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Estimation of spatial demographic maps from polymorphism data using a neural network bioRxiv. Evol. Biol. Pub Date : 2024-03-17 Chris C R Smith, Gilia C Patterson, Peter L. Ralph, Andrew D. Kern
A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and source sink dynamics of dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities. Geographically referenced
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Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease bioRxiv. Evol. Biol. Pub Date : 2024-03-17 Katherine Fleck, Victor Luria, Nitanta Garag, Amir Karger, Trevor Hunter, Daniel Marten, William Phu, Kee-Myoung Nam, Nenad Sestan, Anne H. O'Donnell-Luria, Jelena Erceg
Genome organization is intricately tied to regulating genes and associated cell fate decisions. In this study, we examine the positioning and functional significance of human genes, grouped by their evolutionary age, within the 3D organization of the genome. We reveal that genes of different evolutionary origin have distinct positioning relationships with both domains and loop anchors, and remarkably
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Unraveling the Evolutionary Trajectory of LHCI in Red-Lineage Algae: Conservation, Diversification, and Neolocalization bioRxiv. Evol. Biol. Pub Date : 2024-03-17 Minoru Kumazawa, Kentaro Ifuku
Red algae and the secondary symbiotic algae that engulfed a red alga as an endosymbiont are called red-lineage algae. They comprise key marine taxa including diatoms, Haptophyta, and Cryptophyta. Several photosystem (PS) I-light-harvesting complex I (LHCI) structures have been reported from red-lineage algae, two red algae Cyanidioschyzon merolae (Cyanidiophyceae), Porphyridium purpureum (Rhodophytina)
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Imprinting and DNA methylation in water lily endosperm: implications for seed evolution bioRxiv. Evol. Biol. Pub Date : 2024-03-17 Rebecca A Povilus, Caroline A Martin, Mary Gehring
Endosperm is a key evolutionary innovation associated with the origin of angiosperms (flowering plants). This altruistic seed tissue supports the growth and development of the embryo by mediating the relationship of the mother plant as a nutrient source to the compatriot embryo as a nutrient sink. The endosperm is the primary site of gene imprinting in plants (where expression of an allele depends
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Y-chromosomal microsatellites and expansion from Africa bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Zarus Cenac
Research has suggested that Africa is the continent from which modern humans dispersed around the world. Some diversities are thought to trace this expansion; they decline as distance from Africa accumulates, and they suggest that the expansion originated within a range of locations in Africa. Previously, a decline was found regarding Y-chromosomal microsatellite heterozygosity. However, this diversity
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Evolution of ion channels in cetaceans a natural experiment in the tree of life bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Cristobal Uribe, Mariana Nery, Kattina Zavala, Gonzalo Mardones, Gonzalo Riadi, Juan Opazo
Cetaceans could be seen as a natural experiment within the tree of life in which a mammalian lineage changed from terrestrial to aquatic habitats. This shift involved extensive phenotypic modifications representing an opportunity to explore the genetic bases of phenotypic diversity. Furthermore, the availability of whole genome sequences in representative species of all main cetacean groups means that
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The Mycobacterium tuberculosis complex pangenome is small and driven by sub-lineage-specific regions of difference bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Mahboobeh Behruznia, Maximillian Marin, Maha R Farhat, Jonathan C Thomas, Maria Rosa Domingo-Sananes, Conor J Meehan
The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulence, and antibiotic resistance. While it is known that within MTBC diversity is characterised by large lineage-specific deletions (regions of difference [RD]), a comprehensive
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Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Dominique Colinet, Fanny Cavigliasso, Matthieu Leobold, Appoline Pichon, Serge Urbach, Dominique Cazes, Marine Poullet, Maya Belghazi, Anne-Nathalie Volkoff, Jean-Michel Drezen, Jean-Luc Gatti, Marylene Poirie
Animal venoms and other protein-based secretions that perform a variety of functions, from predation to defense, are highly complex cocktails of bioactive compounds. Gene duplication, accompanied by modification of the expression and/or function of one of the duplicates under the action of positive selection, followed by further duplication to produce multigene families of toxins is a well-documented
