Article
Multidisciplinary Sciences
Sonja Kersten, Jiyang Chang, Christian D. Huber, Yoav Voichek, Christa Lanz, Timo Hagmaier, Patricia Lang, Ulrich Lutz, Insa Hirschberg, Jens Lerchl, Aimone Porri, Yves Van de Peer, Karl Schmid, Detlef Weigel, Fernando A. Rabanal
Summary: Repeated herbicide applications exert strong selection pressure on blackgrass, a major threat to temperate cereal crops, leading to rapid adaptation through target-site resistance (TSR) mutations and non-target-site resistance. We generated a reference genome for A. myosuroides and found that most populations with TSR mutations contained multiple TSR haplotypes, indicating soft sweeps as the norm. Simulation analysis suggested that TSR is primarily driven by standing genetic variation, with de novo mutations playing a minor role.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Kara Ryan, Ryan Greenway, Jake Landers, Lenin Arias-Rodriguez, Michael Tobler, Joanna L. Kelley
Summary: Hydrogen sulfide is a toxic gas that disrupts biological processes, yet fish in the Poecilia mexicana species complex have evolved sulfide tolerance multiple times. This study investigates whether the repeated evolution of tolerance is due to similar genomic changes, finding evidence of both convergence and divergence in gene variation associated with sulfide processes and toxicity.
Article
Biochemistry & Molecular Biology
Cinnamon S. Mittan-Moreau, Crystal Kelehear, Luis Felipe Toledo, Jamie Bacon, Juan M. Guayasamin, Andrew Snyder, Kelly R. Zamudio
Summary: This study investigated the establishment success of cane toads across their introduced range by examining the roles of introduction history and genetic diversity. The researchers found that Florida populations were more closely related to native Central American lineages, and there were high levels of diversity and population structure in the native range, supporting the idea that cane toads are a species complex. The study also revealed that introduced populations have slightly lower genetic diversity compared to native populations.
Article
Biochemistry & Molecular Biology
Katrina B. Harris, Kenneth M. Flynn, Vaughn S. Cooper
Summary: Evolution and diversification of Pseudomonas aeruginosa populations in biofilm-promoting environments show that adaptation and genetic variation are maintained without the usual elimination of diversity by fixation events. Multiple mutations are preserved at intermediate frequencies, suggesting that some environments may expose a larger fraction of the genome and select for many adaptations at once. This challenges the conventional idea that strong selection would normally purge genetic and phenotypic diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Scott T. Small, Carlo Costantini, N'Fale Sagnon, Moussa W. Guelbeogo, Scott J. Emrich, Andrew D. Kern, Michael C. Fontaine, Nora J. Besansky
Summary: The two forms of the major African malaria mosquito Anopheles funestus, which are indistinguishable in morphology but different in their genetic makeup, show evidence of local adaptation to breeding in natural swamps and irrigated rice fields. This rapid adaptation is fueled by standing genetic variation predating the split between the two forms. Differences in inversion frequencies likely facilitated the adaptive divergence between the two forms by suppressing recombination.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Sandra Lorena Ament-Velasquez, Ciaran Gilchrist, Alexandre Rego, Devin P. Bendixsen, Claire Brice, Julie Michelle Grosse-Sommer, Nima Rafati, Rike Stelkens
Summary: This study investigates the dynamics of fitness and genomic changes in yeast populations adapting to different environments. The results show that populations rapidly increase in fitness in stressful environments, while allele frequencies exhibit diverse trajectories. The study also identifies parallel genomic changes within and between environments.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Genetics & Heredity
Olivia L. Johnson, Raymond Tobler, Joshua M. Schmidt, Christian D. Huber
Summary: Recent studies have shown that cosmopolitan Drosophila populations exhibit seasonal fluctuation in allele frequencies at hundreds to thousands of genetic loci, which has raised questions about how genetic variation is maintained in natural populations. This has led to further exploration of the drivers, dynamics, and genome-wide impacts of fluctuating selection through theoretical and experimental studies. In this review, the latest evidence for multilocus fluctuating selection in Drosophila and other taxa is evaluated, with a focus on potential genetic and ecological mechanisms that maintain these loci and their effects on neutral genetic variation.
