Article
Genetics & Heredity
Bingyu Guo, Lingfeng Kong
Summary: In the context of diminishing global biodiversity, this study examines the validity and practicality of species delimitation methods for identifying neglected and undescribed biodiverse species. The results suggest that distance-based methods are generally superior to tree-based methods, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version of GMYC performs better and PTP shows higher efficiency in delimiting species. Additionally, GMYC is significantly influenced by taxonomic rank, performing poorly at the genus level.
Article
Biochemistry & Molecular Biology
Jorge L. Ramirez, Paola Valdivia, Ulises Rosas-Puchuri, Nereida L. Valdivia
Summary: Accurate species delimitation is crucial for biological studies, and the integration of molecular techniques and species delimitation methods can facilitate rapid and accurate biodiversity assessment. Single-gene species delimitation methods can be easily combined with the widely used DNA barcoding approach. We have developed a user-friendly tool called SPdel, which integrates different single-gene species delimitation methods and provides ready-to-publish quality figures for result interpretation. SPdel aims to assist researchers in improving biodiversity studies through the use of species delimitation methods.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Nicolas Puillandre, Sophie Brouillet, Guillaume Achaz
Summary: ASAP is a fast and efficient method for constructing species partitions from single locus sequence alignments. It offers a new scoring system without prior biological insight, and can be used through a graphical web interface or downloaded for local usage.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Microbiology
Sandra Hilario, Micael F. M. Goncalves, Artur Alves
Summary: DNA sequence analysis is crucial for species delimitation in Diaporthe, but combining multiple genes without genealogical concordance criteria complicates species delimitation. Using GCPSR and PTPs methods, the D. eres complex was identified as a single species, contrary to the current recognition of multiple species. Absence of reproductive isolation and low genetic diversity indices suggest D. eres constitutes a population rather than distinct lineages.
Article
Biotechnology & Applied Microbiology
Mario Alejandro Marin, Andres Lopez-Rubio, Alejandra Clavijo, Tomasz Wilhelm Pyrcz, Andre Victor Lucci Freitas, Sandra Ines Uribe, Carlos Federico Alvarez
Summary: This study analyzed high Andean butterflies using DNA barcoding, discovering sixteen potential cryptic species, representing a net richness increase of 11.3% in the assemblage. The genus Vanessa showed higher genetic differentiation at the local level. The research was useful in identifying potential cryptic species in two butterfly complexes along altitudinal and latitudinal gradients.
Article
Biodiversity Conservation
Monika Fajfer, Praveen Karanth
Summary: This study focuses on Geckobia mites infesting geckos in the Gekkonidae family found in Bangalore, India. Through morphological identification and DNA barcode markers, five new species and three known species were identified. The study provides insights into the evolutionary relationships of the mites and highlights Hemidactylus frenatus as the most susceptible gecko species to mite infestations.
Article
Mycology
Sandra Hilario, Liliana Santos, Artur Alves
Summary: The study focused on the delineation of species boundaries within the Diaporthe genus, specifically the D. amygdali complex. Results indicated that the species within this complex do not show clear boundaries, supporting the idea that they constitute a single species.
Article
Zoology
Krzysztof Szpila, Marcin Piwczynski, Wojciech Glinkowski, Lena Lutz, Kamran Akbarzadeh, Arturo Baz, Nikolas P. Johnston, Andrzej Grzywacz
Summary: This study investigates the phylogenetic relationships and species delimitation of the genus Pollenia using molecular markers and morphological data. The results show a congruence between morphology and molecular results in most cases, providing valuable insights into the species relationships and the importance of cluster flies as plant pollinators.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Mycology
F. Sklenar, Z. Jurjevic, J. Houbraken, M. Kolarik, M. C. Arendrup, K. M. Jorgensen, J. P. Z. Siqueira, J. Gene, T. Yaguchi, C. N. Ezekiel, C. Silva Pereira, V Hubka
Summary: The latest research re-evaluated the species boundaries of members in the section Flavipedes, identifying four new species and conducting phenotypic analysis. Additionally, sensitivity assessments of 67 strains to various antifungal drugs revealed some potential clinically relevant differences.
STUDIES IN MYCOLOGY
(2021)
Article
Plant Sciences
A. D. Temraleeva, Yu. S. Bukin
Summary: This study combines morphological identification and DNA-based species delimitation methods for chlorophycean microalgae, revealing unique combinations of features that distinguish members of the Moewusinia clade at the genus and species levels. The congruence between genetic analyses and morphological identification was observed, confirming tentative species hypotheses obtained through DNA-based methods.
