Article
Genetics & Heredity
Gizem Kaya, Chisom Ezekannagha, Dominik Heider, Georges Hattab
Summary: Sustained efforts in next-generation sequencing technologies are changing the field of taxonomy. In order to support evolutionary and taxonomic studies, researchers have developed an interactive web tool called Context-Aware Phylogenetic Trees (CAPT). This tool enhances the traditional phylogenetic tree view with taxonomic icicle view, providing context and interactive techniques for exploring and validating the data.
FRONTIERS IN GENETICS
(2022)
Article
Biodiversity Conservation
Daijiang Li
Summary: Despite the availability of phylogenetic hypotheses for many taxonomic groups, most do not include all species. In phylogenetic ecology, there is a demand for phylogenies that encompass all species in a study. Existing software tools for grafting species to megatrees are limited to specific taxonomic groups. The new R package 'rtrees' aims to provide an easy, flexible, and reliable way to assemble phylogenies from megatrees, facilitating progress in phylogenetic ecology.
Article
Biochemical Research Methods
Yasamin Tabatabaee, Kowshika Sarker, Tandy Warnow
Summary: This article presents Quintet Rooting (QR), a method for rooting species trees based on a proof of identifiability of the rooted species tree under the multi-species coalescent model. The method is shown to be generally more accurate than other rooting methods, except under extreme levels of gene tree estimation error.
Article
Microbiology
Vanessa Nascimento Brito, Janaina Lana Alves, Kaliane Sirio Araujo, Tiago de Souza Leite, Casley Borges de Queiroz, Olinto Liparini Pereira, Marisa Vieira de Queiroz
Summary: In this study, 30 endophytic Trichoderma isolates obtained from wild Hevea spp. in the Brazilian Amazon were analyzed. The analysis revealed known Trichoderma species as well as four new species. This study contributes to our understanding of the diversity of endophytic Trichoderma species in Neotropical forests and identifies potential biocontrol agents for plant disease management.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Zoology
Emmanouela Karameta, Petros Lymberakis, Heinz Grillitsch, Cetin Ilgaz, Aziz Avci, Yusuf Kumluta, Kamil Candan, Philipp Wagner, Spyros Sfenthourakis, Panayiotis Pafilis, Nikos Poulakakis
Summary: Situated in the Eastern Mediterranean, the region offers an ideal setting to study the effects of palaeogeography, ecology, and long human presence on animal evolution. The study on Laudakia stellio reveals its high morphological variation and suggests that it represents three distinct evolutionary entities. The research also highlights the role of humans in shaping the present distribution patterns and the importance of specific areas as refugia and diversity hotspots.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Microbiology
Mei-Xiang Li, Gang Wu, Zhu L. Yang
Summary: In this study, four new species of the genus Hemileccinum were identified based on morphological and molecular evidence, expanding the diversity within the genus. The study also provided insights into the pileipellis structure and basidiospore surface characteristics of the studied species.
Article
Microbiology
Xiu-Lan Xu, Fei-Hu Wang, Chao Liu, Han-Bo Yang, Zhen Zeng, Bao-Xin Wang, Ying-Gao Liu, Chun-Lin Yang
Summary: This study investigated the fungi associated with three walnut species in Sichuan province and identified ten fungi, including two new species. The findings contribute to updating the checklist of fungi associated with Sichuan walnuts and provide important insights.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Naoki Konno, Yusuke Kijima, Keito Watano, Soh Ishiguro, Keiichiro Ono, Mamoru Tanaka, Hideto Mori, Nanami Masuyama, Dexter Pratt, Trey Ideker, Wataru Iwasaki, Nozomu Yachie
Summary: This study proposes a deep distributed computing framework, FRACTAL, for inferring large-scale cell lineages. The framework constructs lineages from a large number of input sequences through recursive iteration, significantly enhancing scalability, and demonstrates its utility in different experiments.