TRENDS IN GENETICS
(2023)
Article
Plant Sciences
Chengchuan Zhou, Yang Feng, Gengyun Li, Mengli Wang, Jinjing Jian, Yuguo Wang, Wenju Zhang, Zhiping Song, Linfeng Li, Baorong Lu, Ji Yang
Summary: The feralization of crop plants has attracted increasing interest due to its impact on crop production and the evolution of weedy forms. Weedy rice in eastern and northeastern China showed divergence in seed germination timing controlled by a temperature-sensing mechanism. An integrative analysis revealed extreme allele frequency differences and correlations between gene expression and feral phenotypes, indicating that weedy rice utilized pre-existing alleles for local adaptation and feralization. Activation of formerly silent alleles exposed cryptic phenotypes, promoting the evolution and persistence of weedy forms.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Haruna Nakamura, Mitsuto Aibara, Rei Kajitani, Hillary D. J. Mrosso, Semvua Mzighani, Atsushi Toyoda, Takehiko Itoh, Norihiro Okada, Masato Nikaido
Summary: The cichlids of Lake Victoria exhibit rapid adaptive radiation, with low genetic differentiation among species and highly differentiated genes related to vision playing a crucial role in speciation. Comparative genomic analyses of three Lake Victoria cichlid species in different habitats revealed distinct patterns of population history and identified novel adaptive candidate genes, some with long divergent haplotypes between species, indicating selective sweep events. Phylogenetic analyses showed that much of the allelic diversity among Lake Victoria cichlids originated from standing genetic variation before the adaptive radiation. The study uncovered the species-specific adaptation processes and complex genomic substrate that facilitated this adaptation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Quiterie Haenel, Laurent Guerard, Andrew D. C. MacColl, Daniel Berner
Summary: Adaptation to derived habitats can stem from standing genetic variation, with variants favored in new habitats potentially being neutral in ancestral populations. This suggests a potential mechanism for the maintenance of genetic variation that has been underappreciated.
Article
Ecology
Lindi M. Wahl, Mark M. Tanaka
Summary: The cost of sexual reproduction provides a significant advantage for derived asexual organisms, but their phylogenetic distribution suggests a higher risk of extinction compared to those engaging in sexual reproduction. Bacteria and archaea, on the other hand, have been able to persist for billions of years without sexual reproduction due to their large population sizes. However, asexual populations undergoing selective sweeps may still lose genetic variation and experience a reduction in effective population size, ultimately increasing the risk of extinction.
AMERICAN NATURALIST
(2022)
Article
Biology
Nico Fuhrmann, Celine Prakash, Tobias S. Kaiser
Summary: Genomic analysis confirms the recent establishment of different ecotypes in marine midges of the genus Clunio, which are characterized by variations in timing of adult emergence, oviposition behavior, and larval habitat. QTL mapping and genome screens reveal that polygenic adaptation from standing genetic variation, particularly involving circadian clock genes, sensory perception genes, and nervous system development genes, plays a central role in ecotype formation. These findings suggest that adaptive ecotype formation can occur rapidly through ongoing gene flow and the re-assortment of existing alleles.
Article
Agronomy
Seema Yadav, Xianming Wei, Priya Joyce, Felicity Atkin, Emily Deomano, Yue Sun, Loan T. Nguyen, Elizabeth M. Ross, Tony Cavallaro, Karen S. Aitken, Ben J. Hayes, Kai P. Voss-Fels
Summary: Non-additive genetic effects are important in the expression of complex traits in sugarcane, and including non-additive effects in genomic prediction models significantly improves the prediction accuracy of clonal performance. The study showed that prediction accuracies for TCH were improved using extended-GBLUP model, but no improvement was observed for CCS and Fibre.
THEORETICAL AND APPLIED GENETICS
(2021)
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
Physics, Fluids & Plasmas
Diego Cirne, Paulo R. A. Campos
Summary: In the past two decades, there has been improved understanding of adaptive evolution in natural populations under constant environments. However, understanding the effects of environmental changes on adaptation remains challenging. This study investigates the impact of the rate of environmental variation on the predictability of evolution using the adaptive-walk approximation method.
Article
Genetics & Heredity
Alison F. Feder, Pleuni S. Pennings, Dmitri A. Petrov
Summary: This paper demonstrates the use of time series data to bound evolutionary parameters, complementing and informing traditional population genetic approaches. By studying drug-induced resistance evolution in HIV, we show new evidence that early HIV treatment failure was driven by soft sweeps.
Article
Genetics & Heredity
Nandita R. Garud, Philipp W. Messer, Dmitri A. Petrov
Summary: The debate over whether hard sweeps or soft sweeps dominate adaptation has continued, with the authors proposing that soft sweeps are prevalent in North American Drosophila melanogaster. Another study by Harris et al. has raised doubts about the reliability of soft sweeps detected, instead suggesting that hard sweeps may be more likely. However, upon reanalysis, the authors confirm that soft sweeps are the dominant mode of adaptation in North American Drosophila melanogaster.
Article
Biology
Alison F. Feder, Kristin N. Harper, Chanson J. Brumme, Pleuni S. Pennings
Summary: Triple-drug therapies have transformed HIV from a fatal condition to a chronic one, significantly reducing the risk of drug resistance evolution, but not eliminating it entirely.
