Article
Ecology
Yuanzhen Liu, Jan Henkel, Alexis Beaurepaire, Jay D. Evans, Peter Neumann, Qiang Huang
Summary: Invasive species are a major driver of ecological and environmental changes affecting human health, food security, and biodiversity. The molecular mechanisms underlying adaptations in invasive parasitic species are poorly understood, but a study on the small hive beetle Aethina tumida has identified candidate gene loci related to growth, reproduction, and body size control in response to environmental cues. These findings suggest that functional investigation of these loci could enhance the understanding of local adaptation mechanisms in invasive species.
ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Joao A. A. Ascensao, Kelly M. M. Wetmore, Benjamin H. H. Good, Adam P. P. Arkin, Oskar Hallatschek
Summary: Ascensao et al. engineered knockout libraries of a nascent bacterial community and found that ecological and epistatic patterns combine to shape adaptive landscapes, despite idiosyncratic behavior of individual knockouts. The study also revealed that fitness effects are correlated with evolutionary outcomes for certain conditions, indicating shifting patterns of adaptation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Qingyun Liu, Haican Liu, Li Shi, Mingyu Gan, Xiuqin Zhao, Liang-Dong Lyu, Howard E. Takiff, Kanglin Wan, Qian Gao
Summary: The study shows that Mycobacterium tuberculosis has adapted and diversified locally in the high-altitude Tibet region after sequential introductions of ancestral strains. Genetic evidence from the Tibetan population suggests unique mutations and positive selection in DNA repair enzymes, indicating adaptation to local environments in Tibet.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Qiong Wang, Xianyun Ren, Ping Liu, Jitao Li, Jianjian Lv, Jiajia Wang, Haien Zhang, Wei Wei, Yuxin Zhou, Yuying He, Jian Li
Summary: The genome assembly of the Chinese shrimp Fenneropenaeus chinensis revealed a significant contraction in genome size compared to other penaeid species, with expanded gene families related to cellular processes and metabolic processes under selection pressure of migration and cold environment. Targeted artificial selection of growth, vision, and behavior during domestication was also identified, providing valuable information for further genetic mechanism analysis and research of genetic changes during evolution.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Aurelie Mesnil, Maude Jacquot, Celine Garcia, Delphine Tourbiez, Lydie Canier, Audrey Bidois, Lionel Degremont, Deborah Cheslett, Michelle Geary, Alessia Vetri, Ana Roque, Dolors Furones, Alison Garden, Petya Orozova, Isabelle Arzul, Mathieu Sicard, Guillaume M. Charriere, Delphine Destoumieux-Garzon, Marie-Agnes Travers
Summary: This article investigates the evolutionary mechanisms of Vibrio aestuarianus, a pathogen causing oyster mortality in France and Ireland, and reveals its classical epidemic population structure. The acquisition of a copper-containing island may have facilitated the emergence of pathogenic lineages specialized in oysters.
Article
Biochemistry & Molecular Biology
Petri Kemppainen, Zitong Li, Pasi Rastas, Ari Loytynoja, Bohao Fang, Jing Yang, Baocheng Guo, Takahito Shikano, Juha Merila
Summary: This study identified the genomic regions responsible for repeated pelvic reduction in three crosses between nine-spined stickleback populations. In one cross, PR was mapped to LG7 containing the Pitx1 gene, while in the other two crosses, PR was polygenic and attributed to 10 novel QTL. The variability in genetic architecture of PR is hypothesized to be due to heterogeneity in the spatial distribution of standing genetic variation caused by different population structuring and genetic isolation in nine-spined sticklebacks compared to three-spined sticklebacks.
Article
Biochemistry & Molecular Biology
Saura R. Silva, Vitor F. O. Miranda, Todd P. Michael, Bartosz J. Plachno, Ramon G. Matos, Lubomir Adamec, Sergei L. K. Pond, Alexander G. Lucaci, Daniel G. Pinheiro, Alessandro M. Varani
Summary: This study explores the genetic differences in the plastome and mitochondrial genes of Utricularia and Genlisea species. The findings suggest that these genes may be influenced by both phylogenetic history and lifestyle. These insights contribute to our understanding of the phylogenetic and taxonomic knowledge of these plants.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Alejandro V. Cano, Hana Rozhonova, Arlin Stoltzfus, David M. McCandlish, Joshua L. Payne
Summary: This study investigates the influence of mutation spectrum on the spectrum of adaptive substitutions, demonstrating that the mutation spectrum has a proportional influence on the spectrum of adaptive substitutions in all three species, but the predictive power of the model differs substantially between the species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Ecology
Matilda W. Gikonyo, Seung-Joon Ahn, Maurizio Biondi, Frank Fritzlar, Yu Okamura, Heiko Vogel, Tobias G. Koellner, Ismail Sen, David Hernandez-Teixidor, Chi-Feng Lee, Harald Letsch, Franziska Beran
Summary: Flea beetles of the genus Psylliodes have specialized interactions with plant species from different families, including Brassicaceae, Solanaceae, and Fagaceae. This study investigates the evolution of their host use and the emergence of a glucosinolate-specific detoxification mechanism. The phylogenetic analysis shows that Psylliodes species are divided into four clades, with different preferences for host plants. Ancestral state reconstructions suggest that Psylliodes were initially associated with Brassicaceae and then expanded their host range. The evolution of glucosinolate-specific detoxification enzymes coincides with the radiation of Psylliodes on Brassicaceae.