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Global climate change effect on Asian Mus musculus; Implication from last glacial maximum to the end of the 21st century bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Yaser Amir Afzali
Global climate change poses unprecedented challenges to biodiversity, prompting urgent investigations into its effects on various species. This study focuses on Mus musculus, a small rodent species and a crucial indicator of ecosystem health. Spanning from the last glacial maximum to the end of the 21st century, employed Species Distribution Models (SDMs) to assess the impacts of climate change on
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Transcriptomic response to pyrethroid treatment in closely related bed bug strains varying in resistance bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Chloe Haberkorn, Zainab Belgaidi, Romain Lasseur, Fabrice Vavre, Julien Varaldi
The common bed bug, Cimex lectularius, is one of the main human parasites. The world-wide resurgence of this pest is mainly due to globalization, and the spread of insecti- cide resistance. A few studies have compared the transcriptomes of susceptible and resistant strains. However, these studies usually relied on strains originating from distant locations, possibly explaining their extended candidate
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FST and genetic diversity in an island model with background selection bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Syed Asad Hasan, Michael C. Whitlock
Background selection, by which selection on deleterious alleles reduces diversity at linked neutral sites, influences patterns of total neutral diversity, πT, and genetic differentiation, FST, in structured populations. The theory of background selection may be split into two regimes: the background selection regime, where selection pressures are strong and mutation rates are sufficiently low such
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Repatterning of mammalian backbone regionalization in cetaceans bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Amandine Gillet, Katrina E Jones, Stephanie E Pierce
The reinvasion of the aquatic realm by cetaceans is one of the most iconic ecological transitions that led to drastic modifications of the mammalian body plan, especially the axial skeleton. Relative to the vertebral column of other mammals that is subdivided into numerous anatomical regions, regional boundaries of the cetacean backbone appear obscured. Whether the traditional mammalian regions are
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Population structure and genetic diversity of the Critically Endangered bowmouth guitarfish (Rhina ancylostomus) in the Northwest Indian Ocean bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Marja J Kipperman, Rima W Jabado, Alifa Banthe Haque, Daniel Fernando, P.A.D.L Anjani, Julia LY Spaet, Emily Humble
The bowmouth guitarfish (Rhina ancylostomus) is a unique and relatively understudied species of wedgefish with a distribution spanning the Indo-Pacific Oceans. Due to targeted and bycatch fisheries, this species is experiencing serious declines across its range. It is now considered among the most threatened species of elasmobranch. Despite this, species-specific management is limited, particularly
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Fast and recurrent evolution of temperature preference among drosophilids bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Tane Kafle, Manuel Grub, Panagiotis Sakagiannis, Martin Paul Nawrot, J. Roman Arguello
Small-bodied ectotherms are acutely vulnerable to temperature changes but diverse thermotactic behaviours have contributed to their ability to inhabit broad climatic niches. Understanding how - and how fast - these behaviours evolve are outstanding biological questions that are also relevant to conservation. Among insects, Drosophila melanogaster is a preeminent ectothermic model for temperate sensing
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Phylogeny-aware modeling uncovers molecular functional convergences associated with complex multicellularity in Eukarya bioRxiv. Evol. Biol. Pub Date : 2024-03-16 Francisco Pereira Lobo, Dalbert Benjamim da Costa, Thieres Tayroni Martins da Silva, Maycon Douglas de Oliveira
A major trait of Eukarya is the independent evolution of complex multicellular lineages of animals and plants with specialized cell types organized in tissues, organs and systems. The number of cell types (NCT) has been commonly adopted as a proxy in comparative studies investigating the genomic evolution of biological complexity. Although expansions of homologous genes playing roles in extracellular
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Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Katia Bougiouri, Sophy Charlton, Alex Harris, Alberto Carmagnini, Giedre Piliciauskiene, Tatiana R. Feuerborn, Lachie Scarsbrook, Kristina Tabadda, Povilas Blazevicius, Heidi G. Parker, Shyam Gopalakrishnan, Greger Larson, Elaine A. Ostrander, Evan K. Irving-Pease, Laurent A. F. Frantz, Fernando Racimo
