Article
Microbiology
Jean-Baptiste Leducq, Emilie Seyer-Lamontagne, Domitille Condrain-Morel, Genevieve Bourret, David Sneddon, James A. Foster, Christopher J. Marx, Jack M. Sullivan, B. Jesse Shapiro, Steven W. Kembel
Summary: In two temperate forests, research found that Methylobacterium has considerable diversity on leaf surfaces, influenced by seasonality, geography, and growth strategies. Cultivated at different temperatures, Methylobacterium diversity was impacted by temperature adaptation, large and small-scale geographical factors, host tree species, and seasonal dynamics.
Article
Microbiology
Jean-Baptiste Leducq, Emilie Seyer-Lamontagne, Domitille Condrain-Morel, Genevieve Bourret, David Sneddon, James A. Foster, Christopher J. Marx, Jack M. Sullivan, B. Jesse Shapiro, Steven W. Kembel
Summary: This study discovered a significant diversity of Methylobacterium on plant leaves and demonstrated the biogeographic, seasonal, and growth strategy characteristics of this diversity. The results revealed the temperature adaptation, geographical and seasonal structuring of Methylobacterium diversity. The study also revealed a progressive replacement of lineages with different growth strategies at the end of the growing season.
Article
Biochemistry & Molecular Biology
Cindy Bessey, Yuan Gao, Yen Bach Truong, Haylea Miller, Simon Neil Jarman, Oliver Berry
Summary: Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. This study compares the effectiveness of nine membrane materials for passively collecting fish eDNA and finds that most materials can collect comparable amounts of eDNA and species richness to that of conventional filtering within short periods of submersion. The collected eDNA particles show a diversity in size and structure. This passive approach is cost-effective, time-efficient, and suitable for biological surveys in remote areas or with limited equipment.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Medicine, Legal
Yanlei Liu, Chao Xu, Wenpan Dong, Xueying Yang, Shiliang Zhou
Summary: This study demonstrates how environmental plant DNA metabarcoding technology was used to determine a criminal suspect. By extracting DNA, amplifying genes, sequencing, and bioinformatics analysis, the suspect was successfully identified. This indicates that plant DNA in environmental soil can be a new source of evidence with high potentials for applications in criminal cases.
FORENSIC SCIENCE INTERNATIONAL
(2021)
Article
Biodiversity Conservation
Jan Perret, Oceane Cobelli, Adrien Taudiere, Julien Andrieu, Yildiz Aumeeruddy-Thomas, Jamila Ben Souissi, Guillaume Besnard, Gabriele Casazza, Pierre-Andre Crochet, Thibaud Decaens, Francoise Denis, Philippe Geniez, Michael Loizides, Frederic Medail, Vanina Pasqualini, Claudia Speciale, Vincent Battesti, Pierre Chevaldonne, Christophe Lejeusne, Franck Richard
Summary: The study examines the distribution of biodiversity research efforts within the Mediterranean Basin hotspot and suggests rebalancing sampling efforts towards poorly known regions and using molecular data to refine hotspot definition.
BIOLOGICAL CONSERVATION
(2023)
Article
Plant Sciences
Satbay Nurashov, Gaukhar Jumakhanova, Sophia Barinova, Roman Romanov, Elmira Sametova, Aibek Jiyenbekov, Saule Shalgimbayeva, Thomas Edward Smith
Summary: The research conducted in south and southeast Kazakhstan from 2019 to 2022 aimed to document the species richness, distribution, and ecology of charophytes (Characeae) and estimate the need for species protection. Ten species and one variety were found across 54 sites, with some species being more common and widespread than others. The study also investigated the relationship between environmental variables and species distribution.
