Editorial Material
Microbiology
Daniel Falush
Summary: The genome of Helicobacter pylori undergoes extensive mixing through homologous recombination, resulting in significant free recombination within populations. A recent study reveals that the UvrC gene in H. pylori has evolved an additional function, allowing very short DNA tracts to be imported into the genome during natural transformation.
Article
Biochemistry & Molecular Biology
Yue Wang, Jianping Xu
Summary: Candida auris is a multidrug-resistant pathogenic yeast that has recently emerged as a global health threat. In this study, genetic analyses based on whole-genome sequences were conducted to investigate potential recombination events in natural populations of C. auris. The results revealed limited evidence for recombination both before and after the divergence of different clades within the species. However, the frequency of recombination was higher before the clade divergence and was observed to be limited in regions associated with antifungal resistance. These findings imply the possibility of ongoing genetic exchange in natural populations of this important yeast pathogen.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Evolutionary Biology
Michael Lynch, Zhiqiang Ye, Lina Urban, Takahiro Maruki, Wen Wei
Summary: By analyzing the whole genome of a microcrustacean, researchers have discovered certain characteristics of the recombination landscape in gene evolution, such as the uniformity of recombination rates, consistent patterns of linkage disequilibrium, and the involvement of recombination mechanisms unrelated to crossing-over. These findings challenge the traditional LD equilibrium model.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Saber Qanbari, Robert D. Schnabel, Dorte Wittenburg
Summary: By evaluating the map coordinates of SNP markers using population genetic metrics, this study identified a panel of misplaced markers in cattle. These misplaced markers account for a small proportion of the SNP genotyping array and it is recommended to remove them in association mapping studies.
Article
Genetics & Heredity
Ling Jin, Zitong Li, Chongnv Wang, Yingnan Wang, Xinxin Li, Jian Yang, Yahui Zhao, Baocheng Guo
Summary: Genetic differentiation in aquatic organisms is influenced by drainage connectivity. Tibetan loaches on the Qinghai-Tibet Plateau show contrasting population differentiation patterns and adaptive mechanisms to salinity change. Despite limited genetic signals of parallel adaption, a catalog of genes related to adaptation to salinity change is identified in Triplophysa loaches.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Lydia K. Wooldridge, Beth L. Dumont
Summary: This study constructed broad- and fine-scale sex-averaged recombination maps in nine geographically isolated wild house mouse populations using a coalescent-based approach. The results showed low conservation of recombination maps across subspecies and populations, with most hotspots being unique to one population due to minimal sharing of Prdm9 alleles. Additionally, population-specific differences in the degree and direction of sex dimorphism for recombination were observed. Overall, this study highlights the variability of recombination landscape in M. musculus and emphasizes the functional impact of Prdm9 allelic variation in wild populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Parul Johri, Charles F. Aquadro, Mark Beaumont, Brian Charlesworth, Laurent Excoffier, Adam Eyre-Walker, Peter D. Keightley, Michael Lynch, Gil McVean, Bret A. Payseur, Susanne P. Pfeifer, Wolfgang Stephan, Jeffrey D. Jensen
Summary: The field of population genomics has grown rapidly, but there is a tendency to focus on specific models at the expense of exploring underlying evolutionary processes. We need to pay more attention to statistical inference and theory and establish relevant baseline models for each analysis.
Article
Plant Sciences
Sajal R. Sthapit, Travis M. Ruff, Marcus A. Hooker, Deven R. See
Summary: The population structure and genetic diversity of wheat varieties in the United States were examined using a panel of historical and modern varieties. The results showed that population structure was related to growth habit and kernel characteristics, which also corresponded with geographic distribution. Market class classification accounted for the greatest amount of variation. There was no evidence of decreased genetic diversity after the release of the first semidwarf wheat variety in 1961, and some varieties even showed increases in genetic diversity. The findings suggest that overall genetic diversity in wheat varieties has not declined in the long term, despite occasional fluctuations.
Editorial Material
Biochemistry & Molecular Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: This article addresses recent claims regarding the importance of indirect selection, arguing that it is not a new or poorly studied phenomenon and that alternative explanations exist for the patterns described by the authors.
Article
Genetics & Heredity
Kieran Samuk, Mohamed A. F. Noor
Summary: Accurate estimation of recombination rate is crucial for evolutionary research. Current linkage disequilibrium-based methods make simplifying assumptions and gene flow can affect the accuracy of recombination rate estimation, resulting in overestimation or underestimation of recombination rates, as well as incorrect detection of interpopulation differences in recombination rate.
G3-GENES GENOMES GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Irene Novo, Pilar Ordas, Natalia Moraga, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The estimation of historical Ne provided by the software GONE can be substantially biased by recent mixture of populations, low rates of continued migration, and high frequencies of chromosomal inversions. Population structure analyses and restriction of estimation to differentiated groups can help mitigate biases. Removing genomic regions involved in inversions can also improve the accuracy of Ne estimates.