The multi-millenia long history between dogs and humans has justly placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the huge diversity of breeds today. Although ancient genomes provide
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Emergent time scales of epistasis in protein evolution bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Leonardo Di Bari, Matteo Bisardi, Sabrina Cotogno, Martin Weigt, Francesco Zamponi
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution encompasses random nucleotide mutations, insertions and deletions, and models selection using a fitness landscape, which is inferred via a generative probabilistic model for
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Lysine-Cysteine-Serine-Tryptophan Inserted into the DNA-Binding Domain of Human Mineralocorticoid Receptor Increases Transcriptional Activation by Aldosterone bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Yoshinao Katsu, Jiaweng Zhang, Michael E. Baker
Due to alternative splicing in the DNA-binding domain (DBD) of the mineralocorticoid receptor (MR), humans contain two almost identical MR transcripts with either 984 amino acids (MR-984) or 988 amino acids (MR-988), in which their DBDs differ by only four amino acids, Lys,Cys,Ser,Trp (KCSW). Human MRs also contain mutations at two sites, codons 180 and 241, in the amino terminal domain (NTD). Together
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Haplore: An alternative approach for Y chromosomal haplogroup identification bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Lukkaet Laoprapaipan, Kittichai Phusawang, Peerapan Laorchairangsi, Arnond Kitnitchee, Hataitip Wachirawanitchkit, Bun Suwanparsert, Pattarapon Promnun
Identification of Y chromosomal haplogroups holds significance in the study of human evolution. In this context, an alternative approach named Haplore was introduced for identifying Y chromosomal haplogroups. This approach relied on the algorithm of matched and unmatched informative SNPs extracted from the reference phylogenetic tree, implemented in Python. Haplore demonstrated high accuracy in identifying
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Socioecological drivers of injuries in female and male rhesus macaques (Macaca mulatta) bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Melissa A. Pavez Fox, Erin Siracusa, Samuel Ellis, Clare Kimock, Nahiri Rivera-Barreto, Josue Negron-Del Valle, Daniel Phillips, Angelina Ruiz-Lambides, Noah Snyder-Mackler, James Higham, Lauren Brent, Delphine De Moor
Competition over access to resources, such as food and mates, is believed to be one of the major costs associated with group living. Two socioecological factors suggested to predict the intensity of competition are group size and the relative abundance of sexually active individuals. However, empirical evidence linking these factors to injuries and survival costs is scarce. Here, we leveraged 10 years
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Gene expression shifts in Emperor penguin adaptation to the extreme Antarctic environment bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Josephine R Paris, Flávia A Nitta Fernandes, Federica Pirri, Samuele Greco, Marco Gerdol, Alberto Pallavicini, Marine Benoiste, Clément Cornec, Lorenzo Zane, Brian Haas, Céline Le Bohec, Emiliano Trucchi
Gene expression can accelerate ecological divergence by rapidly tweaking the response of an organism to novel environments, with more divergent environments exerting stronger selection and, supposedly, requiring faster adaptive responses. Organisms adapted to extreme environments provide ideal systems to test this hypothesis, particularly when compared to related species with milder ecological niches
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Genome streamlining: effect of mutation rate and population size on genome size reduction bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Juliette Luiselli, Jonathan Rouzaud-Cornabas, Nicolas Lartillot, Guillaume Beslon
Genome streamlining, i.e. genome size reduction, is observed in bacteria with very different life traits, including endosymbiotic bacteria and several marine bacteria, raising the question of its evolutionary origin. None of the hypotheses proposed in the literature is firmly established, mainly due to the many confounding factors related to the diverse habitats of species with streamlined genomes
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Assessing tooth wear progression in primates: A longitudinal study using intraoral scanning technology bioRxiv. Evol. Biol. Pub Date : 2024-03-15 Ian Towle, Kristin L. Krueger, Raquel Hernando, Leslea J. Hlusko