Article
Biology
Christian M. M. Gagnon, Hannes Svardal, Anna J. J. Jasinska, Jennifer Danzy Cramer, Nelson B. B. Freimer, J. Paul Grobler, Trudy R. R. Turner, Christopher A. A. Schmitt
Summary: In the last 300 thousand years, the Chlorocebus genus expanded from equatorial Africa to the southernmost latitudes of the continent. The expansion is significantly associated with solar irradiance and winter precipitation, suggesting adaptations to non-shivering thermogenesis.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mugdha Mohkhedkar, Siva Sai Krishna Venigalla, Vani Janakiraman
Summary: The study identifies 28 human proteins with regions homologous to SARS-CoV-2 peptides as potential autoantigens, explaining the occurrence of autoimmune conditions following COVID-19 infection. These autoantigens are found to be distributed widely in tissues, suggesting their involvement in multi-organ manifestations through molecular mimicry. The report may guide future antigen-specific studies for management of extrapulmonary symptoms of COVID-19.
MOLECULAR IMMUNOLOGY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Georgina L. Brennan, Ramiro Logares
Summary: Ocean microbes play a fundamental role in the Earth system, yet our understanding of their evolution in response to global change is limited. Although microbes can quickly adapt to environmental stressors, there is currently scarce genetic evidence of contemporary evolution in wild microbes. The development of coordinated microbial 'genomic' observatories can provide an unprecedented opportunity to track contemporary microbial evolution and investigate how it enables wild microbes to respond to global change.
TRENDS IN MICROBIOLOGY
(2023)
Article
Biology
Samsad Razzaque, Robert W. Heckman, Thomas E. Juenger
Summary: Seed mass is an important ecological trait that varies among different ecotypes. However, the role of seed mass in local adaptation is not clear due to limited studies on its impacts on adult life-history traits. This study examined the relationship between seed mass, seedling and reproductive traits in Panicum hallii, which has two distinct ecotypes adapted to different habitats. The results showed that seed mass differed significantly among P. hallii genotypes and was correlated with various seedling and reproductive traits. Field experiments demonstrated that selection favored large seeds in upland habitat and small seeds in lowland habitat, supporting the concept of local adaptation. These findings highlight the central role of seed mass in ecotypic differences and its importance in seedling and adult recruitment, providing insights into ecotype formation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Evolutionary Biology
Marina Escalera-Zamudio, Sergei L. Kosakovsky Pond, Natalia Martinez de la Vina, Bernardo Gutierrez, Rhys P. D. Inward, Julien Theze, Lucy van Dorp, Hugo G. Castelan-Sanchez, Thomas A. Bowden, Oliver G. Pybus, Ruben J. G. Hulswit
Summary: Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Rafaela A. Almeida, Pieter Lemmens, Luc De Meester, Kristien Brans
Summary: The study evaluated the local genetic adaptation of populations of the non-target aquatic species Daphnia magna to organic and conventional agriculture practices. The results showed that D. magna populations exhibit different levels of adaptation to local pesticide use, with populations near conventional agriculture areas showing increased resistance to chlorpyrifos and populations near organic agriculture areas showing more resistance to deltamethrin.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Ecology
H. Ikeda, S. Sakaguchi, V. Yakubov, V. Barkalov, H. Setoguchi
Article
Ecology
Yan Hou, Charlotte Sletten Bjora, Hajime Ikeda, Christian Brochmann, Magnus Popp
JOURNAL OF BIOGEOGRAPHY
(2016)
Article
Ecology
Daijiro Hata, Hiroyuki Higashi, Valentin Yakubov, Vyacheslav Barkalov, Hajime Ikeda, Hiroaki Setoguchi
JOURNAL OF BIOGEOGRAPHY
(2017)
Article
Plant Sciences
Shinichiro Kameoka, Hitoshi Sakio, Harue Abe, Hajime Ikeda, Hiroaki Setoguchi
