Article
Evolutionary Biology
Veronika N. Laine, Tiina Savilammi, Niklas Wahlberg, Katarina Meramo, Gonzalo Ossa, Joseph S. Johnson, Anna S. Blomberg, Aidyn B. Yeszhanov, Veronica Yung, Steve Paterson, Thomas M. Lilley
Summary: By analyzing the whole-genome of three closely related species in the Eptesicus (Histiotus) subgenus, it was found that there is recent gene flow and hybridization between Eptesicus (Histiotus) montanus and Eptesicus (Histiotus) macrotus, while Eptesicus (Histiotus) magellanicus tends to be more isolated. The results of this study demonstrate the importance of both nuclear and mitochondrial DNA in resolving phylogenetic relationships and species histories.
GENOME BIOLOGY AND EVOLUTION
(2023)
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.
Review
Biodiversity Conservation
Emmanuel Nyongesa Waswa, Elizabeth Syowai Mutinda, Elijah Mbandi Mkala, Daniel Mutavi Katumo, Millicent Akinyi Oulo, Wyclif Ochieng Odago, Sara Getachew Amenu, Shi-Xiong Ding, Guang-Wan Hu
Summary: The genus Sambucus is known for its morphological and genetic variations, making its taxonomic delimitation uncertain. Intraspecific variations and interspecific hybridizations within Sambucus species contribute to taxonomic complications.
Article
Biochemistry & Molecular Biology
Joan Ferrer Obiol, Jose M. Herranz, Josephine R. Paris, James R. Whiting, Julio Rozas, Marta Riutort, Jacob Gonzalez-Solis
Summary: Speciation is a complex process influenced by multiple evolutionary forces. The taxonomic classification of Puffinus shearwaters has been debated extensively, but our study shows that current taxonomies are not supported by genomic data. We propose a more accurate taxonomy based on integrating genomic information with other evidence, emphasizing the potential of genomic data in resolving taxonomic uncertainties.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(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)
Review
Microbiology
Ashley Stengel, Kimberly M. Stanke, Amanda C. Quattrone, Joshua R. Herr
Summary: Species concepts have been a topic of debate among biologists for a long time, contributing to interdisciplinary communication and advancements in research areas such as evolution, population biology, ecology, natural history, and disease epidemiology. The challenges in fungal taxonomy have made taxonomic delimitation difficult, but methodological approaches that improve discrimination of genetic and functional traits, combined with eco-evolutionary theory and integrative taxonomy, show promise in resolving ambiguity. Bioinformatics tools and modeling approaches, along with advancements in genomic and phenomic methods, hold great potential in expanding our knowledge of fungal biodiversity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ariadne F. Sabbag, Maria Tereza C. Thome, Mariana L. Lyra, Cinthia A. Brasileiro, Emily Moriarty Lemmon, Alan Lemmon, Celio F. B. Haddad
Summary: The study utilized genetic data to analyze the Thoropa miliaris + T. taophora species complex in the southeastern Atlantic Forest of Brazil, revealing high genetic diversity and co-evolution among the lineages. The research found that these lineages are relatively independent in evolution and may all represent distinct species that diverged during the Pliocene and Pleistocene epochs.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Miguel Calixto-Rojas, Andres Lira-Noriega, Miguel Rubio-Godoy, Gerardo Perez-Ponce de Leon, Carlos D. Pinacho-Pinacho
Summary: In this study, an integrative taxonomy approach was used to test species boundaries in the profundulid fishes in Guerrero and Oaxaca states, Mexico. By combining molecular and morphological data, 15 valid species were identified and five potential new lineages were discovered.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Plant Sciences
Yunheng Ji, Jin Yang, Jacob B. Landis, Shuying Wang, Lei Jin, Pingxuan Xie, Haiyang Liu, Jun-Bo Yang, Ting-Shuang Yi
Summary: The taxonomic confusion of Paris L. section Axiparis H. Li (Melanthiaceae) has been resolved by reducing the number of species from nine to two based on morphological and geographic analyses. Through genome sequencing and different species delimitation methods, two taxonomic units with distinct morphology, distribution, and genetic characteristics were identified. This study clarifies the species boundaries within Paris L. section Axiparis and facilitates taxonomic revision.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Entomology
Zhen Liu, Sheng-Jie Yang, Yu-Yuan Wang, Yan-Qiong Peng, Hua-Yan Chen, Shi-Xiao Luo
Summary: Species of the family Scoliidae are larval parasitoids of scarabaeoid beetles and pollinators of various plants. By using an integrative approach of morphology and molecular data, researchers identified multiple species, including an undescribed cryptic species and newly recorded species.
Article
Biochemistry & Molecular Biology
Ivan Prates, Mark N. N. Hutchinson, Sonal Singhal, Craig Moritz, Daniel L. L. Rabosky
Summary: This study investigates the taxonomic intractability in an Australian lizard clade, the Ctenotus inornatus species group, and reveals the challenges in resolving species boundaries due to decoupled genetic and phenotypic breaks, uncertain geographic ranges, and idiosyncratic patterns of introgression. The study highlights the importance of spatial variation in species boundaries and its impact on genetic and phenotypic variation.
Article
Entomology
Zhuo Ma, Jinliang Ren, Runzhi Zhang
Summary: This study analyzed the genetic distance variation of species in the subfamily Entiminae to determine parameters for species identification. The results showed that there is no universal genetic distance threshold at the subfamily level, but a threshold of 9.18% can delimit more than 88% of Entiminae species.
Article
Ecology
Stefanie Agne, Gavin J. P. Naylor, Michaela Preick, Lei Yang, Ralf Thiel, Simon Weigmann, Johanna L. A. Paijmans, Axel Barlow, Michael Hofreiter, Nicolas Straube
Summary: The lantern shark family, Etmopteridae, is the most diverse shark family with over 50 species. Due to the remote sampling sites, many species are described based on a few individuals, and recollecting specimens is often difficult. Previous taxonomic studies relied mainly on morphological analysis, while DNA sequence information has rarely been used. Recent advances in ancient DNA techniques have allowed for the recovery of DNA sequences from wet-collection type specimens. In this study, mitochondrial DNA sequences obtained from two wet-collection lantern shark paratype specimens were analyzed to support species identification. The results suggest that E. benchleyi is synonymous with E. litvinovi, but E. pycnolepis is a distinct species. This study highlights the importance of wet-collection type specimens as genetic resources for taxonomic research.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
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
Ecology
Lars Dietz, Jonas Eberle, Christoph Mayer, Sandra Kukowka, Claudia Bohacz, Hannes Baur, Marianne Espeland, Bernhard A. A. Huber, Carl Hutter, Ximo Mengual, Ralph S. S. Peters, Miguel Vences, Thomas Wesener, Keith Willmott, Bernhard Misof, Oliver Niehuis, Dirk Ahrens
Summary: Species recognition is crucial for science and society, and molecular methods have become popular for animal species identification. In this study, genomic data from nine animal lineages were used to explore the use of metazoan-level universal single-copy orthologs (metazoan USCOs) for species delimitation. The results showed that USCOs outperformed classical mitochondrial DNA barcoding in distinguishing closely related species and accurately assigning samples to different taxonomic levels.
METHODS IN ECOLOGY AND EVOLUTION
(2023)