Editorial Material
Biochemistry & Molecular Biology
Joshua A. Thia
Summary: The paper explores how genetic architecture and life history impact invasive success, using the example of European green crabs spreading on the North American west coast. It highlights the role of chromosomal inversions in facilitating rapid adaptive evolution in introduced populations.
Review
Genetics & Heredity
Manas Joshi, Adamandia Kapopoulou, Stefan Laurent
Summary: The study highlights the significant role of genetic variation within cis-regulatory elements (CREs) in influencing gene expression, phenotypic changes, and potentially speciation. Recent advancements in high-throughput sequencing technologies have furthered the understanding of the impact of such variation on local adaptation and evolution within natural populations.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Banu Sebnem Onder, Cansu Fidan Aksoy
Summary: This study examines the variation in wing size and shape in a population of Drosophila melanogaster over different seasons and years. The results show that environmental variables such as temperature, precipitation, and humidity have significant effects on the fluctuating patterns of wing size and shape, with humidity having a more pronounced effect in male flies.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Anubhab Khan, Kaushalkumar Patel, Harsh Shukla, Ashwin Viswanathan, Tom van der Valk, Udayan Borthakur, Parag Nigam, Arun Zachariah, Yadavendradev Jhala, Marty Kardos, Uma Ramakrishnan
Summary: Habitat fragmentation leads to small populations, increasing the risk of inbreeding depression. Small populations can reduce inbreeding depression by purging deleterious recessive alleles. The study on Indian tiger populations found differences in inbreeding levels and mutation load between small and large populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Marty Kardos, Gordon Luikart
Summary: The genetic architecture underlying heritability significantly impacts population viability during environmental change, with polygenic trait architectures showing higher viability compared to architectures with large-effect loci. Initial frequency of large-effect beneficial alleles also plays a crucial role in population viability, with moderately low initial allele frequencies conferring higher viability. Integrating information on trait genetic architecture into analysis will improve understanding and prediction of evolutionary and demographic responses to environmental change.
AMERICAN NATURALIST
(2021)
Article
Biochemistry & Molecular Biology
Benedikt Kirsch-Gerweck, Leonard Bohnenkaemper, Michel T. Henrichs, Jarno N. Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Joachim Burger, Jens Stoye, Yoan Diekmann
Summary: We developed an efficient haplotype-based approach to detect positive selection in large genomic datasets. By combining pattern matching and model-based inference, our method achieves high sensitivity and specificity with low computational resource requirements. Evaluation using UK Biobank data indicates scalability to population genomic datasets with millions of individuals. Our approach serves as an algorithmic blueprint for big data genomics, combining a combinatorial core with statistical inference in closed form.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Evolutionary Biology
John K. Kelly
Summary: This study characterizes the evolution of SNPs in a population of yellow monkeyflower. It finds that most SNPs exhibit minimal change over time, consistent with neutral evolution. However, a subset of SNPs display strong fluctuations in frequency, which are driven by selection and have a ripple effect on genome-wide variation.
Article
Multidisciplinary Sciences
Nan Wang, Xietian Song, Junli Ye, Siqi Zhang, Zhen Cao, Chenqiao Zhu, Jianbing Hu, Yin Zhou, Yue Huang, Shuo Cao, Zhongjie Liu, Xiaomeng Wu, Lijun Chai, Wenwu Guo, Qiang Xu, Brandon S. Gaut, Anna M. G. Koltunow, Yongfeng Zhou, Xiuxin Deng
Summary: The study reveals the mechanism and evolution of apomixis in Citrinae. Multiple embryos of a maternal genotype form directly from nucellar cells, utilizing endosperm for growth, enabling asexual reproduction of the maternal genetic constitution. This mechanism poses a significant barrier to breeding in Citrinae. Genetic and molecular analyses suggest that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae, and introgression may be involved in apomixis in some varieties of Fortunella. The FhRWP gene, associated with apomixis, contains heterozygous structural variants that facilitate nucellar embryogenesis.
NATIONAL SCIENCE REVIEW
(2022)
Article
Biochemistry & Molecular Biology
Soraia Barbosa, Kimberly R. Andrews, Amanda R. Goldberg, Digpal S. Gour, Paul A. Hohenlohe, Courtney J. Conway, Lisette P. Waits
Summary: This study examines the neutral and adaptive processes in species and population differentiation using recently diverged sister species of ground squirrels. The results highlight the importance of neutral and adaptive differentiation in understanding genetic structure and environmental adaptation, with implications for conservation efforts.
