Article
Plant Sciences
Mohammed Al-Dakhil, Salem Alghamdi, Hussein Migdadi, Muhammad Afzal, Ahmed Abdelrahim Ali
Summary: This study investigated ten duckweed isolates from different regions in Saudi Arabia and identified Lemna gibba as a dominant species in many regions, with L. gibba, L. minor, and L. punctata being the most widely distributed species in the country. Variations in morphological traits were observed among the clones, suggesting potential diversity within the duckweed species in the studied areas. Further research on adaptability, molecular genetics, and functional genomics is needed for the commercial utilization of these species in Saudi Arabia.
Article
Microbiology
Jiayuan Qin, Yu Feng, Xiaoju Lu, Zhiyong Zong
Summary: This study identified two novel Acinetobacter species, corrected the classification of two strains previously thought to be different species, and curated 56 new tentative species, expanding the total number of Acinetobacter species to 144. The study also found that Acinetobacter is indeed a single genus despite the large number of species, highlighting the importance of precise species identification in bacterial taxonomy.
Article
Microbiology
Zhiqin Wang, Yao Wang, Quanying Dong, Qi Fan, Van-Minh Dao, Hong Yu
Summary: This study reports five new species of the important fungal resource Samsoniella, providing morphological descriptions, phylogenetic placements, associated hosts, and comparisons with allied taxa. These new species were determined to be located in the clade of Samsoniella and had similar morphologies to other species in the genus.
Article
Multidisciplinary Sciences
Caitriona Brady Halmschlag, Carina Carneiro de Melo Moura, Fabian Brambach, Iskandar Z. Siregar, Oliver Gailing
Summary: Molecular biodiversity surveys are valuable tools for rapid species assessment in tropical regions. This study applied morphological taxonomy and DNA barcoding to assess Lamiaceae species in converted land-use systems in Sumatra, Indonesia, and found that changes in species composition are associated with land-use intensification. Conservation of forest genetic resources and accurate species identification are important for sustainable agricultural production and conservation planning.
Article
Ecology
Wenzhu Lu, Shimiao Shao, Lingling Zu, Xu Luo, Yubao Duan
Summary: By characterizing the body morphology and beak shape of six species of Aethopyga birds in China, it was found that the main distinguishing characteristics included body size, body weight ratio, beak and tarsal length ratio, tail length, wing length, and beak shape (slender/straight vs. thick/decurved). No significant phylogenetic signals were found in the morphological traits. Altitude was significantly correlated with beak shape and tarsus length. The distance matrix of beak morphological characteristics showed a significant correlation with the altitudinal distance matrix.
ECOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
Hui Shang, Zhi-Qing Xue, Zhen-Long Liang, Michael Kessler, Rossarin Pollawatn, Ngan Thi Lu, Yu-Feng Gu, Xue-Ping Fan, Yun-Hong Tan, Liang Zhang, Xin-Mao Zhou, Xia Wan, Li-Bing Zhang
Summary: Based on an expanded taxon sampling and six molecular markers, a new phylogeny is reconstructed for the fern genus Didymochlaena. The study reveals the differentiation of Didymochlaena into a New World clade and an Old World clade, with further subdivisions into an African clade and an Asian-Pacific clade. It also recognizes 22 species in the genus, highlighting the diversity and evolution of this important fern lineage.
Article
Multidisciplinary Sciences
Vinodh Kandavalli, Praneeth Karempudi, Jimmy Larsson, Johan Elf
Summary: The authors present a method for performing phenotypic antibiotic susceptibility testing at the single-cell level using a microfluidic chip, allowing for subsequent genotyping with in situ FISH. They demonstrate its application in a mixed sample of seven species and four antibiotics.
NATURE COMMUNICATIONS
(2022)
Article
Agricultural Engineering
Xinran Chong, Yunlong Li, Minlei Yan, Yue Wang, Mingzhi Li, Yanwei Zhou, Hong Chen, Xiaoqing Lu, Fan Zhang
Summary: The genus Ilex includes economically important ornamental and medicinal plant species. This study describes the complete chloroplast genome sequences of three Ilex species and develops DNA barcodes for species identification. The findings provide resources for further research on the identification, genetic engineering, evolution, and phylogeny of Ilex species.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Microbiology
Xiao-Yun Ou, Yuan-Yuan Shao, Hai-Fu Zheng, Bin Liu
Summary: This study reports the discovery of four new species and three new record species of Orbiliaceous fungi from China. The identification was done based on morphological characteristics and phylogenetic analysis of genetic sequences. The study also compared and discussed the differences between these new species and their close relatives.