Intraoral scanners are widely used in a clinical setting for orthodontic treatments and tooth restorations, and are also useful for assessing dental wear and pathology progression. In this study, we assess the utility of using an intraoral scanner and associated software for quantifying dental tissue loss in non-human primates. An upper and lower second molar for 31 captive hamadryas baboons (Papio
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Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Tristan P. W. Dennis, Poppy Pescod, Sonia Barasa, Louise Teixeira Cerdeira, Eric R Lucas, Chris S Clarkson, Alistair Miles, Alex Asidi, Emile Z. Manzambi, Emery Metelo, Josue Zanga, Steve N. Salambi, Seth R. Irish, Martin James Donnelly, David Weetman, Francis Wat'senga Tezzo
The Democratic Republic of Congo (DRC) suffers from one of the highest malaria burdens worldwide, but information on its Anopheles vector populations is relatively limited. Preventative malaria control in DRC is reliant on pyrethroid-treated nets, raising concerns over the potential impacts of insecticide resistance. We sampled Anopheles gambiae from three geographically distinct populations (Kimpese
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Pseudogenisation of NK3 Homeobox 2 (Nkx3.2) in Monotremes Provides Insight into Unique Gastric Anatomy and Physiology bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Jackson Bryce Dann, Zhipeng Qu, Linda Shearwin-Whyatt, Rachel van der Ploeg, Frank Grutzner
The enzymatic breakdown and regulation of food thoroughfare through the vertebrate antral stomach and pyloric sphincter (antropyloric region) is a trait conserved over 450 million years. Development of the structures involved is underpinned by a highly conserved developmental pathway involving the hedgehog, bone morphogenetic protein (BMP) and Wingless/Int-1 (Wnt) protein families. Monotremes are one
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Evolution of Virulence in Emerging Epidemics: From Theory to Experimental Evolution and Back bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Wakinyan Benhamou, François Blanquart, Marc Choisy, Thomas W Berngruber, Rémi Choquet, Sylvain Gandon
The experimental validation of theoretical predictions is a significant step in the demonstration of the predictive power of a model. In a previous study, we monitored the evolution of the temperate phage λ spreading in continuous cultures of Escherichia coli. This experimental work confirmed the influence of the epidemiological dynamics on the evolution of transmission and virulence of the virus.
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Experimental evolution of an RNA virus in Caenorhabditis elegans bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Victoria G. Castiglioni, María J Olmo-Uceda, Susana Martín, Marie Anne Félix, Rubén González, Santiago F. Elena
The discovery of Orsay virus (OrV), the first virus infecting wild populations of Caenorhabditis elegans, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that C. elegans offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary
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Characterisation of Skoliomonas gen. nov., a haloalkaliphilic anaerobe related to barthelonids (Metamonada). bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Yana Eglit, Shelby K. Williams, Andrew J. Roger, Alastair G.B. Simpson
Metamonads are a large and exclusively anaerobic clade of protists. Additionally, metamonads are one of the three clades with a proposed 'excavate' ancestral cell morphology, characterised by a conspicuous ventral groove often accompanied by a posterior flagellum with a vane. Here, we characterise four isolates of an anaerobic bacterivorous flagellate from hypersaline and alkaline soda lake environments
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Convergent gene expression in epithelial cells illuminates the evolution of uterine receptivity bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Axelle Brulport, Malgorzata Anna Gazda, Maelle Daunesse, Eulalie Liorzou, Bruno Raquillet, Anthony Lepelletier, Maria Sopena-Rios, Pierrick Regnard, Lyne Fellmann, Lucie Faccin, Slaveia Garbit, Alexia Cermolacce, Ivanela Kondova, Mariam Raliou, Louis Marcellin, Carole Abo, Ludivine Doridot, Camille Berthelot
The independent evolution of convergent embryo implantation mechanisms in humans and mice, differing from the ancestral mammalian phenotype, is poorly understood. Endometrial epithelial cells are the first maternal interface encountered by the embryo. We combined organoid models and single-cell transcriptomics to investigate how gene expression has evolved in endometrial epithelial cells between human
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The evolutionary history of the ancient weevil family Belidae (Coleoptera: Curculionoidea) reveals the marks of Gondwana breakup and major floristic turnovers, including the rise of angiosperms bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Xuankun Li, Adriana E. Marvaldi, Rolf G. Oberprieler, Dave Clarke, Brian D. Farrell, Andrea Sequeira, M. Silvia Ferrer, Charles O'Brien, Shayla Salzman, Seunggwan Shin, William Tang, Duane D. McKenna
