Review
Biochemistry & Molecular Biology
Hanna Maerkle, Sona John, Amandine Cornille, Peter D. Fields, Aurelien Tellier
Summary: Host-parasite coevolution is a widespread phenomenon that shapes genetic and phenotypic diversity, as well as the evolutionary trajectory of interacting species. Recent advances in high throughput sequencing technologies allow for a more detailed study of the genetic basis, dynamics, and genomic consequences of coevolution. Three newly developed approaches leverage host and parasite full genome data to pinpoint coevolving loci and infer coevolutionary history, offering insight into the molecular underpinnings of coevolution.
Article
Biochemistry & Molecular Biology
Yibo Hu, Lijun Yu, Huizhong Fan, Guangping Huang, Qi Wu, Yonggang Nie, Shuai Liu, Li Yan, Fuwen Wei
Summary: This study investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms. The research revealed that the parasitic roundworms did not phylogenetically coevolve with their hosts but showed coevolution in specific proteins during protein interaction. Additionally, roundworms in both pandas exhibited unique genetic features related to metallopeptidase genes and fast larval development.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jianing Liu, R. Kelly Dawe
Summary: Through analyzing 26 complete maize genomes, it was found that haplotype divergence in low recombination regions, such as centromeres, occurred as far back as 450 thousand years ago, indicating the presence of ancient diversity in maize populations.
Article
Multidisciplinary Sciences
Layla Hockerstedt, Elina Numminen, Ben Ashby, Mike Boots, Anna Norberg, Anna-Liisa Laine
Summary: This study found that isolated host populations are more affected by pathogen infection, while connected host populations have higher levels of resistance diversity. Spatial structure and host gene flow play important roles in the impacts of pathogens on hosts.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Yi-Ye Liang, Yong Shi, Shuai Yuan, Biao-Feng Zhou, Xue-Yan Chen, Qing-Qing An, Par K. Ingvarsson, Christophe Plomion, Baosheng Wang
Summary: Natural selection plays a key role in shaping genetic diversity within and between species, with selective sweeps and background selection influencing genomic variation. Results from studying oak species genomes show the impact of different types of selection models and the importance of linked selection in shaping genetic diversity.
Review
Ecology
Isabel Blasco-Costa, Alexander Hayward, Robert Poulin, Juan A. Balbuena
Summary: It is crucial to integrate advances from ecology and evolutionary biology into cophylogeny for deeper mechanistic insights and to turn cophylogeny into a platform for understanding interspecific interactions and diversification. Key directions include trait reconstruction integration and consideration of multiple scales of network organization, with recent developments providing opportunities for implementation. A new quantitative framework is proposed to allow the integration of relevant information and assessment of individual mechanisms' contributions to cophylogenetic patterns.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Genetics & Heredity
Abdessamad Ouhrouch, Simon Boitard, Frederic Boyer, Bertrand Servin, Anne Da Silva, Francois Pompanon, Abdelmajid Haddioui, Badr Benjelloun
Summary: Sheep farming is a major source of meat in Morocco and plays a key role in the country's agriculture. The study revealed that Moroccan local sheep breeds exhibit high genetic diversity and a large set of adaptive variations, making them a valuable genetic resource for the conservation of sheep in the context of climate change.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Magnus Wolf, Menno de Jong, Sverrir Daniel Halldorsson, Ulfur Arnason, Axel Janke
Summary: Large-scale whaling in the 19th and 20th century led to a significant reduction in cetacean populations, but its impact on the genomic diversity of the fin whale remained unclear. This study examined the effect of whaling on the North Atlantic fin whale and found a noticeable drop in population size a century ago. However, the genome-wide heterozygosity and inbreeding indicators did not show significant changes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Toomas Kivisild, Lehti Saag, Ruoyun Hui, Simone Andrea Biagini, Vasili Pankratov, Eugenia D'Atanasio, Luca Pagani, Lauri Saag, Siiri Rootsi, Reedik Magi, Ene Metspalu, Heiki Valk, Martin Malve, Kadri Irdt, Tuuli Reisberg, Anu Solnik, Christiana L. Scheib, Daniel N. Seidman, Amy L. Williams, Kristiina Tambets, Mait Metspalu
Summary: The Finnish population, a genetic isolate, shows unexpected high levels of genetic connectedness with Estonians over the past eight centuries, despite clear differentiation in allele frequencies. This shared genetic heritage may originate from a migration event from North Estonia to Finland between the 8th-10th centuries.
AMERICAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Astronomy & Astrophysics
Junyao Li, John D. Silverman, Takuma Izumi, Wanqiu He, Masayuki Akiyama, Kohei Inayoshi, Yoshiki Matsuoka, Masafusa Onoue, Yoshiki Toba
Summary: The correlation between the mass of supermassive black holes and their host galaxies in the reionization epoch is studied. The results show that the observed distribution can be explained assuming that the underlying SMBH population at z~6 follows the relationship in the local universe. However, the evolution of the mass ratio and various uncertainties need to be considered to break the degeneracies.