Article
Plant Sciences
Zhen Peng, Hongge Li, Gaofei Sun, Panhong Dai, Xiaoli Geng, Xiao Wang, Xiaomeng Zhang, Zhengzhen Wang, Yinhua Jia, Zhaoe Pan, Baojun Chen, Xiongming Du, Shoupu He
Summary: The paper introduces a cotton genomic variation database, CottonGVD, which provides cotton researchers with a comprehensive tool to exhibit genomic variations and GWAS results. Users can easily retrieve, browse, query, and visualize various cotton-related data using built-in tools and interactive maps provided in the database.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Loke von Schmalensee, Pauline Caillault, Katrin Hulda Gunnarsdottir, Karl Gotthard, Philipp Lehmann
Summary: Seasons impose different selection pressures on organisms, leading to varying adaptive strategies. This study investigates the resolution of seasonal conflicts in two closely related butterfly species through field experiments, laboratory work, and citizen science data analyses. The results reveal differences in fitness and population dynamics between Pieris rapae and P. napi across seasons, driven by physiological and behavioral traits. P. rapae maximizes gains during growth seasons but suffers from higher winter mortality, while P. napi minimizes harm during adverse seasons.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
William C. Rosenthal, John M. Fennell, Elizabeth G. Mandeville, Jason C. Burckhardt, Annika W. Walters, Catherine E. Wagner
Summary: This study examined the relative fitness and reproductive strategies of hybridizing populations of Yellowstone cutthroat trout and rainbow trout. The results showed that Yellowstone cutthroat trout outperformed rainbow trout in terms of reproduction and there was slight female preference for males of similar ancestry. These findings provide insights into the effects of natural selection and hybridization on population dynamics.
Article
Genetics & Heredity
Anne Slavotinek, Shannon Rego, Nuriye Sahin-Hodoglugil, Mark Kvale, Billie Lianoglou, Tiffany Yip, Hannah Hoban, Simon Outram, Beatrice Anguiano, Flavia Chen, Jeremy Michelson, Roberta M. Cilio, Cynthia Curry, Renata C. Gallagher, Marisa Gardner, Rachel Kuperman, Bryce Mendelsohn, Elliott Sherr, Joseph Shieh, Jonathan Strober, Allison Tam, Jessica Tenney, William Weiss, Amy Whittle, Garrett Chin, Amanda Faubel, Hannah Prasad, Yusuph Mavura, Jessica Van Ziffle, W. Patrick Devine, Ugur Hodoglugil, Pierre-Marie Martin, Teresa N. Sparks, Barbara Koenig, Sara Ackerman, Neil Risch, Pui-Yan Kwok, Mary E. Norton
Summary: This study evaluated the diagnostic yield of exome sequencing (ES) in individuals of European and underrepresented minority (URM) and underserved (US) patients. The results showed a higher diagnostic rate in pediatric patients compared to prenatal patients, but there was no significant difference in diagnostic yield or inconclusive findings between URM/non-URM and US/non-US patients. These findings support the use of ES to identify clinically relevant variants in patients from diverse populations.
NPJ GENOMIC MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Lucy Peters, Jisca Huisman, Loeske E. B. Kruuk, Josephine M. Pemberton, Susan E. Johnston
Summary: Sexually selected traits exhibit large variation and rapid evolution in the animal kingdom, yet genetic variation persists within populations despite directional selection. Understanding the genetic architecture of sexually selected traits, such as antler morphology in red deer, can shed light on evolutionary drivers and constraints at the genomic level. The study on red deer antler traits revealed high repeatability, heritability, and polygenic architecture, suggesting that genetic covariances among traits and pleiotropy may contribute to the maintenance of genetic variation in antler morphology.