GENETICS SELECTION EVOLUTION
(2023)
Article
Evolutionary Biology
Jeffrey D. Wall, Jacqueline A. Robinson, Laura A. Cox
Summary: This study investigates crossover and noncrossover recombination in olive baboons and compares the results to linkage disequilibrium-based recombination estimates. The study finds gender differences in recombination rates and a bimodal distribution of noncrossover tract lengths. Additionally, the study demonstrates the use of crossover and linkage disequilibrium-based recombination estimates in identifying genome assembly errors.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Immunology
Anja Klussmeier, Kathrin Putke, Steffen Klasberg, Maja Kohler, Juergen Sauter, Daniel Schefzyk, Gerhard Schoefl, Carolin Massalski, Gesine Schaefer, Alexander H. Schmidt, Axel Roers, Vinzenz Lange
Summary: MICA is a stress-induced ligand that stimulates immune responses. The study reveals high frequencies of MICA copy number variations in different ethnic groups, which may have implications for disease associations. These variations are likely caused by nonallelic homologous recombination events between MICA and MICB.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Vivian Link, Yuomi Jhony A. Zavaleta, Rochelle-Jan Reyes, Linda Ding, Judy Wang, Rori V. Rohlfs, Michael D. Edge
Summary: The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are widely used in forensic genetics in the United States. Although CODIS loci were previously believed to contain limited information about ancestry or traits, recent research has shown that the regions surrounding CODIS loci are enriched with trait-related variants.
Article
Biochemistry & Molecular Biology
Tin-Yu J. Hui, Jon Hael Brenas, Austin Burt
Summary: The study extends current methods for estimating contemporary effective population size by allowing the use of multiple linked loci to provide more accurate results. By deriving the covariance of changes in allele frequency at linked loci to account for between-locus correlation-induced extra sampling variance, the new method ensures reliability and accuracy in estimating Ne.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Ecology
Tetsuya Akita, Shohei Takuno, Hideki Innan
Article
Genetics & Heredity
Takahiro Sakamoto, Hideki Innen
Review
Evolutionary Biology
Jeffrey A. Fawcett, Hideki Innan
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Jeffrey A. Fawcett, Fumio Sato, Takahiro Sakamoto, Watal M. Iwasaki, Teruaki Tozaki, Hideki Innan
Article
Genetics & Heredity
Hideki Innan, Reiner Veitia, Diddahally R. Govindaraju
Article
Biochemistry & Molecular Biology
Watal M. Iwasaki, T. E. Kijima, Hideki Innan
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Multidisciplinary Sciences
Kazuki K. Takahashi, Hideki Innan
SCIENTIFIC REPORTS
(2020)
Article
Multidisciplinary Sciences
Atsushi Niida, Takanori Hasegawa, Hideki Innan, Tatsuhiro Shibata, Koshi Mimori, Satoru Miyano
Article
Ecology
T. Sakamoto, H. Innan
THEORETICAL POPULATION BIOLOGY
(2020)
Review
Genetics & Heredity
Diddahally R. Govindaraju, Hideki Innan, Reiner A. Veitia
TRENDS IN GENETICS
(2020)
Article
Multidisciplinary Sciences
Yu Sugihara, Kwabena Darkwa, Hiroki Yaegashi, Satoshi Natsume, Motoki Shimizu, Akira Abe, Akiko Hirabuchi, Kazue Ito, Kaori Oikawa, Muluneh Tamiru-Oli, Atsushi Ohta, Ryo Matsumoto, Paterne Agre, David De Koeyer, Babil Pachakkil, Shinsuke Yamanaka, Satoru Muranaka, Hiroko Takagi, Ben White, Robert Asiedu, Hideki Innan, Asrat Asfaw, Patrick Adebola, Ryohei Terauchi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Genetics & Heredity
Takahiro Sakamoto, Hideki Innan
Summary: The turnover process of sex-determining loci consists of a stochastic phase and a deterministic phase. During the stochastic phase, a new sex-determining allele arises and random genetic drift plays a significant role, while during the deterministic phase, the allele increases in frequency through positive selection. Theoretical results suggest that the turnover of a newly arisen sex-determining locus benefits from selection at a linked locus under sexually antagonistic selection.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Shotaro Sakimura, Satoshi Nagayama, Mitsuko Fukunaga, Qingjiang Hu, Akihiro Kitagawa, Yuta Kobayashi, Takanori Hasegawa, Miwa Noda, Yuta Kouyama, Dai Shimizu, Tomoko Saito, Atsushi Niida, Yusuke Tsuruda, Hajime Otsu, Yoshihiro Matsumoto, Hiroki Uchida, Takaaki Masuda, Keishi Sugimachi, Shin Sasaki, Kazutaka Yamada, Kazuki Takahashi, Hideki Innan, Yutaka Suzuki, Hiromi Nakamura, Yasushi Totoki, Shinichi Mizuno, Masanobu Ohshima, Tatsuhiro Shibata, Koshi Mimori
Summary: This study revealed the significant role of copy number aberrations in cancer evolution, as well as the importance of neoantigens and diverse T cell receptor repertoire in postoperative recurrence. The comparison of driver mutations and immune response-related molecules between early and metastatic sites showed differences, and the postoperative recurrence was associated with neoantigen levels and TCR diversity in the metastatic sites.
Article
Biochemistry & Molecular Biology
Hideki Innan, Daniel Vaiman, Reiner A. Veitia
Summary: With the increasing lifespan and societal changes, women are now able to marry and have children later than in previous centuries. However, pathogenic genetic variants in the population can cause female subfertility or infertility before the average age of menopause, leading to counter-selection of these harmful alleles. It is speculated that as a logical consequence, menopause may occur later and women's reproductive lifespan may be extended. Factors such as medical interventions and lifestyle also play a role in female fertility.
Article
Multidisciplinary Sciences
Hideki Innan, Takahiro Sakamoto
Summary: Diffusion theory is commonly used in describing allele frequency behavior in one-locus one-population models, but handling it in models with multiple loci or populations is challenging. Multi-dimensional diffusion equations have shown strong potential in addressing evolutionary questions in population genetics.
PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
(2021)