NATURE BIOTECHNOLOGY
(2022)
Article
Microbiology
Mingzhen Ma, Yuqing Li, Qingxiang Yuan, Xuetong Zhao, Khaled A. S. Al-Rasheid, Jie Huang, Honggang Ma, Xiangrui Chen
Summary: This study investigated the morphological and molecular characteristics of four suctorian ciliates collected from a freshwater lake in Ningbo, China. Phylogenetic analysis revealed that they belong to three monophyletic suctorian orders, with the family Heliophryidae now being transferred from Evaginogenida to Endogenida based on evidence of endogenous budding reproduction by the type genus Heliophrya.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Tong-Kai Zong, Heng Zhao, Xiao-Ling Liu, Li-Ying Ren, Chang-Lin Zhao, Xiao-Yong Liu
Summary: Four new species within the genus Absidia, characterized by unique morphological traits and molecular evidence, are proposed in this study. Phylogenetic analyses based on rDNA sequences supported the novelty of these species. An identification key to all known Absidia species in China is provided, along with illustrations of the new species.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Forestry
Chang Xu, Zhi-Qun Liang, Ming-Sheng Su, Shuai Jiang, Yun Chen, Yu-Guang Fan, Nian-Kai Zeng
Summary: Austroboletusbrunneisquamus, a newly described species from a tropical rainforest in China, is characterized by its scaly pileal surface and fine cristate ornamentation on basidiospores.
Article
Plant Sciences
Fabio Conti, Christoph Oberprieler, Marco Dorfner, Erik Schabel, Fabrizio Bartolucci
Summary: This article describes a new subspecies, Pedicularis rostratospicata subsp. marsica, based on morphological and molecular analyses. The new taxon is endemic to specific locations within the Abruzzo, Lazio and Molise National Park in Central Italy. It can be distinguished from the other two accepted subspecies by its taller stems, shorter petioles, narrower basal leaf blades, longer inflorescences with more flowers, and longer calyx lobes. Molecular analysis confirms the distinctiveness of the new taxon. The article also proposes and discusses the conservation status assessment of the new subspecies and provides an analytical key for the three subspecies of P. rostratospicata.
Article
Plant Sciences
Eugeny Boltenkov, Elena Artyukova, Anna Trias-Blasi
Summary: This study revised the taxonomy of Iris subser. Chrysographes through molecular and morphological studies, confirming its monophyletic nature and identifying four distinct lineages within the group. Additionally, it provided a revised taxonomic treatment and an identification key for the species in this group.
Article
Microbiology
Kanad Das, Aniket Ghosh, Dyutiparna Chakraborty, Sudeshna Datta, Ishika Bera, Ranjith Layola Mr, Farheen Banu, Alfredo Vizzini, Komsit Wisitrassameewong
Summary: Through morphological and molecular phylogenetic studies, it has been discovered that European and American names of wild mushrooms were often mistakenly applied to Asian lookalikes in the past. Consequently, taxonomical research on wild mushrooms has been intensified in Asian countries, including India, in recent years to reveal the true mushroom diversity. In this study, four new species and two species new to India were identified and established based on morphology and molecular phylogeny.
Article
Multidisciplinary Sciences
Bine Xue, Yun-Yun Shao, Chun-Fen Xiao, Ming-Fai Liu, Yongquan Li, Yun-Hong Tan
Summary: Meiogyne oligocarpa sp. nov. is a newly described species from Yunnan Province in Southwest China, distinguished by its unique characteristics and confirmed through a phylogenetic analysis. Additionally, paraffin sectioning was conducted to study the specific structures on its inner petals.
Article
Fisheries
Ingo S. Wehrtmann, Dayan Hernandez-Diaz, Neil Cumberlidge
LATIN AMERICAN JOURNAL OF AQUATIC RESEARCH
(2019)
Article
Marine & Freshwater Biology
Savel R. Daniels, Theo Busschaul, Neil Cumberlidge
JOURNAL OF CRUSTACEAN BIOLOGY
(2019)
Article
Environmental Sciences
Louisa E. Wood, Sammy De Grave, Neil Cumberlidge, Adam Kennerley, Savel R. Daniels
AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS
(2019)
Article
Zoology
Fengxin Yao, Boyang Shi, Xiaoqi Wang, Da Pan, Ming Bai, Jie Yan, Neil Cumberlidge, Hongying Sun
INTEGRATIVE ZOOLOGY
(2020)
Article
Biodiversity Conservation
Tim Caro, Haji Hamad, Rashid Suleiman Rashid, Ulrike Kloiber, Victoria M. Morgan, Ossi Nokelainen, Barnabas Caro, Ilaria Pretelli, Neil Cumberlidge, Monique Borgerhoff Mulder
Summary: The coconut crab, the largest terrestrial decapod, is threatened by habitat destruction and overharvesting due to human activities. Research has shown that larger subpopulations are found in areas with crops and away from human activities, while the largest adult coconut crabs are located on more remote islands and in areas where they are not exploited. Protection and remote locations offer hope for the survival of this species, with opportunities for conservation through community involvement and tourism revenue.