The rise of angiosperms to ecological dominance and the breakup of Gondwana during the Mesozoic marked major transitions in the evolutionary history of insect-plant interactions. To elucidate how contemporary trophic interactions were influenced by host plant shifts and palaeogeographical events, we integrated molecular data with information from the fossil record to construct a timetree for ancient
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De novo evolution of transmissible tumors in Hydra bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Sophie Tissot, Jordan Meliani, Justine Boutry, Lionel Brazier, Jácint Tökkölyi, Benjamin Roche, Beata Ujvari, Aurora M Nedelcu, Frédéric Thomas, Antoine M Dujon
While most cancers are not transmissible, there are rare cases where cancer cells have acquired the ability to spread vertically or horizontally to other individuals, and sometimes species, causing epidemics in their hosts. However, as these transmissible cancers are usually detected once they are relatively well disseminated in host populations, the conditions associated with their origin remain poorly
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Ant queens cannibalise infected brood to contain disease spread and recycle nutrients bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Flynn Bizzell, Christopher D Pull
Filial cannibalism, where parents eat their own offspring, is a taxonomically widespread behaviour with a multitude of potential adaptive explanations. Of these, the impact of parasites on the expression of filial cannibalism is particularly poorly understood. On one hand, cannibalising young with low survival probability may enable parents to reinvest valuable resources into future reproduction; on
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Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence bioRxiv. Evol. Biol. Pub Date : 2024-03-14 Nathan Rives, Vinita Lamba, C.-H. Christina Cheng, Xuan Zhuang
Determining the origins of novel genes and the genetic mechanisms underlying the emergence of new functions is challenging yet crucial for understanding evolutionary innovations. The novel fish antifreeze proteins, exemplifying convergent evolution, represent excellent opportunities to investigate the evolutionary origins and pathways of new genes. Particularly notable is the near-identical type I
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MASCOT-Skyline integrates population and migration dynamics to enhance phylogeographic reconstructions bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Nicola Felix Müller, Remco R Bouckaert, Chieh-Hsi Wu, Trevor Felix Bedford
The spread of infectious diseases is shaped by spatial and temporal aspects, such as host population structure or changes in the transmission rate or number of infected individuals over time. These spatiotemporal dynamics are imprinted in the genome of pathogens and can be recovered from those genomes using phylodynamics methods. However, phylodynamic methods typically quantify either the temporal
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"This training is bound for glory": selection by experimental evolution of a bacteriophage with expanded host-range and increased virulence bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Amandine Maurin, Marie Vasse, Carlos Zarate-Chaves, Cecile breyton, Sarah Bouzidi, Juliette hayer, Jacques Dainat, Margaux Mesleard-Roux, Francois-Xavier Weill, Ignacio G Bravo, Alexandre Feugier, Remy Froissart
Phage host-range expansion is predicted to be at the cost of lower mean fitness. We aimed at following the adaptive walks of a virulent phage (Tequintavirus) evolving in a spatially variable environment composed of four susceptible and four resistant strains (Salmonella enterica enterica pv Tennessee, sequence types ST5018 and ST319 respectively). We evolved a single ancestor through serial passages
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Time-resolved oxidative signal convergence across the algae-embryophyte divide bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Tim P Rieseberg, Armin Dadras, Tatyana Darienko, Sina Post, Cornelia Herrfurth, Janine MR Fuerst-Jansen, Nils Hohnhorst, Romy Petroll, Stefan A Rensing, Thomas Proeschold, Sophie de Vries, Iker Irisarri, Ivo Feussner, Jan de Vries
The earliest land plants faced a significant challenge in adapting to environmental stressors. Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood. Here
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Fixation times of de novo and standing beneficial variants in subdivided populations bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Vitor Sudbrack, Charles Mullon
The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficial de novo mutations, as well as fixation time from standing genetic variation. We investigate