Article
Biology
Ahmed M. Hashim, Aishah Alatawi, Faris M. Altaf, Sameer H. Qari, Mohamed E. Elhady, Gamal H. Osman, Heba H. Abouseadaa
Summary: By studying the DNA barcodes of nine endangered endemic plant species, it was found that rbcL, ITS, and ycf1 barcodes were more capable of identifying the genetic relationships among plant species, while SCoT polymorphism could only group plant species belonging to the same genus.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Environmental Sciences
Alfonso Peralbo-Moreno, Sara Baz-Flores, Raul Cuadrado-Matias, Patricia Barroso, Roxana Triguero-Ocana, Saul Jimenez-Ruiz, Cesar Herraiz, Carmen Ruiz-Rodriguez, Pelayo Acevedo, Francisco Ruiz-Fons
Summary: Tick abundance is determined by multiple factors at small spatial scales and understanding these determinants is crucial for effective tick management strategies. The study reveals that tick burdens on wild ungulates in Donana National Park, Spain, are influenced by environment, host population, host individual, and land-use. The findings emphasize the importance of host aggregation areas with favorable traits for ticks as hotspots for tick and vector-borne pathogen transmission.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Maria Eugenia Molina-Paniagua, Pablo Hendrigo Alves de Melo, Santiago Ramirez-Barahona, Alexandre K. Monro, Carlos Manuel Burelo-Ramos, Hector Gomez-Dominguez, Andres Ernesto Ortiz-Rodriguez
Summary: The mountain karst forests of Mexico, occupying 2.07% of the country's land surface, are one of the most diverse biomes in Mexico. They are covered by tropical rainforests, montane cloud forests, and tropical deciduous forests. These forests are vital for global climate regulation and biodiversity conservation.
Review
Chemistry, Multidisciplinary
Junyun Cheng, Jie Liao, Xin Shao, Xiaoyan Lu, Xiaohui Fan
Summary: Barcoding technology has improved throughput in single-cell RNA sequencing studies by reducing processing time and costs. Focus on DNA-based barcoding methods for sample multiplexing, with guidelines for choosing appropriate techniques. Future applications include predicting severity of COVID-19 in patients of different demographics.
Article
Entomology
Haiguang Zhang, Wenjun Bu
Summary: Insecta is the most diverse group in the animal kingdom, and COI gene is commonly used for species delimitation. However, high intra-specific genetic variation in insects can lead to false positives in COI-based species delimitation. The threshOpt and localMinima algorithms in the Spider package are recommended for threshold-based species delimitation studies in insects. More comprehensive research is needed on the genetic variation in COI among Insecta, and the abundant COI data in BOLD provides an opportunity for such assessment.
Article
Biology
Hung-Tai Lee, Cheng-Hsin Liao, Te-Hua Hsu
Summary: This study utilized environmental DNA (eDNA) metabarcoding to identify 153 fish species potentially consumed in fish markets and nearby seafood restaurants, demonstrating the feasibility of large-scale seafood identification using this approach. The results suggest that species diversity in traditional seafood may be seriously underestimated, highlighting the importance for conservation and management of marine resources.
Article
Geography, Physical
Yuemin Yue, Xiangkun Qi, Kelin Wang, Chujie Liao, Xiaowei Tong, Martin Brandt, Bo Liu
Summary: The karst area in southwest China has experienced rapid vegetation growth and improvement in ecological conditions due to ecological protection projects. This study provides scientific evidence that restoration efforts contribute to the mitigation of rocky desertification, as well as increasing vegetation resilience and resistance against climate variations.
PROGRESS IN PHYSICAL GEOGRAPHY-EARTH AND ENVIRONMENT
(2022)
Article
Computer Science, Artificial Intelligence
Yiyuan Fang, Shuyi Deng, Cai Li
Summary: This study presents a deep learning framework, Mutation Rate Learner (MuRaL), to predict mutation rates at the nucleotide level using genomic sequences as input. The results demonstrate that MuRaL outperforms current state-of-the-art methods in predictive performance and can build models with few training mutations and individuals, leveraging transfer learning to reduce data and time demands. MuRaL is applied to generate genome-wide mutation rate maps for representative species and used to stratify human genes into different functional groups based on improved mutation rate estimates.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Geosciences, Multidisciplinary
You Xin Shen, Qing He Wang, Zhi Meng Zhao, Chuang Yuan
Summary: Rock outcrops have significant effects on the adjacent soil and plant communities, particularly on fine scales such as physical and chemical parameters as well as biomass.
