, distribution, systematics, ecophysiological adaptations, endemism, and conservation status of podocarps. Through analyzing data on living and extinct macrofossil taxa and combining it with genetic data, an updated phylogeny is reconstructed and historical biogeography is understood. Podocarpaceae includes 20 genera and approximately 219 taxa, distributed in three clades, and shows remarkable adaptations from leaves to seeds, dispersal methods, and plant types, as well as a complex pattern of seed and leaf functional trait evolution.
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
Biochemistry & Molecular Biology
Zhi-Qiong Mo, Jie Wang, Michael Moller, Jun-Bo Yang, Lian-Ming Gao
Summary: Accurate species identification is crucial for conservation and phylogenetic inference. This study used DNA barcodes to test the proportion of misidentified cultivated plants in botanical gardens. The findings highlight the importance of proper species identification in scientific research and conservation efforts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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)