ASTROPHYSICAL JOURNAL LETTERS
(2022)
Review
Genetics & Heredity
Madlen Stange, Rowan D. H. Barrett, Andrew P. Hendry
Summary: The 2019 United Nations Global Assessment Report on Biodiversity and Ecosystem Services estimated that approximately 1 million species are at risk of extinction. Genetics and genomics research can contribute to understanding the adaptive potential of species and communities, ultimately improving the conditions of ecosystems and people.
NATURE REVIEWS GENETICS
(2021)
Article
Biology
Raman Akinyanju Lawal, Uma P. Arora, Beth L. Dumont
Summary: The study leveraged 154 whole-genome sequences from various wild house mouse populations to examine the geographic organization of functional variation and identify signals of positive selection. They found a significant proportion of unique variations in single populations, including many predicted functional alleles, and strong signals of positive selection at genes associated with human diseases. Additionally, they uncovered multiple signals of selection at genes involved in dietary adaptations, suggesting the role of adaptation in shaping genetic variation in wild mouse populations.
Article
Biotechnology & Applied Microbiology
Muhammad Saqib Sohail, Raymond H. Y. Louie, Matthew R. McKay, John P. Barton
Summary: Genetic linkage plays a significant role in determining the fate of new mutations and their effects on fitness in evolving populations. Resolving genetic linkage is crucial for accurately quantifying selection and understanding the impact of mutations on evolutionary histories.
NATURE BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Fatemeh Amini, Guiping Hu, Lizhi Wang, Ruoyu Wu
Summary: Selecting for multiple traits in genomic selection has become increasingly important. This paper proposes a new method called L-shaped selection, which addresses the limitations of index selection and has been proven to find any Pareto optimal solution with appropriate weights. Computational experiments demonstrate the improved performance of L-shaped selection over index selection.
Article
Genetics & Heredity
Shoupu He, Gaofei Sun, Xiaoli Geng, Wenfang Gong, Panhong Dai, Yinhua Jia, Weijun Shi, Zhaoe Pan, Junduo Wang, Liyuan Wang, Songhua Xiao, Baojun Chen, Shufang Cui, Chunyuan You, Zongming Xie, Feng Wang, Jie Sun, Guoyong Fu, Zhen Peng, Daowu Hu, Liru Wang, Baoyin Pang, Xiongming Du
Summary: The study revealed that extensive chromosome inversions on chromosomes A06 and A08 underlies the geographic differentiation in cultivated cotton, and haplotypic diversity from landraces is essential for adaptive evolution. Introgression and association analyses identified new fiber quality-related loci, showing that introgressed alleles from diploid cottons have a large effect on fiber quality improvement.
Article
Gastroenterology & Hepatology
James A. Evans, Emanuela Carlotti, Meng-Lay Lin, Richard J. Hackett, Magnus J. Haughey, Adam M. Passman, Lorna Dunn, George Elia, Ross J. Porter, Mairi H. McLean, Frances Hughes, Joanne ChinAleong, Philip Woodland, Sean L. Preston, S. Michael Griffin, Laurence Lovat, Manuel Rodriguez-Justo, Weini Huang, Nicholas A. Wright, Marnix Jansen, Stuart A. C. McDonald
Summary: This study investigated the distribution of gland phenotypes in Barrett's esophagus (BE) and found that diverse gland phenotypes represent an evolutionary process, with changes in gland diversity potentially playing a role in disease progression.
Article
Virology
Cas Retel, Vienna Kowallik, Lutz Becks, Philine G. D. Feulner
Summary: This study characterized the genomic changes of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. The results showed highly repeatable genetic variants and strong positive selection in the studied populations. The study also identified potential targets of selection during Chlorella-Chlorovirus coevolution.
Article
Multidisciplinary Sciences
Jacob Househam, Timon Heide, George D. Cresswell, Inmaculada Spiteri, Chris Kimberley, Luis Zapata, Claire Lynn, Chela James, Maximilian Mossner, Javier Fernandez-Mateos, Alessandro Vinceti, Ann-Marie Baker, Calum Gabbutt, Alison Berner, Melissa Schmidt, Bingjie Chen, Eszter Lakatos, Vinaya Gunasri, Daniel Nichol, Helena Costa, Miriam Mitchinson, Daniele Ramazzotti, Benjamin Werner, Francesco Iorio, Marnix Jansen, Giulio Caravagna, Chris P. Barnes, Darryl Shibata, John Bridgewater, Manuel Rodriguez-Justo, Luca Magnani, Andrea Sottoriva, Trevor A. Graham
Summary: Genetic and epigenetic variation, as well as transcriptional plasticity, contribute to intratumour heterogeneity in colorectal cancer. However, the impact of intratumour genetic variation on gene expression traits and subclonal evolution is limited. Most intratumour gene expression variation is found to be "plastic" rather than strongly heritable. There may exist potential genetic controls on gene expression, but their association with subclone expansions is limited.
