Article
Multidisciplinary Sciences
Magdalena Bohutinska, Jakub Vlcek, Sivan Yair, Benjamin Laenen, Veronika Konecna, Marco Fracassetti, Tanja Slotte, Filip Kolar
Summary: Parallel adaptation provides insight into evolutionary predictability through replicated natural experiments, showing varying levels of genomic parallelism depending on the genetic divergence between lineages. Studies on Arabidopsis species adapting to alpine environments identified 151 genes under positive selection associated with alpine colonization and response to environmental challenges. The extent of genomic parallelism decreases significantly with increasing genetic divergence, driven by the decreasing probability of repeated selection on the same alleles, highlighting the importance of genetic divergence in genome evolution predictability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Ecology
Johnma J. Rondon, Nicolas Nahuel Moreyra, Vadim A. Pisarenco, Julio Rozas, Juan Hurtado, Esteban Hasson
Summary: Odorant-binding proteins (OBPs) are involved in the perception of olfactory signals in insects and mediate host preference and shifts. Studies on the Drosophila genus show significant variations in OBP gene repertoire among species, suggesting a role in host adaptation. The research indicates potential for rapid evolution and positive selection in specific OBP genes, especially in lineages associated with different ecological scenarios.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Nittay Meroz, Nesli Tovi, Yael Sorokin, Jonathan Friedman
Summary: Managing and engineering microbial communities requires the ability to predict their composition. While little work has been done on predicting compositions on evolutionary timescales, this study shows that community composition typically changes during evolution, but the composition of replicate communities remains similar. These changes were also predictable, suggesting that it may be possible to forecast the evolution of microbial communities even on long timescales.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
Summary: Utilizing a newly developed bioinformatics pipeline, Drosophila melanogaster's Pool-Seq data is mapped to a hologenome to create the largest genomic data repository to date, called DEST, including 271 population samples from over 100 locations worldwide. This dataset can be used to study spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Physics, Multidisciplinary
Angus Leung, Naotsugu Tsuchiya
Summary: This study explores how a system generates conscious experience using integrated information theory. The theory proposes measuring integrated information (phi) and suggests applying it at the scale where the measure is maximized. The study confirms through computational models and neural recordings that phi becomes maximal at specific temporal scales.
Article
Biochemistry & Molecular Biology
Diana J. Rennison, Catherine L. Peichel
Summary: Highly pleiotropic genes are less likely to be used during adaptation, but parallel genomic regions contain genes with higher pleiotropy. Pleiotropy only becomes constraining at high levels, and low or intermediate levels of pleiotropy may be beneficial for adaptation.
Article
Biotechnology & Applied Microbiology
D. De Panis, H. Dopazo, E. Bongcam-Rudloff, A. Conesa, E. Hasson
Summary: Our study reveals different transcriptional strategies in D. buzzatii and D. koepferae to cope with the challenges posed by their natural resources. D. buzzatii exhibits greater transcriptional plasticity, mainly modulated by alkaloids of its secondary host, while D. koepferae shows a more canalized genetic response, associated with the cactus species.