Editorial Material
Microbiology
Nandita Garud
Summary: Microbes can evolve rapidly to adapt to selection pressures, but our understanding of the adaptation in microbiomes is still incomplete. Advances in modeling complex populations and scenarios will help us better understand adaptation in microbiomes and other natural populations experiencing similar complexities.
Article
Virology
Kaho H. Tisthammer, Christopher Kline, Tara Rutledge, Collin R. Diedrich, Sergio Ita, Philana Ling Lin, Zandrea Ambrose, Pleuni S. Pennings
Summary: This study evaluated viral diversity in a non-human primate model of SIV-Mtb co-infection and found changes in viral diversity and divergence over 6-9 weeks. Compartmentalization of viral diversity was observed in different tissues, with the highest diversity in thoracic lymph nodes. Viral diversity in lung granulomas was correlated with CD4+ T cell frequency and inversely correlated with CD8+ T cell frequency.
Article
Biochemical Research Methods
Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud
Summary: The ability to predict human phenotypes and identify disease biomarkers from metagenomic data is important for microbiome-associated disease therapeutics. However, technical variables unrelated to the phenotype can complicate prediction and biomarker discovery. Supervised methods may be limited in correcting for unmeasured variation, while unsupervised approaches can struggle with the unique characteristics of microbiome data. A comparative analysis of denoising transformations and correction methods reveals that unsupervised principal component correction has comparable effectiveness in reducing false discovery as supervised approaches, without requiring knowledge of the sources of variation. However, the unsupervised approach only improves prediction when technical variables contribute to the majority of data variance. Background noise correction will be crucial as more metagenomic datasets become available.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daisy W. Chen, Nandita R. Garud
Summary: By analyzing longitudinal fecal metagenomic data from over 700 infants and their mothers, this study reveals distinct evolutionary dynamics in the infant gut microbiome compared to adults. The rate of evolution and strain turnover in the infant gut is significantly higher than in healthy adults, with gene loss dominating during the mother-infant transition at delivery. These dynamics stabilize within a few months after birth, with an increase in gene gains as the microbiome matures.
Article
Genetics & Heredity
Kaho H. Tisthammer, Caroline Solis, Faye Orcales, Madu Nzerem, Ryan Winstead, Weiyan Dong, Jeffrey B. Joy, Pleuni S. Pennings
Summary: This study applied a frequency-based approach to estimate the fitness costs of mutations at 7957 sites along the HCV genome. The results showed that the fitness costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G.
Article
Genetics & Heredity
Pleuni S. Pennings, C. Brandon Ogbunugafor, Ruth Hershberg
Summary: This study utilizes computational and theoretical approaches to explain experimental evolution findings. It finds that high mutation rates increase the probability of reversion toward the wild type when compensation is only partial. However, the existence of even a single fully compensatory mutation dramatically decreases the probability of reversion to the wild type. These findings help explain the dynamics of compensation and reversion in real-world scenarios.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemical Research Methods
Rochelle-Jan Reyes, Nina Hosmane, Shasta Ihorn, Milo Johnson, Anagha Kulkarni, Jennifer Nelson, Michael Savvides, Duc Ta, Ilmi Yoon, Pleuni S. Pennings
Summary: Science students increasingly need programming and data science skills to be competitive, but our university lacked the necessary courses. To address this, we established a computing applications minor known as PINC. We share our experience and 10 rules, covering course setup, teaching methods, and program management.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Genetics & Heredity
Nandita R. Garud
Summary: Nandita Garud discusses two influential papers by Hermisson and Pennings that offer a framework for determining whether adaptation should occur gradually or rapidly.
NATURE REVIEWS GENETICS
(2023)
Article
Microbiology
Richard Wolff, William Shoemaker, Nandita Garud
Summary: The human gut microbiome exhibits substantial ecological diversity at both the species and strain levels. The majority of species maintain stable genetic diversity over time, and strain abundances can be predicted by a stochastic logistic model, suggesting dynamic stability. Additionally, strain abundances follow macroecological laws known to hold at the species level. These findings highlight the importance of strains as an ecological unit in the human gut microbiome.
Article
Ecology
Maya A. A. Lewinsohn, Trevor Bedford, Nicola F. F. Mueller, Alison F. F. Feder
Summary: A Bayesian state-dependent evolutionary phylodynamic model (SDevo) is used to quantify the difference in division rates between tumour cells at the periphery and interior. This model accurately infers spatially varying birth rates of tumors and outperforms existing methods in analyzing differential sequence evolution. Clinical data shows evidence of higher division rates on the tumor edge. The use of high-resolution, multi-region sequencing can further help investigate spatial growth restrictions and other factors that influence tumor progression.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Microbiology
Maoz Gelbart, Sheri Harari, Ya'ara Ben-Ari, Talia Kustin, Dana Wolf, Michal Mandelboim, Orna Mor, Pleuni S. Pennings, Adi Stern