Article
Evolutionary Biology
Irene de Sosa, Daniel F. Marchan, Marta Novo, Timea Szederjesi, Misel Jelic, Aleksandra Jablonska, Raul Navarro, Ana Almodovar, Dario J. Diaz Cosin
Summary: Eiseniella neapolitana is a semi-aquatic, diploid earthworm that was previously considered a subspecies of Eiseniella tetraedra. Our study using molecular markers and morphology confirmed the synonymy between Eiseniella and Norealidys. Genetic analyses revealed the separation between E. neapolitana and E. andaluciana (= N. andaluciana), and disproved that E. neapolitana is a subspecies of E. tetraedra.
ORGANISMS DIVERSITY & EVOLUTION
(2023)
Article
Biodiversity Conservation
Khaoula Ayati, Kamil Hupalo, Sonia Dhaouadi, Tomasz Rewicz, Michal Grabowski, Christophe Piscart
Summary: The freshwater fauna of the Mediterranean Basin is facing a crisis due to climate change and overexploitation, and conservation priorities need to be defined. This study used molecular and morphological data to investigate freshwater amphipods in Tunisia and found that their diversity is underestimated. The distribution of amphipods is influenced by precipitation, thermal amplitudes, and precipitation fluctuations, indicating the need for adjusted conservation strategies in the face of climate change.
BIODIVERSITY AND CONSERVATION
(2023)
Review
Environmental Sciences
Jonas Jourdan, Mirco Bundschuh, Denis Copilas-Ciocianu, Cene Fiser, Michal Grabowski, Kamil Hupalo, Anita Jemec Kokalj, Jana Kabus, Joerg Roembke, Laura J. Soose, Joerg Oehlmann
Summary: The use of genetic methods has allowed the discovery of previously undistinguishable species based on morphology. However, these cryptic species are rarely considered in ecotoxicology, which can lead to false extrapolations and lack of reproducibility in experiments. It is crucial to address the ecological differentiation and sensitivity of closely related cryptic species for evolutionary ecology, conservation biology, and regulatory ecotoxicology.
ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY
(2023)
Article
Entomology
Vladimir Pesic, Harry Smit
Summary: In this study, we describe a new species, Monatractides corsicus sp. nov., from Corsica, France, using morphological data and DNA barcodes. The new species is a part of the M. stadleri-complex, which consists of at least four distinct genetic lineages in the Western Palaearctic. Morphologically, the new species can be distinguished by its large palp, thick chelicera, and color pattern on the dorsal shield. Additionally, we provide the first DNA barcoding data for M. latissimus (K. Viets, 1936) and M. lusitanicus (Lundblad, 1941).
INTERNATIONAL JOURNAL OF ACAROLOGY
(2023)
Article
Zoology
Vladimir Pesic, Milica Jovanovic, Amalia Espiridiao Oliveira, Ana Pedro, Marvin Freira, Maria Manuela Morais
Summary: This study presents the first results of DNA barcoding of water mites from Portugal. DNA barcodes were obtained from 19 water mite specimens belonging to eight species, seven of which are newly reported from Portugal. Two species, Torrenticola hispanica and A. cultellatus, were rediscovered after more than 80 years since their first description, and a new species, Atractides marizae sp. nov., is described.