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Sexual antagonism and sex determination in three syngnathid species alongside male pregnancy gradient and varying sex roles. bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Arseny Dubin, Jamie Parker, Astrid Boehne, Olivia Roth
The allocation of energy towards gamete production, parental care, mate choice, sex roles, and sexual dimorphism generates divergence in selection between sexes, leading to sexual antagonism (SA). Due to the shared genetic makeup a single genomic locus can contain a gene or allele with differing fitness impacts on each sex. This intralocus sexual conflict is resolved through intersex bias in gene expression
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Environmental and genetic influence on rate and spectrum of spontaneous mutations in Escherichia coli bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Danna R Gifford, Anish Bhattacharyya, Alexandra Geim, Eleanor Marshall, Rok Krašovec, Christopher G Knight
Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests
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Ongoing hybridisation among clownfishes: the genomic architecture of the Kimbe Bay hybrid zone bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Sarah Schmid, Diego A. Hartasanchez, Ashton Gainsford, Geoffrey Jones, Nicolas Salamin
Hybrid zones - locations where genetically distinct lineages interact and reproduce - are remarkable resources for exploring the evolutionary trajectory of species. Not only can we learn from hybrid zones about the mechanisms of speciation and how reproductive isolation is maintained, but we can also study their impact on evolutionary processes. Thanks to the advent of next-generation sequencing, we
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Adaptation to complex environments reveals pervasive trade-offs and genomic targets with large pleiotropic effects bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Alexandre Rêgo, Dragan Stajic, Carla Bautista, Sofia Rouot, Maria de la Paz Celorio-Mancera, Rike Stelkens
Populations in nature rarely adapt to a single stress at a time. Various biotic and abiotic factors come together to produce a complex environment to which populations must adapt. How populations adapt to multiple stressors simultaneously, and how trade-offs evolve between these stressors has been of interest to evolutionary biologists for decades. But natural populations often present logistical challenges
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Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Gholamhossein Jowkar, Julija Pecerska, Manuel Gil, Maria Anisimova
Insertions and deletions (indels) play a significant role in mammalian genomic evolution. Sensible modelling of the evolutionary process of indels is challenging and still an open research question. Several attempts have been made to explicitly model multi-character (long) indels, such as TKF92, by violating the site independence assumption and introducing fragments. However, these methods are computationally
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Environmental similarity between relatives reduces heritability of reproductive timing in wild great tits bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Carys V Jones, Charlotte E Regan, Ella F Cole, Josh A Firth, Ben C Sheldon
Intraspecific variation is necessary for evolutionary change and population resilience, but the extent to which it contributes to either depends on the causes of this variation. Understanding the causes of individual variation in traits involved with reproductive timing is important in the face of environmental change, especially in systems where reproduction must coincide with seasonal resource availability
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Islands promote diversification within the silvereye clade: a phylogenomic analysis of a great speciator bioRxiv. Evol. Biol. Pub Date : 2024-03-13 Andrea Estandia, Nilo Merino Recalde, Ashley T. Sendell-Price, Dominique A. Potvin, Bruce C. Robertson, Sonya M. Clegg
Geographic isolation plays a pivotal role in speciation by restricting gene flow between populations through distance or physical barriers. However, the speciation process is complex, influenced by the interplay between dispersal ability and geographic isolation, especially in 'great speciators' - bird species present on multiple islands that, at the same time, have many subspecies. Comparing population
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Sex-specific viability effects of mutations in Drosophila melanogaster bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Robert H Melde, JoHanna M Abraham, Maryn R Ugolini, Madison P Castle, Molly M Fjalstad, Daniela M Blumstein, Nathaniel P Sharp
