Review
Biology
Christian Schloetterer
Summary: Experimental evolution is a useful tool for testing the predictability of evolution without the confounding effects of inaccurate forecasts. Parallel evolution has been studied in both asexual microorganisms and sexual species, but the predictability varies between different aspects. The predictability of genomic selection response for polygenic traits depends on the founder population and the adaptive architecture in the ancestral populations.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Thomas Rolland, Freddy Cliquet, Richard J. L. Anney, Clara Moreau, Nicolas Traut, Alexandre Mathieu, Guillaume Huguet, Jinjie Duan, Varun Warrier, Swan Portalier, Louise Dry, Claire S. Leblond, Elise Douard, Frederique Amsellem, Simon Malesys, Anna Maruani, Roberto Toro, Anders D. Borglum, Jakob Grove, Simon Baron-Cohen, Alan Packer, Wendy K. Chung, Sebastien Jacquemont, Richard Delorme, Thomas Bourgeron
Summary: The prevalence of autism-associated genetic variants in individuals without a diagnosis of autism is explored. These variants are associated with a decrease in fluid intelligence, qualification level, income, and an increase in metrics related to material deprivation. Autism-associated genes have a larger impact on these phenotypic features than other genes with loss-of-function variants.
Article
Ecology
Maddie E. James, Melanie J. Wilkinson, Diana M. Bernal, Huanle Liu, Henry L. North, Jan Engelstadter, Daniel Ortiz-Barrientos
Summary: The independent and repeated adaptation of populations to similar environments often leads to the evolution of similar forms, known as parallel evolution. This study on multiple coastal ecotypes of Senecio lautus in Australia shows a strong correlation between phenotype and environment, with all populations evolving along the same phenotypic trajectory through mutational changes in different genes. The research sheds light on replicated adaptation at both phenotypic and genotypic levels within populations, highlighting S. lautus as a striking example of phenotypic parallel evolution in nature.
Review
Biochemistry & Molecular Biology
Rik Verdonck, Delphine Legrand, Staffan Jacob, Herve Philippe
Summary: Ciliates have a unique genetic system with two types of nuclei in each cell. The ecological and evolutionary significance of nuclear dimorphism in ciliates has not been well explained. We propose a novel explanation that suggests ciliate nuclear dimorphism can be considered as a tool for phenotypic plasticity by somatic selection at the level of the ciliate clone.
TRENDS IN MICROBIOLOGY
(2022)
Article
Evolutionary Biology
Irina Calic, Simon C. Groen, Jae Young Choi, Zoe Joly-Lopez, Elena Hamann, Mignon A. Natividad, Katherine Dorph, Carlo Leo U. Cabral, Rolando O. Torres, Georgina V. Vergara, Amelia Henry, Michael D. Purugganan, Steven J. Franks
Summary: Accurately predicting responses to selection is crucial in biology and crop breeding. In this study, we investigated constraints to selection for drought resistance in rice. We found that traits related to drought response were heritable and under selection. However, we did not find evidence that factors such as genetic correlations, linkage, or pleiotropy would constrain selection for drought resistance. Genetic correlations had little influence on responses to selection, except for seed mass under drought conditions. Breeding lines with high fitness and yield under drought also performed well under wet conditions, indicating no yield penalty for drought resistance. Multiple genes were found to influence both water use efficiency and days to first flowering, supporting a genetic trade-off between drought escape and avoidance strategies. These findings provide valuable insights for understanding and managing evolutionary constraints and breeding stress-resistant crops.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Multidisciplinary Sciences
Piaopiao Chen, Jianzhi Zhang
Summary: This study analyzed transcriptomic data from multiple species and found that genetic assimilation of environment-induced gene expression is not common, with most genes retaining their expression plasticity after organisms adapt to new environments.