SOUTH AFRICAN JOURNAL OF BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Vedprakash G. Hurdeal, Joyce E. Longcore, E. B. Gareth Jones, D. Rabern Simmons, Kevin D. Hyde, Eleni Gentekaki
Summary: In this study, three chytrids were isolated from northern Thailand and placed into three monotypic genera within Rhizophydiales. The study suggests the existence of multiple species within each genus. This research contributes to the understanding of chytrids, an understudied group in Thailand and worldwide.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Evgeniya N. N. Solovyeva, Evgeniy A. A. Dunayev, Roman A. A. Nazarov, Dmitriy A. A. Bondarenko, Nikolay A. A. Poyarkov
Summary: This study provides a diversity assessment of the agamid genus Phrynocephalus through the analysis of COI mtDNA barcodes. Multiple species delimitation algorithms were applied, revealing nine species groups and demonstrating the underestimation of species diversity in the genus. Thirteen previously unknown potential species were identified.
Article
Biodiversity Conservation
Arnaud Goulpeau, Benoit Penel, Marie-Eugenie Maggia, Daniel Fernandez Marchan, Dirk Steinke, Mickael Hedde, Thibaud Decaens
Summary: This study compared different methods for delimiting operational taxonomic units (OTUs) using DNA barcodes of earthworms. Phylogenetic methods were found to be less suitable for this purpose, while distance-based methods such as ASAP showed efficient results with shorter computation times and fewer mismatches.
Article
Multidisciplinary Sciences
Jinjin Fang, Reyim Mamut, Lidan Wang, Gulmira Anwar
Summary: In this study, the complete mitochondrial genome of Cladonia subulata was sequenced and compared with other Cladonia species. The mitogenome of Cladonia subulata consisted of a circular DNA molecule with 44 genes. Comparison with other Cladonia species revealed variations in tRNAs and cox1 genes, while repeat sequences were found to cause mitogenome rearrangement. The study provides important data for the systematic development and genetic diversity research of Cladonia subulata.
Article
Environmental Sciences
Jinxia Zhang, Lei Xu, Feiyan Du, Quehui Tang, Lianggen Wang, Jiajia Ning, Delian Huang, Yafang Li, Shuangshuang Liu, Xuehui Wang
Summary: This study employed DNA barcoding and molecular identification approaches to explore the species diversity and distribution pattern of marine fish in both the northern and southern sea areas of Hainan Island in the northern South China Sea. A total of 186 sequences were obtained, representing 56 species, 47 genera, 34 families, and 17 orders.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Plant Sciences
Isabel Urena-Vacas, Elena Gonzalez-Burgos, Pradeep Kumar Divakar, M. Pilar Gomez-Serranillos
Summary: This paper provides an overview of the potential biological interest of lichen depsidones as abundant secondary metabolites produced by lichens, showcasing their activities as antioxidants, antimicrobial, and cytotoxic agents. Future research should focus on investigating the mechanism of action of depsidones, evaluating new potential actions, and conducting clinical trials for the most promising depsidones.
Article
Integrative & Complementary Medicine
Isabel Urena-Vacas, Elena Gonzalez-Burgos, Simona De Vita, Padreep K. Divakar, Giuseppe Bifulco, M. Pilar Gomez-Serranillos
Summary: This study evaluated the antioxidant capacity and enzyme inhibitory activities of 14 lichen extracts belonging to the cetrarioid clade. The results showed that certain lichens exhibited strong antioxidant capacity and enzyme inhibitory activities, suggesting their potential use in the treatment of neurodegenerative diseases. The study also identified several promising secondary metabolites in these lichen extracts.
EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE
(2022)
Article
Plant Sciences
Todd J. Widhelm, Anusha Rao, Felix Grewe, H. Thorsten Lumbsch
Summary: Accurate species delimitations are crucial for understanding genetic diversity and conducting research in evolutionary and conservation biology. In lichenized fungi, there has been a debate on whether species pairs with similar morphology and chemistry should be classified as one species or two. Recent analysis using RADseq data has found fixed genetic differences between the two morphs, contradicting earlier conclusions based on limited Sanger sequencing data.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Microbiology
Ana Otero, Alejandrina Barcenas-Pena, H. Thorsten Lumbsch, Felix Grewe
Summary: This study used RADseq technology to analyze the evolutionary history of neuropogonoid lichens. Two new species and three resurrected species were discovered, and the timeframe for neuropogonoid lichen diversification was inferred. This study provided important support for filling the gap of fungal diversity and raised new questions about factors that may trigger complex evolutionary scenarios.
Review
Microbiology
Isabel Urena-Vacas, Elena Gonzalez-Burgos, Pradeep Kumar Divakar, Maria Pilar Gomez-Serranillos
Summary: This review discusses the research findings on the biological effects and mechanisms of action of lichen depsides and tridepsides, which are secondary metabolites found in lichens. Various studies have demonstrated antioxidant, cytotoxic, and antimicrobial activities of these compounds. However, clinical trials have not been conducted yet, and future research should focus on in vivo studies, clinical trials, and evaluating other activities. Additionally, there are many compounds that have yet to be investigated in terms of their pharmacology.