Article
Plant Sciences
Hoi-Yan Wu, Kwan-Ho Wong, Bobby Lim-Ho Kong, Tin-Yan Siu, Grace Wing-Chiu But, Stacey Shun-Kei Tsang, David Tai-Wai Lau, Pang-Chui Shaw
Summary: The pantropical genus Dalbergia consists of 269 species of trees, shrubs, and woody lianas. Due to illegal logging and trafficking driven by the high economic value of its heartwood, this genus is listed in CITES Appendices. However, species identification of Dalbergia timber and herbs is challenging but essential for CITES implementation. In this study, the chloroplast genomes of five Dalbergia species native to Hong Kong, including four medicinal plants, were sequenced and analyzed. Four divergence hotspots in the chloroplast genomes were identified as potential genetic markers for the identification of medicinal Dalbergia species.
Article
Microbiology
Jize Xu, Yi Jiang, Tiantian Wang, Di Zhang, Xiaobin Li, Md. Iqbal Hosen
Summary: Four new species of Agaricales from China, namely Hohenbuehelia tomentosa, Rhodophana qinghaiensis, Rhodophana aershanensis, and Spodocybe tomentosum, are described based on their unique morphological features and molecular evidence. Full descriptions, illustrations, and phylogenetic trees of the four new species are provided in this study.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xavier Arnan, Elena Angulo, Raphael Boulay, Roberto Molowny-Horas, Xim Cerda, Javier Retana
Summary: This study aimed to examine the climatic niche similarity in native and introduced ant species in Europe, and found a strong phylogenetic signal in the optimal climatic niches of the most common ant species in Europe. Introduced species occupied different climatic niches in Europe compared to their native ranges, and their European climatic niches did not resemble those of their closest relative species in Europe.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Guoping Ma, Shuwen Bao, Juan Zhao, Yuan Sui, Xuehong Wu
Summary: The study identified six Alternaria species associated with watermelon leaf blight in China, with A. tenuissima being the most prevalent. Notably, A. infectoria, A. gaisen, and an unclassified Alternaria species were reported as causal agents of leaf blight on watermelon for the first time globally.
Article
Plant Sciences
Yu-Hang Chang, Gang Yao, Jens Neilsen, De-Tuan Liu, Lu Zhang, Yong-Peng Ma
Summary: A new species of Rhododendron, Rhododendron kuomeianum, from Yiliang County, NE Yunnan, China is described and illustrated. Phylogenomic studies confirmed its relationship with other species and highlighted the utility of next-generation sequencing in resolving taxonomic problems in plants.
Article
Microbiology
Jiun-Nong Lin, Chung-Hsu Lai, Shang-Yi Lin, Ching-Chi Lee, Nan-Yao Lee, Po-Yu Liu, Chih-Hui Yang, Yi-Han Huang
Summary: This study evaluated the impact of intraspecific diversity among the multiple copies of the 16S rRNA gene on the accuracy of species identification in the genus Elizabethkingia. The results suggest that 16S rRNA gene sequencing should not be considered the gold standard for the accurate identification of Elizabethkingia species.
MICROBIOLOGY SPECTRUM
(2022)
Article
Psychology, Biological
Monica Tromp, Elizabeth Matisoo-Smith, Rebecca Kinaston, Stuart Bedford, Matthew Spriggs, Hallie Buckley
NATURE HUMAN BEHAVIOUR
(2020)
Article
Anthropology
Charlotte L. King, Hallie R. Buckley, Peter Petchey, Rebecca Kinaston, Andrew Millard, Jana Zech, Patrick Roberts, Elizabeth Matisoo-Smith, Geoff Nowell, Darren R. Grocke
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2020)
Article
Multidisciplinary Sciences
Barbara Pena-Ahumada, Monica Saldarriaga-Cordoba, Olga Kardailsky, Ximena Moncada, Mauricio Moraga, Elizabeth Matisoo-Smith, Daniela Seelenfreund, Andrea Seelenfreund
Article
Multidisciplinary Sciences
E. Lord, C. Collins, S. deFrance, M. J. LeFebvre, F. Pigiere, P. Eeckhout, C. Erauw, S. M. Fitzpatrick, P. F. Healy, M. F. Martinez-Polanco, J. L. Garcia, E. Ramos Roca, M. Delgado, A. Sanchez Urriago, G. A. Pena Leon, J. M. Toyne, A. Dahlstedt, K. M. Moore, C. Laguer Diaz, C. Zori, E. Matisoo-Smith
SCIENTIFIC REPORTS
(2020)
Review
Biology
S. K. McDonald, E. A. Matisoo-Smith, H. R. Buckley, R. K. Walter, H. L. Aung, C. J. Collins, G. M. Cook, O. Kardailsky, J. Krause, M. Knapp
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Ecology
A. L. van der Reis, A. G. Jeffs, S. D. Lavery
MARINE ECOLOGY PROGRESS SERIES
(2020)
Article
Ecology
Sarah J. Withers, Stuart Parsons, Mark E. Hauber, Alistair Kendrick, Shane D. Lavery
Summary: This research examined the genetic population divergence in the North Island Rifleman, revealing several significantly divergent lineages across New Zealand's North Island and indicating isolated populations for extended periods. Modeling suggested a dynamic history of population connectivity with constraints on gene flow between regions but recent re-establishment of connectivity.