Article
Ecology
Gregory Thom, Camila C. Ribas, Eduardo Shultz, Alexandre Aleixo, Cristina Y. Miyaki
Summary: This study explores the historical demographic changes of populations occurring on the floodplains of the Solimoes River in the Amazon Basin and finds that habitat specificity might be an important predictor of population connectivity.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Genetics & Heredity
Chuan Cao, Rodrigo Cogni, Vincent Barbier, Francis M. Jiggins
Article
Ecology
Leandro G. Cosmo, Andre R. Nascimento, Rodrigo Cogni, Andre V. L. Freitas
ARTHROPOD-PLANT INTERACTIONS
(2019)
Article
Biochemistry & Molecular Biology
Julia B. Raices, Paulo A. Otto, Maria D. Vibranovski
Article
Clinical Neurology
Claudia Ismania Samogy-Costa, Elisa Varella-Branco, Frederico Monfardini, Helen Ferraz, Rodrigo Ambrosio Fock, Ricardo Henrique Almeida Barbosa, Andre Luiz Santos Pessoa, Ana Beatriz Alvarez Perez, Naila Lourenco, Maria Vibranovski, Ana Krepischi, Carla Rosenberg, Maria Rita Passos-Bueno
JOURNAL OF NEURODEVELOPMENTAL DISORDERS
(2019)
Article
Biochemistry & Molecular Biology
Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, Matthew A. Streisfeld
Article
Multidisciplinary Sciences
Diomar Vercosa, Rodrigo Cogni, Marcos Nopper Alves, Jose Roberto Trigo
SCIENTIFIC REPORTS
(2019)
Article
Plant Sciences
Leandro G. Cosmo, Lydia F. Yamaguchi, Gabriel M. F. Felix, Massuo J. Kato, Rodrigo Cogni, Martin Pareja
Summary: Plant secondary chemistry influences plant-insect community structure; phytochemical diversity plays a role in shaping the variation in plant secondary chemistry and its impact on community structure. Both compositional and structural dimensions of PD affect herbivory, caterpillar biodiversity, and plant-herbivore network structure at different scales, indicating that PD has distinct roles across biological organization scales.
JOURNAL OF ECOLOGY
(2021)
Article
Genetics & Heredity
Murillo F. Rodrigues, Rodrigo Cogni
Summary: Understanding how animal populations evolve in response to climate change requires overcoming challenges in differentiating genetic adaptation from phenotypic plasticity, mapping genotype, phenotype, and fitness, and considering the effects of neutral demographic processes and natural selection on genetic variation. Classical model organisms like Drosophila melanogaster offer promising opportunities to study adaptation to climate change and lay the groundwork for similar research in non-model systems.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P. Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E. Castedo Ellerman, Jared G. Galloway, Ariella L. Gladstein, Gregor Gorjanc, Bing Guo, Ben Jeffery, Warren W. Kretzschumar, Konrad Lohse, Michael Matschiner, Dominic Nelson, Nathaniel S. Pope, Consuelo D. Quinto-Cortes, Murillo F. Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton, Hugo van Kemenade, Anthony W. Wohns, Yan Wong, Simon Gravel, Andrew D. Kern, Jere Koskela, Peter L. Ralph, Jerome Kelleher
Summary: This article introduces the release of msprime 1.0 and summarizes its numerous features and advantages through a collaborative open source development model. Compared to specialized alternatives, msprime demonstrates excellent performance with faster speed and higher memory efficiency, making it a commonly used simulation tool in population genetics.
Article
Biology
Rodrigo Cogni, Shuai Dominique Ding, Andre C. Pimentel, Jonathan P. Day, Francis M. Jiggins
Summary: Wolbachia has a protective effect on viral infection in a natural population of Drosophila, with individuals infected with Wolbachia being less likely to be infected by viruses. This antiviral effect is specific to certain viruses and contributes to the ecological success of Wolbachia.
COMMUNICATIONS BIOLOGY
(2021)
Article
Ecology
Rodrigo Cogni, Tiago B. Quental, Paulo R. Guimaraes Jr
Summary: The classic paper by Ehrlich and Raven on coevolution has had a significant impact on the study of coevolution and has inspired generations of scientists. Their contributions include exploring the genetic mechanisms of coevolutionary interactions, investigating the association between coevolutionary diversification and ecological network organization, and examining micro- and macroevolutionary mechanisms and patterns under their hypothesis. This paper discusses overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.
Review
Biochemistry & Molecular Biology
Andre C. Pimentel, Camila S. Beraldo, Rodrigo Cogni
Summary: Host shifts, particularly cross-species transmission of pathogens, play a significant role in the emergence of infectious diseases like COVID-19. Current research focuses on understanding the factors that determine whether cross-species transmission leads to spillover or sustained infection, with a particular emphasis on the interactions between Drosophila species and viruses.
GENETICS AND MOLECULAR BIOLOGY
(2021)