Article
Genetics & Heredity
Joshua T. Lange, John C. Rose, Celine Y. Chen, Yuriy Pichugin, Liangqi Xie, Jun Tang, King L. Hung, Kathryn E. Yost, Quanming Shi, Marcella L. Erb, Utkrisht Rajkumar, Sihan Wu, Sabine Taschner-Mandl, Marie Bernkopf, Charles Swanton, Zhe Liu, Weini Huang, Howard Y. Chang, Vineet Bafna, Anton G. Henssen, Benjamin Werner, Paul S. Mischel
Summary: Random segregation of extrachromosomal DNA contributes to intratumoral heterogeneity and facilitates the rapid adaptation of human tumor cells to anticancer drugs. Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Through theoretical models, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, it is shown that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment.
Article
Biology
Janina M. C. Diehl, Vienna Kowallik, Alexander Keller, Peter H. W. Biedermann
Summary: This study experimentally demonstrated that fruit-tree pinhole borers are able to actively shift symbiont communities, thus engaging in active farming. The study also found that the beetles exhibit selective promotion and/or suppression of symbionts, though the exact mechanisms behind this behavior require further investigation.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Cell Biology
Haider Tari, Ketty Kessler, Nick Trahearn, Benjamin Werner, Maria Vinci, Chris Jones, Andrea Sottoriva
Summary: In this study, a Bayesian inference framework was used to quantify spatial subclonal interactions in diffuse midline gliomas (DMGs). The study found that interactions between different subclones may enhance tumor invasion.
Article
Biochemistry & Molecular Biology
David Frei, Pascal Reichlin, Ole Seehausen, Philine G. D. Feulner
Summary: Anthropogenic disturbances have caused the extinction of an endemic whitefish species in Lake Constance, leading to hybridization with surviving species that potentially facilitates adaptation to deep-water habitats. The study identified genomic regions under divergent selection between deep and shallow spawning habitats, with introgression from the extinct species potentially contributing to ongoing deep-water adaptation. These findings support the syngameon hypothesis and highlight the importance of introgression from extinct species in enabling rapid adaptation and ecological recovery.
Article
Microbiology
Vienna Kowallik, Ashutosh Das, Alexander S. Mikheyev
Summary: Microbiomes can enhance the health and evolutionary potential of hosts, but can be disrupted by stressors like antibiotics, leading to harm to host's progeny.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Ana del Arco, Lutz Becks, Inmaculada de Vicente
Summary: The ecological risk assessment of chemicals neglects the ecological and evolutionary interplay in communities. Considering these factors can lead to improved assessments by testing for implications within and across trophic levels and changes in population diversity. This study presents a simple experimental system to evaluate the ecological and evolutionary responses of a microbial community to chemical exposure.
Article
Biochemistry & Molecular Biology
Guenole Le Pennec, Cas Retel, Vienna Kowallik, Lutz Becks, Philine G. D. Feulner
Summary: Through experimental research on a host-parasite system, we found that population structure, selection, and their interaction play a crucial role in genetic diversity. Populations that experience both selection and population structure fluctuations have higher genetic diversity, providing empirical support for improving theoretical models of adaptation during host-parasite co-evolution.
Article
Genetics & Heredity
Luis Zapata, Giulio Caravagna, Marc J. Williams, Eszter Lakatos, Khalid AbdulJabbar, Benjamin Werner, Diego Chowell, Chela James, Lucie Gourmet, Salvatore Milite, Ahmet Acar, Nadeem Riaz, Timothy A. A. Chan, Trevor A. Graham, Andrea Sottoriva
Summary: In cancer, clones that can evade the immune system are selected by evolutionary forces. By analyzing thousands of primary tumors and immune-checkpoint-treated metastases, researchers have measured immune selection using immune dN/dS, which is the ratio of nonsynonymous to synonymous mutations in the immunopeptidome. This analysis helps differentiate between immune-edited and immune-escaped tumors and predicts the response to immunotherapies.
Review
Ecology
Jelena H. Pantel, Lutz Becks
Summary: While the reciprocal effects of ecological and evolutionary dynamics on biodiversity are recognized as important, detecting and understanding these feedbacks remains challenging due to their occurrence at different scales and levels of organization. Recent advances in statistical methods and hypothesis testing provide a promising approach to identifying eco-evolutionary drivers even in non-model systems. This literature review discusses these advances and the challenges of fitting mechanistic models to eco-evolutionary data.
TRENDS IN ECOLOGY & EVOLUTION
(2023)