ECOLOGY AND EVOLUTION
(2021)
Article
Marine & Freshwater Biology
Vanessa Arranz, Vibha Thakur, Shane D. Lavery
Summary: Two unresolved questions in marine population connectivity are addressed by studying two species from New Zealand's rocky shore. The species with greater dispersal potential exhibited greater population differentiation, highlighting the potential for different population structure patterns even among species along the same coast.
Article
Biochemistry & Molecular Biology
Kate D. Lee, Craig D. Millar, Patricia Brekke, Annabel Whibley, John G. Ewen, Melanie Hingston, Amy Zhu, Anna W. Santure
Summary: Next-generation sequencing technology has revolutionized ecological and evolutionary genetics, enabling cost-effective identification of genome-wide variation. In this study, researchers developed a 50K SNP chip for the threatened species hihi by combining RAD-seq and WGS data, demonstrating its utility in identifying SNPs for genotyping and revealing high rates of linkage disequilibrium in the hihi genome, indicative of population bottleneck events.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Anastasija Zaiko, Paul Greenfield, Cathryn Abbott, Ulla von Ammon, Jaret Bilewitch, Michael Bunce, Melania E. Cristescu, Anthony Chariton, Eddy Dowle, Jonathan Geller, Alba Ardura Gutierrez, Mehrdad Hajibabaei, Emmet Haggard, Graeme J. Inglis, Shane D. Lavery, Aurelija Samuiloviene, Tiffany Simpson, Michael Stat, Sarah Stephenson, Judy Sutherland, Vibha Thakur, Kristen Westfall, Susanna A. Wood, Michael Wright, Guang Zhang, Xavier Pochon
Summary: Advances in high-throughput sequencing technology are changing marine monitoring by enabling rapid and accurate detection of species in complex samples. An international experiment showed that while there was variation in results from different laboratories, the primary signal in the data was consistent, with samples grouping by geographical origin. Post hoc data clean-up, such as removing low-quality samples, improved sample classification accuracy significantly.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Environmental Sciences
Vanessa Arranz, Rachel M. Fewster, Shane D. Lavery
Summary: Comparative phylogeography in New Zealand waters reveals consistent genetic divergence patterns among species, highlighting common barriers to marine dispersal. Differences in genetic barriers among species may be more associated with habitat type and marker type rather than dispersal traits.
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2021)
Article
Biodiversity Conservation
Vanessa Arranz, Rachel M. Fewster, Shane D. Lavery
Summary: This study proposes a new method for comparative multi-species meta-analysis of published population genetic data. It uses a genogeographic clustering technique to capture common spatial patterns of genetic diversity among species and enables statistical comparison of these patterns. The method provides a novel approach to discern multiple common spatial patterns and allows for more rigorous comparative studies from diverse published data.
DIVERSITY AND DISTRIBUTIONS
(2022)
Article
Ecology
Priscila M. Salloum, Anna W. Santure, Shane D. Lavery, Pierre de Villemereuil
Summary: Genome scans are powerful tools to understand genetic adaptation to future environmental conditions. However, low gene flow and population structure can lead to errors in these scans. This study compared different methods and identified candidate loci associated with environmental factors in a marine mollusc. The results highlight the importance of careful statistical controls in genome scans and suggest that further research is needed to determine the potential of non-model species to adapt to future environments.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Fisheries
Ahmad Farhadi, Florian Pichlmueller, Bhargavi Yellapu, Shane Lavery, Andrew Jeffs
Summary: Genome-wide SNP typing can improve the management of marine species. In this study, the spiny lobster in the Indo-Pacific region was investigated. The results reveal a genetic break between populations in northern Australia and South East Asia, with significant implications for future fisheries management and aquaculture development.
ICES JOURNAL OF MARINE SCIENCE
(2022)
Article
Ecology
Angela McGaughran, Libby Liggins, Katharine A. Marske, Michael N. Dawson, Lauren M. Schiebelhut, Shane D. Lavery, L. Lacey Knowles, Craig Moritz, Cynthia Riginos
Summary: This article discusses the opportunities and challenges of comparative phylogeography in the genomic age, highlighting the importance of collecting co-distributed species and accruing species-specific ecological knowledge, as well as the availability of bioinformatic skills and user-friendly analytical tools for genomic data analysis.
JOURNAL OF BIOGEOGRAPHY
(2022)