In populations with separate sexes, genetic load due to deleterious mutations may be expressed differently in males and females. Evidence from insect models suggests that selection against mutations is stronger in males, with a positive intersexual correlation for fitness. This pattern will reduce deleterious allele frequencies at the expense of males, such that female mean fitness is greater than
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Genomic consequences of isolation and inbreeding in an island dingo population bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Ana V. Leon-Apodaca, Manoharan Kumar, Andres del Castillo, Gabriel C. Conroy, Robert W. Lamont, Steven Ogbourne, Kylie M. Cairns, Liz Borburgh, Linda Behrendorff, Sankar Subramanian, Zachary A Szpiech
Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). While dingoes on K'gari are protected, dingoes on the mainland are only protected in certain regions, and, because
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Genomics of Natural Populations: Gene Conversion Events Reveal Selected Genes within the Inversions of Drosophila pseudoobscura bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Stephen W Schaeffer, Stephen Richards, Zachary L Fuller
When adaptive phenotypic variation or QTLs map within an inverted segment of a chromosome, researchers often despair because it is thought that the suppression of crossing over will prevent the discovery of selective target genes that contribute to the establishment of the rearrangement. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that
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Gliding towards an understanding of the origin of flight in bats bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Abigail E Burtner, David M Grossnickle, Sharlene E Santana, Chris J Law
Bats are the only mammals capable of powered flight and have correspondingly specialized body plans, particularly in their limb morphology. The origin of bat flight is still not fully understood due to an uninformative fossil record but, from the perspective of a functional transition, it is widely hypothesized that bats evolved from gliding ancestors. Here, we test predictions of the gliding-to-flying
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Functional Diversification of Gene Duplicates under the Constraint of Protein Structure bioRxiv. Evol. Biol. Pub Date : 2024-03-12 kangning guo, yuqing yang, tingting you, kangli zhu
Gene differentiation subsequent to duplication plays a pivotal role in the evolutionary process, facilitating the generation of new functional genes. This dynamic process involves alterations in gene characteristics including protein structure, expression patterns, cellular localization, and enzymatic activity, which collectively contribute to the advent of novel functions. However, there are still
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Adaptive generalization in pollinators: hawkmoths increase fitness to long-tubed flowers, but secondary pollinators remain important bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Katherine E Wenzell, Johnathan Y. Zhang, Krissa A. Skogen, Jeremie B. Fant
Selection on floral traits by animal pollinators is important in the evolution of flowering plants, yet whether floral divergence requires specialized pollination remains uncertain. Longer floral tubes, a trait associated with long-tongued pollinators, can also exclude other pollinators from accessing rewards, a potential mechanism for specialization. Across most of its range, Castilleja sessiliflora
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Natural slab photonic crystals and where to find them among the girdle bands of diatoms bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Matt P. Ashworth, Daryl W. Lam, Martin Lopez-Garcia, Schonna R. Manning, Johannes Wilhelm Goessling
Slab photonic crystals, nanomaterials characterized by periodic pores for manipulating light, have applications in advanced optical technologies. Remarkably, similar materials have been identified in the silica shell of diatoms, in particular the girdle bands. Despite the potential applications and significance for diatom biology, their prevalence remains uncertain due to limited observations across
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Demographic history and the efficacy of selection in the globally invasive mosquito Aedes aegypti bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Tyler Kent, Daniel Schrider, Daniel R Matute
Aedes aegypti is the main vector species of yellow fever, dengue, zika and chikungunya. The species is originally from Africa but has experienced a spectacular expansion in its geographic range to a large swath of the world, the demographic effects of which have remained largely understudied. In this report, we examine whole-genome sequences from 6 countries in Africa, North America, and South America