JOURNAL OF PLANT RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Hajime Ikeda, Pernille Bronken Eidesen, Valentin Yakubov, Vyacheslav Barkalov, Christian Brochmann, Hiroaki Setoguchi
Article
Ecology
Hajime Ikeda, Valentin Yakubov, Vyacheslav Barkalov, Hiroaki Setoguchi
JOURNAL OF BIOGEOGRAPHY
(2018)
Article
Ecology
Asuka Takaishi, Andrey E. Kozhevnikov, Zoya V. Kozhevnikova, Hajime Ikeda, Noriyuki Fujii, Akiko Soejima
ECOLOGY AND EVOLUTION
(2019)
Article
Ecology
Hajime Ikeda, Valentin Yakubov, Vyacheslav Barkalov, Kazuhiro Sato, Noriyuki Fujii
JOURNAL OF BIOGEOGRAPHY
(2020)
Article
Plant Sciences
Hajime Ikeda, Tomomi Suzuki, Yoshito Oka, A. Lovisa S. Gustafsson, Christian Brochmann, Nobuyoshi Mochizuki, Akira Nagatani
Summary: This study suggests that fine tuning the stability of phytochrome (Pfr) is a fundamental mechanism for plants to optimize phytochrome-related traits in their evolution and adaptation to spatially varying environments. The research revealed evolutionary divergence in physiological responses relevant to thermal stability of Pfr between two sister species of Brassicaceae, with the higher latitude species showing stronger responses to light-limited conditions.
Article
Plant Sciences
A. Lovisa S. Gustafsson, Galina Gussarova, Liv Borgen, Hajime Ikeda, Alexandre Antonelli, Lucas Marie-Orleach, Loren H. Rieseberg, Christian Brochmann
Summary: This study finds that post-zygotic reproductive isolation is common in Arctic flora, and this may be associated with glacial cycles and selfing mating systems.
Article
Plant Sciences
Haruna Sata, Midori Shimizu, Takaya Iwasaki, Hajime Ikeda, Akiko Soejima, Andrey E. Kozhevnikov, Zoya Kozhevnikova, Hyoung-Tak Im, Su-Kil Jang, Takayuki Azuma, Atsushi J. Nagano, Noriyuki Fujii
Summary: The study revealed that Viola orientalis originated in northeastern Asia and spread southward through the Korean Peninsula to the Japanese Islands during the last glacial period. This finding supports the previously proposed evolutionary hypothesis regarding the origin and migration routes of the Mansen elements.
JOURNAL OF PLANT RESEARCH
(2021)
Article
Plant Sciences
Hajime Ikeda
Summary: Mountain regions play an important role in supporting biodiversity, especially in East Asia. The high mountains of the Japanese archipelago harbor alpine and arctic-alpine plant populations, which have persisted through climate changes in the Pleistocene. Phylogeographic studies reveal complex range dynamics of these plants and their genetic relationships with northern regions, indicating possible ecological divergence.
JOURNAL OF PLANT RESEARCH
(2022)
Article
Plant Sciences
Tomoka Sakaba, Akiko Soejima, Shinji Fujii, Hajime Ikeda, Takaya Iwasaki, Hiroaki Saito, Yoshihisa Suyama, Ayumi Matsuo, Andrey E. Kozhevnikov, Zoya V. Kozhevnikova, Hongfeng Wang, Siqi Wang, Jae-Hong Pak, Noriyuki Fujii
Summary: A group of temperate grassland plant species, known as the Mansen elements, are found in Japan and continental East Asia. Researchers hypothesized that these species are remnants of continental grasslands in Japan from a colder age, but their migration history remained unclear. To investigate the migration history, the phylogeographic analysis of Tephroseris kirilowii, a member of the group, was conducted using single-nucleotide polymorphisms (SNPs). The results showed that the Japanese populations of T. kirilowii diverged from continental East Asia around 25.2 thousand years ago, with the first divergence within Japan occurring around 20.2 thousand years ago. The study suggested a post-glacial expansion of T. kirilowii in Japan based on limited suitable climate during the last glacial maximum and slight genetic differentiation among Japanese populations.
JOURNAL OF PLANT RESEARCH
(2023)
Editorial Material
Plant Sciences
Hajime Ikeda
Summary: This virtual issue compiles 35 papers on phylogeographic studies from the Journal of Plant Research, focusing on three major topics in biodiversity: biogeography, systematics, and evolution.
JOURNAL OF PLANT RESEARCH
(2023)
Article
Evolutionary Biology
Hajime Ikeda, Hiroaki Setoguchi
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2017)