Article
Biochemistry & Molecular Biology
Marissa M. Spear, Sophie J. Levi, Julie R. Etterson, Briana L. Gross
Summary: Resurrection experiments were conducted to study phenotypic and molecular evolution in response to environmental challenges. The researchers compared plants from seed collections that were 36 years old to modern seed collections from the same area, using molecular and quantitative genetic approaches. They found differentially expressed transcripts between the two groups, with generally higher transcript expression in the modern samples. Admixture analysis suggested gene flow from domesticated to modern populations over time. The study also involved growing one population pair under different environmental conditions, showing that traits differed between the antecedent and modern populations, with modern individuals displaying some coherent trait changes in response to climate changes.
Review
Genetics & Heredity
Maud Fagny, Frederic Austerlitz
Summary: The adaptation of populations to local environments often involves selecting optimal values for polygenic traits. Research has shown the importance of systems biology in understanding the molecular basis of polygenic traits and the evolution of gene regulatory networks. A unified framework merging population genetics, quantitative genetics, and systems biology is needed to better comprehend the molecular basis of polygenic traits adaptation.
TRENDS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Nannan Liu, Yuanhao Du, Marilyn L. Warburton, Yingjie Xiao, Jianbing Yan
Summary: The study found rich phenotypic plasticity variation among maize F-1 hybrids, involving hundreds of quantitative trait loci, most of which contributed little variance. Heterosis in terms of phenotypic plasticity was also observed, which is crucial for understanding the genetic structure and breeding of maize.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
James Baxter-Gilbert, Julia L. Riley, Celine H. Frere, Martin J. Whiting
Summary: Urban wildlife, such as Australian water dragons, face unique challenges that result in selective pressure leading to population-level changes. Urban hatchlings show distinct morphological differences compared to those from natural populations, with shorter body lengths and longer limbs, while urban adult males exhibit shorter body lengths. However, developmental environment in urban-style enclosures influences body size of yearlings, with no significant differences in performance capacity observed between urban and natural reared dragons.
Article
Biology
Jacopo Franzoni, Giovanni Astuti, Lorenzo Peruzzi
Summary: By studying the relationship between genetic divergence at neutral loci, phenotypic variation, and geographic and environmental distances, micro-evolutionary scenarios involving natural selection and neutral evolution can be analyzed. In this study, we examined the patterns of intraspecific genetic and phenotypic variation along an elevational gradient using Dianthus virgineus as a study system. We found a weak genetic structure related to geographic distance, but genetic drift was not the primary factor driving phenotypic traits. The high degree of phenotypic differentiation in relation to genetic divergence at neutral loci suggests that selection, possibly driven by changing conditions at different sites, may explain the observed patterns of variation.
Article
Genetics & Heredity
Varun Warrier, Xinhe Zhang, Patrick Reed, Alexandra Havdahl, Tyler M. Moore, Freddy Cliquet, Claire S. Leblond, Thomas Rolland, Anders Rosengren, David H. Rowitch, Matthew E. Hurles, Daniel H. Geschwind, Anders D. Borglum, Elise B. Robinson, Jakob Grove, Hilary C. Martin, Thomas Bourgeron, Simon Baron-Cohen
Summary: Comprehensive factor analysis of core diagnostic features provides insights into the complex genetic architecture underlying phenotypic heterogeneity in autism. The study found that common genetic variants were associated with the core factors of autism, but not de novo variants. Higher autism polygenic scores were associated with a lower likelihood of co-occurring developmental disabilities, and autistic females showed a stronger over-inheritance of autism PGS compared to males.
Article
Ecology
Alexander Lalejini, Austin J. Ferguson, Nkrumah A. Grant, Charles Ofria
Summary: Populations with adaptive phenotypic plasticity undergo less evolutionary change than non-plastic populations, making it easier for them to retain new adaptive traits. Adaptive phenotypic plasticity helps stabilize populations against environmental fluctuations.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biology
Giovanni Pezzulo, Thomas Parr, Karl Friston
Summary: This article discusses the evolution of brain architectures for predictive processing, arguing that these mechanisms emerged gradually from simpler predictive loops and were key to solving adaptive regulation problems. The article formalizes the evolution from simpler to more complex brains using generative models and explores the expansion, duplication, and deepening of predictive control in response to different spatial and temporal scales. The proposal aligns neuroscientific theories with evolutionary and comparative data on brain architectures.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Ecology
Thomas Dorey, Florian P. Schiestl
Summary: Many organisms exhibit phenotypic plasticity in response to the environment. This study investigates the link between plasticity and selection using Brassica rapa plants. The researchers observed strong plasticity in morphology, nectar, and floral scent in response to different soil types and aphid herbivory. Positive selection was found on nectar and morphological traits in hand- and bumblebee-pollinated plants.