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Gene expression is the main driver of purifying selection in large penguin populations bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Emiliano Trucchi, Piergiorgio Massa, Francesco Giannelli, Thibault Latrille, Flavia A.N. Fernandes, Lorena Ancona, Nils Chr Stenseth, Joan Ferrer Obiol, Josephine Paris, Giorgio Bertorelle, Celine Le Bohec
Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate fewer deleterious mutations between divergent species' lineages (known as E-R anticorrelation), pointing towards gene expression as an additional driver of purifying selection. However,
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Preventing multiple resistance above all: new insights for managing fungal adaptation bioRxiv. Evol. Biol. Pub Date : 2024-03-12 Agathe Ballu, Claire Ugazio, Clementine Duplaix, Alicia Noly, Juerg Wullschleger, Stefano F. F. Torriani, Anne Deredec, Florence Carpentier, Anne-Sophie Walker
Sustainable crop protection is crucial for food security, but is threatened by the adaptation of diverse, evolving pathogen population. Resistance can be managed by maximizing selection pressure diversity, by dose variation and the spatial and temporal combination of active ingredients. We explored the interplay between operational drivers for maximizing management strategy sustainability relative
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Genetic load, eco-evolutionary feedback and extinction in metapopulations bioRxiv. Evol. Biol. Pub Date : 2024-03-11 Oluwafunmilola Olusanya, Ksenia A. Khudiakova, Himani Sachdeva
Habitat fragmentation poses a significant threat to the persistence of populations, by generating increased genetic drift (and thus higher genetic load) as well as demographic stochasticity. Higher load causes population numbers to decline, which reduces the efficiency of selection and further increases load, resulting in a positive feedback which may drive entire populations to extinction. Here, we
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A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates bioRxiv. Evol. Biol. Pub Date : 2024-03-11 Christopher J. Johnson, Zheng Zhang, Haifeng Zhang, Renjie Shang, Katarzyna M. Piekarz, Pengpeng Bi, Alberto Stolfi
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is only expressed in post-metamorphic multinucleated muscles, but is absent
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Frequency-dependent ecological interactions increase the prevalence and shape the distribution of pre-existing drug resistance bioRxiv. Evol. Biol. Pub Date : 2024-03-11 Jeff Maltas, Dagim Shiferaw Tadele, Arda Durmaz, Christopher D McFarland, Michael Hinczewski, Jacob G Scott
The evolution of resistance remains one of the primary challenges for modern medicine from infectious diseases to cancers. Many of these resistance-conferring mutations often carry a substantial fitness cost in the absence of treatment. As a result, we would expect these mutants to undergo purifying selection and be rapidly driven to extinction. Nevertheless, pre-existing resistance is frequently observed
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Connecting species-specific extents of genome reduction in mitochondria and plastids bioRxiv. Evol. Biol. Pub Date : 2024-03-11 Konstantinos Giannakis, Luke Richards, Kazeem Dauda, Iain Johnston
Mitochondria and plastids have both dramatically reduced their genomes since the endosymbiotic events that created them. The similarities and differences in the evolution of the two organelle genome types has been the target of discussion and investigation for decades. Ongoing work has suggested that similar mechanisms may modulate the reductive evolution of the two organelles in a given species, but
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Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations bioRxiv. Evol. Biol. Pub Date : 2024-03-11 Minako Izutsu, Devin M. Lake, Zachary W. D. Matson, Jack P. Dodson, Richard E. Lenski
Population bottlenecks are common in nature, and they can impact the rate of adaptation in evolving populations. On the one hand, each bottleneck reduces the genetic variation that fuels adaptation. On the other hand, each founder that survives a bottleneck can undergo more generations and leave more descendants in a resource-limited environment, which allows surviving beneficial mutations to spread
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Idiosyncrasies unveiled: examining the pace, patterns and predictors of biotic diversification in peninsular India bioRxiv. Evol. Biol. Pub Date : 2024-03-11 Pragyadeep Roy, Jahnavi Joshi
Understanding the tempo and mode of diversification and its consequence for tropical biodiversity remains a key challenge as different clades and regions exemplify distinct patterns and processes. The evolution of the Peninsular Indian biota, one of the oldest regions of differentiation in tropical Asia with a complex geological history and high species diversity with endemism, remains poorly explored