Article
Biodiversity Conservation
Ram Sharan Dani, Pradeep Kumar Divakar, Chitra Bahadur Baniya
Summary: Studies on species richness patterns along elevation gradients have been conducted to estimate the patterns and determinants of species richness. More than half of the studies found unimodal hump-shaped richness patterns, followed by a monotonic decline, in different plant taxa. Both hemispheres showed similar patterns of species richness. Some taxa showed bimodality or multi-model patterns. The mid-domain effect and elevation range influenced the patterns. More regional research focusing on specific taxa and factors is needed.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Plant Sciences
Luis Fernando Coca, Salome Gomez Gomez, Jorge Guzman Guillermo, Edwin Trujillo Trujillo, Laura Clavijo, Alejandro Zuluaga, Manuela Dal Forno, H. Thorsten Lumbsch
Summary: A new species of Sulzbacheromyces was discovered during botanical and lichenological expeditions in the Colombian Andean-Amazonian Piedmont, Brazilian Amazon, and Veracruz, Mexico. S. leucodontium is distinguished by its white basidiomata and colonial algae in the thallus, and it has the widest distribution of the genus in the Americas, from Mexico to Brazil. Furthermore, this study presents the most complete phylogenetic reconstruction of the genus and provides a key to the known species of Sulzbacheromyces in the Neotropics.
Article
Plant Sciences
Patsakorn Tiwutanon, Kasidis Chaiyasut, H. Thorsten Lumbsch, Ekaphan Kraichak
Summary: This study re-evaluated the taxonomic status of Leucobryum scalare using phylogenetic and morphometric approaches. The results showed that it should be resurrected as a separate species from Leucobryum aduncum. This work highlights the need for a more thorough revision of Leucobryum to clarify the actual level of diversity in this genus.
Article
Plant Sciences
Nopparat Anantaprayoon, Jason Hollinger, Abigail Robison, Ekaphan Kraichak, Heather Root, Steven D. Leavitt
Summary: Species of lichen-forming fungi exhibit a variety of geographical distribution patterns, with some species having their diversity and biogeographical patterns masked by unrecognized diversity or taxonomic limitations. This study reveals that the widely distributed Lecidea atrobrunnea s. lat. is likely a complex of distinct species-level lineages, with unsettled species boundaries in both phenotype and molecular-based approaches.
Article
Plant Sciences
Mohammad Sohrabi, Steven D. Leavitt, Walter Obermayer, Helmut Mayrhofer
Summary: A new manna lichen species, Circinaria nimisii sp. nov., is described and illustrated in this study. It is the fourth known manna lichen in Europe and was found on Mount Olympus in Greece. The distinct morphological and molecular characteristics differentiate this species from closely related congeners. Additionally, the study proposes Agrestia zerovii to be a new synonym of Circinaria hispida.
Article
Microbiology
Michael Kerr, Steven D. Leavitt
Summary: DNA barcoding approaches provide powerful tools for characterizing fungal diversity, but are limited by poor representation of species-level diversity in fungal sequence databases. This study created a regional ITS database for lichen-forming fungi in the Intermountain West of the United States and found that species-level identification rates were significantly improved using the regional database compared to the widely used UNITE database.
Article
Microbiology
Steven D. Leavitt, Ann DeBolt, Ethan McQuhae, Jessica L. Allen
Summary: The Florida Perforate Cladonia (FPC), a federally endangered species, remains imperiled in isolated populations in the Florida scrub. Reference genomes of threatened and endangered species like FPC provide crucial insights into genomic diversity and adaptations. In this study, the first draft nuclear and mitochondrial genomes were assembled for FPC, and genetic diversity within and among populations in southeastern Florida was assessed. The genomic resources generated here are important for informed conservation efforts for the FPC.
Article
Chemistry, Analytical
David Alors, Pradeep Kumar Divakar, Anjuli Calchera, Imke Schmitt, Ana Crespo, Maria Carmen Molina
Summary: Lichens produce bioactive compounds, but their slow growth rate and environmental damage make massive collection impractical. Cultivation of lichens in the lab is an alternative, and our study focused on two lichen species cultured for over 550 days. We found that the mycobiont cultures produced different secondary metabolites than those found in natural lichen thalli, indicating their potential for bioactive compound production.
Article
Plant Sciences
Paul M. Kirika, H. Thorsten Lumbsch, Elisa Garrido Huescar, Taylor S. Quedensley, Pradeep K. Divakar
Summary: Recent studies have found cryptic species in lichen-forming fungi, especially in parmelioid lichens. This study focuses on Canoparmelia texana, a sorediate species, and finds that it actually consists of two distinct lineages.
Article
Biochemistry & Molecular Biology
Isabel Urena-Vacas, Elena Gonzalez-Burgos, Pradeep Kumar Divakar, Maria Pilar Gomez-Serranillos
Summary: This study evaluates the neuroprotective role of methanol extracts from Dactylina arctica, Nephromopsis stracheyi, Tuckermannopsis americana, and Vulpicida pinastri in an oxidative stress model. The results show that these lichen extracts can prevent cell death and morphological changes, and increase antioxidant enzyme activities.
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)