Article
Biochemistry & Molecular Biology
Taro Nojiri, Laura A. B. Wilson, Camilo Lopez-Aguirre, Vuong Tan Tu, Shigeru Kuratani, Kai Ito, Hiroki Higashiyama, Nguyen Truong Son, Dai Fukui, Alexa Sadier, Karen E. Sears, Hideki Endo, Satoshi Kamihori, Daisuke Koyabu
Summary: The study found that laryngeal echolocation in bats may have multiple origins, supporting the hypothesis of a non-echolocating bat ancestor and independent gain of echolocation in Yinpterochiroptera and Yangochiroptera. Additionally, there were no developmental differences in the hearing apparatus between non-echolocating bats and terrestrial non-bat mammals.
Article
Ecology
Marcello Mezzasalma, Jeffrey W. Streicher, Fabio M. Guarino, Marc E. H. Jones, Simon P. Loader, Gaetano Odierna, Natalie Cooper
Summary: This study used chameleons as model organisms and found that fusion of microchromosomes played a major role in reducing the chromosome number. This tendency of fusion was a characteristic of the ancestral chameleon genome and not influenced by ecological, physiological, and biogeographical factors.
Article
Microbiology
Adriano de Bernardi Schneider, Carla Osiowy, Reilly Hostager, Henrik Krarup, Malene Borresen, Yasuhito Tanaka, Taylor Morriseau, Joel O. Wertheim
Summary: A study found that a high percentage of Greenland's Inuit population are chronically infected with HBV, with 39 novel HBV/D sequences forming a new quasi-subgenotype that differs from traditional HBV sequences.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh
Summary: Sequence simulators are important in phylogenetics for evaluating methods, hypothesis testing, and generating data. AliSim is a new tool that efficiently simulates biologically realistic alignments, outperforming popular software in terms of speed and efficiency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Sophie Teullet, Marie-Ka Tilak, Amandine Magdeleine, Roxane Schaub, Nora M. Weyer, Wendy Panaino, Andrea Fuller, W. J. Loughry, Nico L. Avenant, Benoit de Thoisy, Guillaume Borrel, Frederic Delsuc
Summary: The consumption of ants and termites by myrmecophagous mammals is an example of dietary convergence. The gut microbiome of these mammals plays an important role in their dietary adaptation, particularly the digestion of chitinous exoskeletons. By sequencing fecal samples, researchers identified chitin-degrading bacteria in the gut microbiota of myrmecophagous species, highlighting the potential role of these bacteria in their convergent adaptation to ant and termite consumption.
Article
Biochemistry & Molecular Biology
Han Yan, Zhirui Hu, Gregg W. C. Thomas, Scott Edwards, Timothy B. Sackton, Jun S. Liu
Summary: The paper introduces PhyloAcc-GT, a method that extends PhyloAcc by modeling gene tree heterogeneity, to effectively identify lineage-specific accelerations in substitution rate while accounting for incomplete lineage sorting. The method outperforms other methods in detecting complex patterns of rate shifts and is robust to population size parameter specification.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Sudhir Kumar
Summary: Molecular evolutionary analysis requires computationally intensive steps that have a significant environmental impact. However, innovative methods and heuristics can reduce the carbon footprint, lower environmental costs, and promote green evolutionary computing.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Yuqi Huang, Minghao Sun, Lenan Zhuang, Jin He
Summary: This study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, revealing loss or gain of AIG members in different species during evolution. The findings can be used for future functional characterization of AIGs.
Article
Oncology
Antonia Chroni, Sayaka Miura, Lauren Hamilton, Tracy Vu, Stephen G. Gaffney, Vivian Aly, Sajjad Karim, Maxwell Sanderford, Jeffrey P. Townsend, Sudhir Kumar
Summary: By analyzing the genetic heterogeneity of tumors in cancer patients, we found that the migration histories of metastasis are often best described by a hybrid model of metastatic tumor evolution. We discovered that new tumor seedings arise from clones of pre-existing metastases as frequently as they do from clones from primary tumors. Additionally, there were many clone exchanges between the source and recipient tumors.
Article
Evolutionary Biology
Daniele Salvi, Manal Al-Kandari, P. Graham Oliver, Emanuele Berrilli, Matteo Garzia
Summary: Animal biodiversity, especially for intertidal benthic organisms like oysters, is often underestimated in nontemperate marine regions. This study focused on small oysters from Kuwait and identified a new species called Ostrea oleomargarita. The study also revealed inconsistencies in the classification of the Ostrea genus and highlighted the Arabian Gulf as a key region for discovering marine animal diversity, suggesting a possible biogeographic divide between the Eastern and Western Indo-Pacific.
JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH
(2022)
Article
Biology
Jory Thiel, Muzaffar A. Khan, Roel M. Wouters, Richard J. Harris, Nicholas R. Casewell, Bryan G. Fry, R. Manjunatha Kini, Stephen P. Mackessy, Freek J. Vonk, Wolfgang Wuster, Michael K. Richardson
Summary: Convergence is the phenomenon where similar phenotypes evolve independently in different lineages. Resistance to toxins in animals is an example of convergence, where molecular adaptations have evolved to counteract the harmful effects of toxins. However, resistance adaptations may carry fitness costs if they disrupt the normal physiology of the resistant animal.
BIOLOGICAL REVIEWS
(2022)
Article
Evolutionary Biology
Jeremias N. Brand, Luke J. Harmon, Lukas Schaerer
Summary: Traumatic insemination is a mating behavior in which sperm is injected into the recipient's body through the epidermis, bypassing the female genitalia. This behavior has evolved independently at least nine times in the flatworm genus Macrostomum, involving convergent shifts in male and female reproductive traits. The evolution of traumatic insemination is driven by sexual selection and conflict, allowing donors to bypass postcopulatory control mechanisms of recipients.
Article
Biochemistry & Molecular Biology
Kazumi Sakai, Hiroki Ikeuchi, Chihiro Fujiyabu, Yasushi Imamoto, Takahiro Yamashita
Summary: Opsins are universal photoreceptive proteins in animals that play a role in regulating cyclic nucleotide signaling. Different types of opsins in different animals form different active states during photoconversion, and the position of the negatively charged counterion varies. Through analyzing a distinct group of opsins, researchers found that the counterion position change is related to the efficiency of signaling. This study provides insights into the evolutionary process of opsins and their signaling efficiency.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Evolutionary Biology
Leticia Chiara Baldassio de Paula, Rodrigo de Vilhena Perez Dios, Filipe Macedo Gudin, Marcelo Domingos de Santis, Deivys Moises Alvarez-Garcia, Manuel Antunes Junior, Beatriz Vieira Freire, Fernando Portella de Luna Marques, Daniel Jose Galafasse Lahr, Silvio Shigueo Nihei
Summary: Tachinidae is the second largest and species-rich family in Diptera, with all members being parasitoids. This study presents the first phylogenomic analysis of Tachinidae using transcriptomic data, revealing the subfamilial relationships and the existence of a fifth lineage.
Article
Microbiology
Vishnu Raghuram, Ashley M. Alexander, Hui Qi Loo, Robert A. Petit, Joanna B. Goldberg, Timothy D. Read
Summary: This study investigates the mutations in the agr operon of Staphylococcus aureus and their impact on strain characteristics. The study shows a close association between agr type and S. aureus clonal complex, and a strong linkage between agrBDC alleles. More than 5% of the genomes analyzed have frameshift mutations in the agr operon. The recurring mutations in different clonal lineages suggest that strains with agr frameshifts are short-lived in evolution.
MICROBIOLOGY SPECTRUM
(2022)
Article
Limnology
Renata Manconi, Dirk Erpenbeck, Jane Fromont, Gert Woerheide, Roberto Pronzato
Summary: The recent discovery of freshwater sponges in an unexplored hydrographic basin in north-western Australia provided the opportunity to investigate the genus Corvospongilla Annandale using integrative systematics. A new Australasian Corvospongilla species was identified through comparative analysis of morphological traits and biogeographic patterns, and a phylogenetic and phylogeographic tree was established for some Asian, Afrotropical and Australasian lineages based on molecular analyses.
Article
Biochemistry & Molecular Biology
Sergio Vargas, Thorsten Zimmer, Nicola Conci, Martin Lehmann, Gert Woerheide
Summary: While many coral reef species are threatened by overfishing, some octocorals show resilience to anthropogenic environmental changes and may replace stony corals in the future. Research has found that the molecular mechanisms of octocorals, such as Pinnigorgia flava, exhibit resilience to heat and seawater acidification stress. This provides insights into their adaptive responses to anthropogenically driven environmental changes.