Article
Biochemistry & Molecular Biology
Karin Rengefors, Raphael Gollnisch, Ingrid Sassenhagen, Karolina Harnstrom Aloisi, Marie Svensson, Karen Lebret, Dora Certnerova, William A. Cresko, Susan Bassham, Dag Ahren
Summary: The study investigated the genetic structure and dispersal pathways of G. semen using RAD tag sequencing. It revealed a distinct population genetic structure with western and eastern populations likely representing different lineages. Despite significant genetic differentiation among lakes, there was limited isolation by distance, and gene flow was observed from the northeast/east towards the southwest/west. This suggests that migratory birds may act as dispersal vectors for G. semen propagules.
Article
Genetics & Heredity
Christine H. O'Connor, Kristin L. Sikkink, Thomas C. Nelson, Janna L. Fierst, William A. Cresko, Patrick C. Phillips
Summary: The study used experimental evolution to dissect the genetic architecture of acute heat stress and oxidative stress response in the nematode C. remanei, finding that these traits are polygenic and complex, involving hundreds of genomic regions. Contrary to expectation, the genetic bases of acute heat stress and oxidative stress response in C. remanei appear to be largely independent, suggesting that rapid adaptation can be generated by changes at multiple sites in the genome.
G3-GENES GENOMES GENETICS
(2021)
Article
Cell Biology
Allison M. Fuiten, William A. Cresko
Summary: A significant sequence divergence of a highly conserved hindbrain hoxa2b enhancer element was found in the family syngnathidae, despite its previous recognition as highly conserved across vertebrates. Modifications in binding element sequence motifs and spacing suggest potential roles of natural mutations in phenotypic diversity within pipefish and seahorse species. The study highlights the importance of investigating diverse taxa for understanding gene regulatory evolution and the impact of natural mutations on deeply conserved pathways.
DEVELOPMENT GENES AND EVOLUTION
(2021)
Article
Microbiology
Hannah F. Tavalire, Diana M. Christie, Leslie D. Leve, Nelson Ting, William A. Cresko, Brendan J. M. Bohannan
Summary: The study found that early life home environment significantly influences the gut microbiome in children, with a shared home environment being the strongest predictor of overall microbiome similarity. The abundance of certain microbial taxa is more influenced by host genetic similarity, while the presence of certain taxa depends more on a shared home environment.
Review
Genetics & Heredity
Emily A. Beck, Hope M. Healey, Clayton M. Small, Mark C. Currey, Thomas Desvignes, William A. Cresko, John H. Postlethwait
Summary: EMMs provide unique avenues to study gene-by-environment interactions and mutations in noncoding regions, improving our understanding of complex diseases. Fish, as the most diverse group of vertebrates, exhibit specialized phenotypes that could be pathogenic in humans but are adaptive in their specialized habitats.
TRENDS IN GENETICS
(2022)
Article
Genetics & Heredity
Katja R. Kasimatis, Megan J. Moerdyk-Schauwecker, Ruben Lancaster, Alexander Smith, John H. Willis, Patrick C. Phillips
Summary: Sexual reproduction is a complex process that contributes to differences between the sexes and divergence between species. This study investigates the role of pre- and post-insemination sexual selection in the evolution of male reproductive success using an experimental evolution approach. The results show that enhanced post-insemination competition is more effective than pre-insemination competition in driving the evolution of male reproductive success. Surprisingly, enhanced pre-insemination competition hinders selection and slows down the rate of evolution. Post-insemination selection leads to a strong polygenic response at the whole-genome level.