Article
Biochemistry & Molecular Biology
Sylvia M. Durkin, Mahul Chakraborty, Antoine Abrieux, Kyle M. Lewald, Alice Gadau, Nicolas Svetec, Junhui Peng, Miriam Kopyto, Christopher B. Langer, Joanna C. Chiu, J. J. Emerson, Li Zhao
Summary: Studying the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii using a comparative species framework involving behavioral, gene expression, and genomic analyses. The study showed a gradual transition to ripe fruit oviposition preference in D. suzukii compared to closely related species and identified a species-specific preference for stiff substrates driving their choice for ripe fruits. High-quality genome sequencing of D. subpulchrella allowed the identification of candidate genes involved in D. suzukii's ability to target ripe fruits and adapt to a new ecological niche.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: Experimental evolution combined with whole-genome sequencing is a powerful method to study the adaptive architecture of selected traits. This study shows that the presence of a second stressor affects the genomic selection response, and the combination of temperature and laboratory adaptation results in widespread synergistic effects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Evolutionary Biology
Aude E. Caizergues, Jeremy Le Luyer, Arnaud Gregoire, Marta Szulkin, Juan-Carlos Senar, Anne Charmantier, Charles Perrier
Summary: This study investigated the genomic and epigenomic changes in the Great tit bird in response to urban life. The findings reveal that urbanization induces polygenic and nonparallel genomic and epigenomic responses, with changes mainly occurring in regions associated with gene expression and biological functions related to the nervous system, immunity, behavior, hormones, and stress responses.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Immunology
JooHee Choi, Eric C. Keen, Meghan A. Wallace, Skye Fishbein, Jerome Prusa, Madsen Zimbric, Carlos R. Mejia-Chew, Shail B. Mehta, Thomas C. Bailey, Lindsay J. Caverly, Carey-Ann D. Burnham, Gautam Dantas
Summary: Comparative genomics of 175 Mycobacterium abscessus isolates revealed nonrandom parallel mutations in 22 genes. We identified altered macrolide susceptibility co-occurring with a nonsynonymous whiB1 mutation and the loss of a 23-kb mercury-resistance plasmid during M. abscessus in-host adaptation.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Ecology
Mats Ittonen, Alexandra Hagelin, Christer Wiklund, Karl Gotthard
Summary: Daylength affects diapause induction in butterflies, but northern populations are able to adapt rapidly to their local daylength conditions during range expansions.
Article
Biochemistry & Molecular Biology
Matthew K. Brachmann, Kevin Parsons, Skuli Skulason, Oscar Gaggiotti, Moira Ferguson
Summary: Sympatric adaptive phenotypic divergence of benthic and pelagic morphs in Icelandic Arctic charr is underlined by genomic differentiation. The divergence histories were reconstructed using coalescent modeling and single nucleotide polymorphisms. Genomic differentiation was characterized by outlier loci and was associated with phenotypic and ecological variation, suggesting a genomic basis for adaptive divergence. Little evidence was found for a parallel genomic basis of differentiation among populations.
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
Multidisciplinary Sciences
Robert K. Robbins, Qian Cong, Jing Zhang, Jinhui Shen, Julia Quer Riera, Debra Murray, Robert C. Busby, Christophe Faynel, Winnie Hallwachs, Daniel H. Janzen, Nick Grishin
Summary: The research team found that the evolution of cycad feeding and conspicuous coloration in Eumaeus was accompanied by little genomic change. After its origin, Eumaeus split into two fast-evolving lineages instead of forming a clump of close relatives. This indicates parallel evolution among the two lineages of Eumaeus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Sai Li, Eric Bo Zheng, Li Zhao, Shixin Liu
Article
Biology
Evan Witt, Sigi Benjamin, Nicolas Svetec, Li Zhao
Article
Ecology
Orna Levran, Eran Even-Tov, Li Zhao
Article
Biochemistry & Molecular Biology
Samuel Khodursky, Nicolas Svetec, Sylvia M. Durkin, Li Zhao
Article
Biochemistry & Molecular Biology
Evan Witt, Nicolas Svetec, Sigi Benjamin, Li Zhao
Summary: Evolutionarily young genes tend to be preferentially expressed in the testis, while older genes are more likely to be biased towards ovary expression in Drosophila. The relationship between gene age and expression is strongest in the ovary and weakest in the testis. Furthermore, upstream transcription factor (TF) expression is highly predictive of gene expression in the ovary, while testis gene expression is influenced by both TF expression and open promoter chromatin.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Sylvia M. Durkin, Mahul Chakraborty, Antoine Abrieux, Kyle M. Lewald, Alice Gadau, Nicolas Svetec, Junhui Peng, Miriam Kopyto, Christopher B. Langer, Joanna C. Chiu, J. J. Emerson, Li Zhao
Summary: Studying the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii using a comparative species framework involving behavioral, gene expression, and genomic analyses. The study showed a gradual transition to ripe fruit oviposition preference in D. suzukii compared to closely related species and identified a species-specific preference for stiff substrates driving their choice for ripe fruits. High-quality genome sequencing of D. subpulchrella allowed the identification of candidate genes involved in D. suzukii's ability to target ripe fruits and adapt to a new ecological niche.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Evan Witt, Zhantao Shao, Chun Hu, Henry M. Krause, Li Zhao
Summary: This study explored dosage compensation in Drosophila testis at the single-cell level, revealing that certain germ cell types exhibit X chromosome expression similar to autosomes, indicating dosage compensation activity. Genes near chromatin entry sites showed higher expression in cell types with dosage compensation, providing additional evidence of this process. Lack of expression of most dosage compensation complex genes suggests a potential noncanonical mechanism mediating observed pre-meiotic dosage compensation. These findings offer new insights into the understanding of sex chromosomes.