Article
Marine & Freshwater Biology
Neil Cumberlidge, Julia B. Soma, Ellen M. Leever, Savel R. Daniels
JOURNAL OF CRUSTACEAN BIOLOGY
(2020)
Article
Ecology
Boyang Shi, Da Pan, Yufang Sun, Xiaorui Liu, Xiulin Lv, Neil Cumberlidge, Hongying Sun
Summary: This study explores how past regional climatic differences have influenced the biogeographic history of endemic freshwater crabs in China. By studying the Sinopotamon yangtsekiense species complex, researchers found that divergence of crab lineages across the Qinling Mountains-Huaihe River Line was linked to significant past variations in monsoon intensity and the location of multiple refuges. The phylogeographical isolation observed in these crabs today is a result of different populations being isolated in separate refuges during the Last Glacial Maximum.
JOURNAL OF BIOGEOGRAPHY
(2021)
Article
Zoology
Pierre A. Mvogo Ndongo, Thomas von Rintelen, Neil Cumberlidge
Summary: A new species of freshwater crab genus Potamonemus was described in this study, with distinguishing characteristics of the carapace and chelipeds. Phylogenetic analysis based on mitochondrial DNA genes confirmed the new species as a distinct lineage. The study also compared the new species to existing species of Potamonemus and discussed the conservation status of the genus.
Article
Infectious Diseases
Muriel Rabone, Joris Wiethase, Paul F. Clark, David Rollinson, Neil Cumberlidge, Aidan M. Emery
Summary: Paragonimiasis is a neglected disease caused by zoonotic trematodes of Paragonimus spp., particularly in Africa. Recent transmission was found in Southeast Nigeria, Cote d'Ivoire, and Cameroon, with higher prevalence of P. uterobilateralis than P. africanus. More studies are urgently needed to determine the distribution and diversity of Paragonimus species in Africa.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Zoology
Neil Cumberlidge, Pierre A. Mvogo Ndongo, Paul F. Clark
Summary: The taxonomic status of the freshwater crab Sudanonautes granulatus in West and Central Africa has been revised to reveal that it consists of at least 4 species. Diagnoses, illustrations, and distribution maps are provided for these species and compared with congeners in the region.
Article
Plant Sciences
Neil Cumberlidge, Emily Johnson, Paul F. Clark, Martin J. Genner
Summary: The taxonomic status of the freshwater crab Potamonautes lirrangensis sensu lato has been revised to identify four separate species, based on morphological and molecular evidence. These species include P. lirrangensis s. str., P. kisangani sp. nov., P. amosae sp. nov., and P. orbitospinus, each with diagnostic information, illustrations, distribution maps, and comparisons to similar species in Central and Southern Africa.
EUROPEAN JOURNAL OF TAXONOMY
(2021)
Article
Marine & Freshwater Biology
Neil Cumberlidge, Emily C. Johnson, Ellen M. Leever, Julia B. Soma, Kaitlyn M. Ahles, Seyit A. Kamanli, Paul F. Clark
Summary: This study provides descriptions and images of female characters for primary freshwater crabs, introducing a new dataset for family-level comparisons. It identifies two groups of primary freshwater crabs: Potamoidea and Trichodactyloidea.
JOURNAL OF CRUSTACEAN BIOLOGY
(2021)
Article
Biodiversity Conservation
Pierre A. Mvogo Ndongo, Salieu K. Sankoh, Paul F. Clark, Thomas von Rintelen, Christian Albrecht, Neil Cumberlidge
Summary: The current status of two Sierra Leone Afrithelphusa freshwater crabs is unknown, with one species considered possibly extinct and the other not reported for a long time. Fresh material from both species was collected in 2021, providing detailed information on their habitats.
JOURNAL OF NATURAL HISTORY
(2021)
Article
Marine & Freshwater Biology
Neil Cumberlidge, Julia B. Soma, Ellen M. Leever, Paul F. Clark, Savel R. Daniels
Summary: A new genus of freshwater crab, Crosnautesn. gen., and two species, C. ranomafanan. sp. and C. alainusn. sp., have been described from forested highlands in southeastern Madagascar. The new genus and species can be distinguished from other Malagasy genera based on phylogenetic and morphological characteristics.
JOURNAL OF CRUSTACEAN BIOLOGY
(2021)