Article
Zoology
Denis Copilas-Ciocianu, Dmitry Palatov, Tomasz Rewicz, Arthur F. Sands, Kestutis Arbaciauskas, Ton Van Haaren, Paul D. N. Hebert, Michal Grabowski, Ivan Marin
Summary: Amphipods in the Ponto-Caspian region have diversified significantly. The taxonomy of Trichogammarus trichiatus, a common invader in European inland waters, has been investigated using an integrative approach. Analyses of DNA markers, measurements, and imaging reveal that T. trichiatus and C. tenellus major are distinct species, with the former being an endemic species in the Caucasus and the latter being an invader in Europe. Furthermore, T. trichiatus is unexpectedly nested within Chaetogammarus ischnus, despite morphological and geographical differences. The study also reassigns T. trichiatus to Chaetogammarus and establishes a new genus, Spirogammarus, for C. tenellus major.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Entomology
Vladimir Pesic, Harry Smit, Ekaterina S. Konopleva
Summary: This study provides the first calibrated phylogeny of the Hygrobates fluviatilis-complex, revealing that its most recent common ancestor originated in the Oligocene. Phylogenetic and dating analyses show three monophyletic lineages within this complex, with the earliest branching lineage being the H. turcicus-clade. The diversification and speciation processes started from the Oligocene-Miocene and continued during the Miocene. Evidence of multiple colonization of Corsica and the presence of two endemic lineages, H. corsicus and H. cyrnusensis sp. nov., were also found in this study.
Article
Agriculture, Dairy & Animal Science
Rafal Maciaszek, Wieslaw Swiderek, Sebastian Prati, Chih-Yang Huang, Kamil Karaban, Anita Kaliszewicz, Aleksandra Jablonska
Summary: This study reports the discovery of epibiotic species associated with Neocaridina davidi shrimp collected from the wild, aquaculture ponds, and aquaria. Among 900 imported shrimp from Taiwan, three-quarters of them host at least one of the recorded epibionts. Two new species, Cladogonium kumaki sp. nov. and Monodiscus kumaki sp. nov., were found, along with the redescriptions of Holtodrilus truncatus and Scutariella japonica. The highest number of epibionts is found in shrimp from aquaculture ponds, while the lowest is found in individuals from aquaria. The occurrence of epibionts differs across designated microhabitats. Their presence may affect shrimp breeding rates, thus requiring more control measures.
Article
Biodiversity Conservation
Tomasz Rewicz, Grzegorz Tonczyk, Lukasz Trebicki, Piotr Gadawski, Tomasz Mamos, Vladimir Pesic, Andrzej Zawal, Michal Grabowski
Summary: Lake Skadar and its surrounding areas are highly diverse freshwater ecosystems in the Mediterranean region and are crucial for biodiversity conservation in Europe. However, they are facing threats from climate change and rapid tourism development. This study provides the first comprehensive DNA barcode library for aquatic Heteroptera in the area and reveals potential taxonomic inconsistencies and cryptic diversity. It emphasizes the need for more research in understudied hotspots like Lake Skadar and highlights the value of DNA-barcoding-based surveys for biomonitoring and taxonomy.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Zoology
Harry Smit, Vladimir Pesic
Article
Zoology
Andrzej Zawal, Aleksandra Bankowska, Maja Krakowiak, Zuzanna Krzynowek, Vladimir Pesic, Grzegorz Michonski
Article
Environmental Sciences
Monika Mysliwy, Vladimir Pesic
Summary: River valleys, although valuable, are heavily influenced by human activities. This study conducted the first detailed investigation of tall herb communities in riverside vegetation in Montenegro. The variability of vegetation was found to be related to land use type and river size.
Article
Entomology
Harry Smit, Vladimir Pesic
Summary: This article describes two new species of the genus Anisitsiellides from Australia and provides a key for the Australian Anisitsiellides species. One of the new species has a dorsal shield with five pairs of glandularia, which requires an emendation of the genus diagnosis.
Article
Entomology
Tapas Chatterjee, Ajaz Ali Ahmed Khan, Ravail Singh, Malcolm Vidrine, Andrzej Zawal, Vladimir Pesic
Summary: This study presents a new host record of Unionicola (Myanamaratax) savadiensis from Lamellidens corrianus in India. The study also found associations between U. savadiensis and two other mussel species, Lamellidens marginalis and Corbicula cashmiriensis, but DNA evidence confirms the parasite-host relationship between U. (M.) savadiensis and L. corrianus. This report highlights the importance of interdisciplinary collaboration to understand the nature of mite-mussel associations.
Article
Entomology
Harry Smit, Vladimir Pesic, Nathalie J. Mary
Summary: This article presents new records of water mites from La Reunion Island, including one newly discovered species and one species reported for the first time on the island.