Article
Biochemistry & Molecular Biology
Ramon E. Rivera-Vicens, Catalina A. Garcia-Escudero, Nicola Conci, Michael Eitel, Gert Woerheide
Summary: The use of RNA sequencing and de novo transcriptome assembly is crucial for ecological and evolutionary studies, especially for nonmodel organisms lacking genome information. A multi-assembler approach, followed by a reduction step, is often employed to improve the assembly quality. TransPi is a comprehensive pipeline for de novo transcriptome assembly that achieves higher completeness percentages and reduces duplication rates compared to single assembler approaches. It is easy to configure and can be seamlessly deployed using Conda, Docker, and Singularity.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biology
Brian W. Strehlow, Astrid Schuster, Warren R. Francis, Donald E. Canfield
Summary: This article presents the raw data of metagenome sequencing for the sponge Halichondria panicea and its microbiome, and compares the assembly results of different sequencing methods. Although the assembly results are incomplete, these data can provide reference for future studies and suggest possibilities for improving assembly methods and limitations of the applied methods.
BMC RESEARCH NOTES
(2022)
Article
Zoology
Stefanie Agne, Merrick Ekins, Adrian Galitz, Michael Hofreiter, Michaela Preick, Nicolas Straube, Gert Woerheide, Dirk Erpenbeck
Article
Paleontology
Ailin Chen, Luis Porras, Haidan Ma, Xianguang Hou, Gert Woerheide
Summary: In this paper, we describe a new sponge with unique characteristics, indicating its relevance to the evolution of ancient sponges. This new taxon shows similarities to the total group of Silicea and a combination of filtering sponges, suggesting a potential connection between two major types of Early Palaeozoic sponge body plans. A more accurate definition of the Cambro-Ordovician groups and the creation of a total evidence framework that integrates extinct and extant sponge morphology into the phylogenetic scenario derived from phylogenomics seem to be essential steps for the improvement of our understanding of early sponge evolution.
Article
Multidisciplinary Sciences
Ksenia Juravel, Luis Porras, Sebastian Hoehna, Davide Pisani, Gert Woerheide
Summary: An accurate understanding of the evolution and ecology of animals relies on an accurate phylogeny. However, there are still unresolved nodes in the animal tree, including the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. In this study, we utilized newly assembled genome gene content and morphological datasets to investigate these difficult nodes. Our results support the idea that sponges are the sister group of all other animals, Xenacoelomorpha is the sister group of other Bilateria, and provide tentative support for the monophyly of Deuterostomia.
Article
Zoology
Merrick Ekins, John N. A. Hooper
Summary: This research discovered three new species of carnivorous sponges from the Cladorhizidae family in the Great Barrier Reef, Queensland, Australia: Abyssocladia falkor sp. nov., Abyssocladia jeanvaceleti sp. nov., and Axoniderma wanda sp. nov. These specimens were collected by ROV during the FK200802-Seamounts, Canyons & Reefs of the Coral Sea Cruise on the RV Falkor from the Schmidt Ocean Institute. Additionally, the presence of two complete specimens enabled the redescription of two previously known Australian species of carnivorous sponge (Chondrocladia (Chondrocladia) zygainadentonis Ekins et al., 2020a and Asbestopluma (Asbestopluma) maxisigma Ekins et al., 2020a), which were previously only based on incomplete specimens from the East coast of Australia.
Article
Zoology
Dirk Erpenbeck, Rob W. M. Van Soest, Gert Woerheide, Michelle Kelly
Article
Zoology
Merrick Ekins, Dirk Erpenbeck, Cecile Debitus, Sylvain Petek, Tepoerau Mai, Gert Woerheide, John N. A. Hooper
Summary: This study examines the taxonomy of sponge specimens with unique chemistry collectively known as Fascaplysinopsis reticulata. The results revealed that Fascaplysinopsis reticulata is a species complex comprising the genus Fascaplysinopsis, as well as two new genera: Skolosachlys gen. nov. and Rubrafasciculus gen. nov. Several new species were described within these genera.
Article
Zoology
Merrick Ekins, Soraya Baker, John N. A. Hooper
Summary: Four new species of encrusting Hamacantha (Vomerula) were discovered in the bathyal depths of seamounts in southeast Australia, along with a re-description of a previously known species from New Caledonia. A comparison table of all known species of H. (Vomerula) was provided, bringing the total number of known species in the subgenus to 26. This study also marks the first record of the genus Hamacantha in the Australian Exclusive Economic Zone.
Article
Zoology
Merrick Ekins, Dirk Erpenbeck, Gert Woerheide, John N. A. Hooper
Summary: This study reports on new deep water sponge species discovered in the East Coast of Australia and the Lord Howe and Norfolk Ridges in the Tasman Sea. In addition, two previously known species have been redescribed based on the new collections.