Article
Biochemistry & Molecular Biology
Junhui Peng, Nicolas Svetec, Li Zhao
Summary: Proteins are essential for cell functions, and understanding their molecular evolution is crucial. Previous studies have shown that adaptation often occurs at the protein surface, but it is unclear whether adaptive sites are randomly distributed throughout the genome or associated with specific structural or functional characteristics. This study found that protein sequence adaptation is more related to function than structure, and strongly differentiated amino acids across geographic regions in protein-coding genes are mostly adaptive, contributing to long-term adaptive evolution. The results highlight the importance of intermolecular interactions and coadaptation in protein adaptive evolution at both species and population levels.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Julie M. Cridland, Alex C. Majane, Li Zhao, David J. Begun
Summary: Research on de novo gene discovery in Drosophila has revealed significant differences in gene abundance and expression between different tissues, particularly in the testis and accessory gland. While other properties such as transcript length and chromosomal distribution are more similar, regulatory mechanisms may vary and interact with selection to produce differences in de novo genes expressed in male reproductive tissues.
Article
Biology
Eric B. Zheng, Li Zhao
Summary: Using a mass-spectrometry-first computational approach, the study identifies a large number of unannotated open reading frames with evidence of translation in Drosophila melanogaster, suggesting their de novo origin. Contrary to expectations, the fastest-evolving open reading frames are not the youngest. The study also reveals a higher occurrence of these open reading frames in the brain compared to the testis. The results indicate significant diversity in de novo protein evolution, suggesting different evolutionary trajectories.
Article
Biology
Krithika Venkataraman, Nadav Shai, Priyanka Lakhiani, Sarah Zylka, Jieqing Zhao, Margaret Herre, Joshua Zeng, Lauren A. Neal, Henrik Molina, Li Zhao, Leslie B. Vosshall
Summary: Female Aedes aegypti mosquitoes face climate challenges due to rising global temperatures, causing suboptimal conditions for egg-laying. In the laboratory, under drought-like conditions, these mosquitoes retain mature eggs until suitable conditions for laying eggs arise. The genes tweedledee and tweedledum are found to play a crucial role in this extended egg retention.
Article
Ecology
Evan Witt, Christopher B. B. Langer, Nicolas Svetec, Li Zhao
Summary: Older fathers may pass on more paternally derived de novo mutations, possibly due to the decreased ability to remove mutations during spermatogenesis. This study provides new insights into the impact of paternal age on genetic mutations.
NATURE ECOLOGY & EVOLUTION
(2023)
Editorial Material
Genetics & Heredity
Li Zhao
Summary: The research reviews a 2006 paper by Levine et al. that identified a few de novo genes and proposed a potentially universal process of de novo gene birth, which greatly advanced this field of study.
NATURE REVIEWS GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Samuel Khodursky, Eric B. Zheng, Nicolas Svetec, Sylvia M. Durkin, Sigi Benjamin, Alice Gadau, Xia Wu, Li Zhao
Summary: The study investigates the sequence determinants of chromatin accessibility in different species and tissues of Drosophila using deep neural networks. The results show that the sequence determinants are highly conserved and accessible regions are mutationally robust. The study also identifies motifs predictive of accessibility, recovering both novel and previously known motifs.
Article
Multidisciplinary Sciences
Samuel Khodursky, Caroline S. Jiang, Eric B. Zheng, Roger Vaughan, Daniel R. Schrider, Li Zhao
Summary: Understanding phenotypic sex differences is important in biology. Analysis of RNA-seq and single-cell RNA sequencing data reveals sex differences in gene expression variability, which are associated with important biological functions and sex-biased diseases. These genes also show increased selective constraint and may have a genetic basis. A simple evolutionary model is proposed to explain the emergence of sex differences in variability.