Article
Genetics & Heredity
Hope M. Healey, Susan Bassham, William A. Cresko
Summary: Single-cell RNA sequencing is a powerful technique, but incomplete 3'-UTR annotations can impede analysis. In this study, we demonstrate that combining single-cell isoform sequencing with single-cell RNA sequencing can rapidly improve 3'-UTR annotations and enhance the identification of cell types and gene expression patterns.
Article
Multidisciplinary Sciences
Clayton M. Small, Hope M. Healey, Mark C. Currey, Emily A. Beck, Julian Catchen, Angela S. P. Lin, William A. Cresko, Susan Bassham
Summary: Seadragons are a remarkable lineage of teleost fishes known for male pregnancy. By producing gene-annotated, chromosome-scale genome models for seadragons, we have identified interesting genomic features specific to seadragons, as well as syngnathid-specific gene losses. These resources serve as important tools for future evolutionary studies and conservation efforts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Fisheries
Mark C. Currey, Charline Walker, Susan Bassham, Hope M. Healey, Emily A. Beck, William A. Cresko
Summary: Gynogenetic embryos can be created by fertilizing eggs with radiation-treated sperm, and these organisms have many applications in aquaculture, evolutionary biology and genomics. Previous methods of assessing paternal contribution have focused on a small subset of the genome, but this study used genome-wide assessments and found evidence of paternal genetic material in gynogenetic diploids. This study highlights the need for more comprehensive assessments of paternal contributions to gynogenetic animals.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Genetics & Heredity
Sophia Frantz, Clayton M. Small, William A. Cresko, Nadia D. Singh
Summary: Wolbachia is a maternally transmitted endosymbiotic bacteria that infects a wide variety of arthropod and nematode hosts. The effects of Wolbachia on host biology are far-reaching and include changes in host gene expression. However, previous work on the host transcriptional response has generally been investigated in the context of a single host genotype. Thus, the relative effect of Wolbachia infection versus vs. host genotype on gene expression is unknown.
G3-GENES GENOMES GENETICS
(2023)
Article
Microbiology
Clayton M. Small, Emily A. Beck, Mark C. Currey, Hannah F. Tavalire, Susan Bassham, William A. Cresko
Summary: This study demonstrates a positive association between host genetic dissimilarity and microbiome dissimilarity in stickleback fish. The findings provide insight into the genomic architecture of gut microbiome variation and highlight the influence of host genome on microbiome diversity.
Article
Biology
Zachary C. Stevenson, Megan J. Moerdyk-Schauwecker, Stephen A. Banse, Dhaval S. Patel, Hang Lu, Patrick C. Phillips
Summary: High-throughput transgenesis using synthetic DNA libraries is a powerful method for exploring genetic function. However, the need for library transgenesis has restricted its application to single-cell models. In this study, we present TARDIS, a method that overcomes these limitations and enables large-scale transgenesis in multicellular systems. We demonstrate its utility in Caenorhabditis elegans and show that transformation yields can be increased up to approximately 1000-fold compared to current methods.
Article
Genetics & Heredity
Martin Stervander, William A. Cresko
Summary: The fish order Syngnathiformes, including commercially important species like red mullets and diverse seahorses, have unique adaptations such as male pregnancy. The mandarinfish within this order has a highly contiguous genome assembly, with potential for research on genetic underpinnings of novel pigmentation. This genomic resource will likely serve as an outgroup for syngnathid fish and contribute to the understanding of evolution and pigmentation.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Katja R. Kasimatis, Abin Abraham, Peter L. Ralph, Andrew D. Kern, John A. Capra, Patrick C. Phillips
Summary: Sex and sexual differentiation are common in various species, leading to different selection pressures between sexes. However, studies on autosomal loci in humans did not find clear evidence of sexually antagonistic viability selection, possibly due to cross-hybridization with sex chromosome regions at these loci.