-
Evolution of primate protomusicality via locomotion bioRxiv. Evol. Biol. Pub Date : 2021-01-14 David M Schruth; Christopher N Templeton; Darryl J Holman; Eric Alden Smith
Animals communicate acoustically to report location and identity to conspecifics. More complex patterning of calls can also function as displays to potential mates and as territorial advertisement. Music and song are terms often reserved only for humans and birds, but elements of both forms of acoustic display are also found in non-human primates. While theories on proximate functions abound, ultimate
-
Genes encoding teleost orthologs of human haplo-insufficient and monoallelic genes remain in duplicate more frequently than the whole genome bioRxiv. Evol. Biol. Pub Date : 2021-01-14 Philippe Monget; Floriane Picolo; Anna Grandchamp; Benoît Piégu; Reiner Veitia
Gene dosage is important is an important issue both in cell and evolutionary biology.Most genes are present in two copies in eukaryotic cells. The first outstanding exception is monoallelic gene expression (MA) that concerns genes localized on the X chromosome or in regions undergoing parental imprinting in eutherians, and many other genes scattered throughout the genome. The second exception concerns
-
A theoretical approach for quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Thibault Latrille; Nicolas Lartillot
Molecular sequences are shaped by selection, where the strength of selection relative to drift is determined by effective population size (Ne). Populations with high Ne are expected to undergo stronger purifying selection, and consequently to show a lower substitution rate for selected mutations relative to the substitution rate for neutral mutations (ω=dN/dS). However, computational models based on
-
Evolutionary Perspective And Expression Analysis Of Intronless Genes Highlight The Conservation On Their Regulatory Role bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Katia Avina-Padilla; Jose Antonio Ramirez Rafael; Gabriel Emilio Herrera-Oropeza; Vijaykumar Muley; Dulce Valdivia; Erick Diaz Valenzuela; Andres Garcia-Garcia; Alfredo Varela-Echavarria; Maribel Hernandez-Rosales
Eukaryotic gene structure is a combination of exons generally interrupted by intragenic non-coding DNA regions termed introns removed by RNA splicing to generate the mature mRNA. Thus, eukaryotic genes can be either single exon genes (SEGs) or multiple exon genes (MEGs). Among SEGs, intronless genes (IGs) are a subgroup that additionally lacks introns at their UTRs, and code for proteins essentially
-
Inferring long-term effective population size with Mutation-Selection models bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Thibault Latrille; Vincent Lanore; Nicolas Lartillot
Mutation-selection phylogenetic codon models are grounded on population genetics first principles and represent a principled approach for investigating the intricate interplay between mutation, selection and drift. In their current form, mutation-selection codon models are entirely characterized by the collection of site-specific amino-acid fitness profiles. However, thus far, they have relied on the
-
Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae) bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Lindsey L Bechen; Matthew G Johnson; Geoffrey T Broadhead; Rachel A Levin; Rick P Overson; Tania Jogesh; Jeremie B Fant; Robert A Raguso; Krissa A Skogen; Norman J Wickett
Background: Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+
-
The landscape of transcriptional and translational changes over 22 years of bacterial adaptation bioRxiv. Evol. Biol. Pub Date : 2021-01-13 John S Favate; Shun Liang; Srujana Samhita Yadavalli; Premal Shah
Organisms can adapt to an environment by taking multiple mutational paths. This redundancy at the genetic level, where many mutations have similar phenotypic and fitness effects, can make untangling the molecular mechanisms of complex adaptations difficult. Here we use the E. coli long-term evolution experiment (LTEE) as a model to address this challenge. To bridge the gap between disparate genomic
-
Predicting lifestyle and host from positive selection data and genome properties in oomycetes bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Daniel Gómez-Pérez; Eric Kemen
Host and niche shifts are a source of genomic and phenotypic diversification as evidenced in parasitism. Most characteristic is metabolism reduction as parasites adapt to a particular host. However, selection pressures acting on such organisms are not fully understood. Here, we developed a comparative genomic approach to study underlying adaptive trends in oomycetes, eukaryotes with a broad range of
-
Diversification dynamics and (non-)parallel evolution along an ecological gradient in African cichlid fishes bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Alexandra Anh-Thu Weber; Jelena Rajkov; Kolja Smailus; Bernd Egger; Walter Salzburger
Understanding the drivers and dynamics of diversification is a central topic in evolutionary biology. Here, we investigated the dynamics of diversification in the cichlid fish Astatotilapia burtoni that diverged along a lake-stream environmental gradient. Whole-genome and morphometric analyses revealed that divergent selection was essential at the early stages of diversification, but that periods in
-
Reticulate Evolutionary History in a Recent Radiation of Montane Grasshoppers Revealed by Genomic Data bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Vanina Tonzo; Adrià Bellvert; Joaquín Ortego
Inferring the ecological and evolutionary processes underlying lineage and phenotypic diversification is of paramount importance to shed light on the origin of contemporary patterns of biological diversity. However, reconstructing phylogenetic relationships in recent evolutionary radiations represents a major challenge due to the frequent co-occurrence of incomplete lineage sorting and introgression
-
High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Mathias Scharmann; Anthony G Rebelo; John Pannell
The males and females of many dioecious plants differ in morphological (Dawson and Geber 1999; Barrett and Hough 2013; Tonnabel et al. 2017), physiological (Juvany and Munne-Bosch 2015), life-history (Delph 1999), and defence traits (Cornelissen and Stiling 2005). Ultimately, such sexual dimorphism must largely be due to differential gene expression between the sexes (Ellegren and Parsch 2007), but
-
Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Kevin M Sutherland; Lewis M Ward; Chloé-Rose Colombero; David T Johnston
The ability of aerobic microorganisms to regulate internal and external concentrations of the reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous enzymes that perform the same function. Thus
-
Neuromodulation of Behavioral Specialization: Tachykinin Signaling Inhibits Task-Specific Behavioral Responsiveness in Honeybee Workers bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Bin Han; Qiaohong Wei; Fan Wu; Han Hu; Chuan Ma; Lifeng Meng; Xufeng Zhang; Mao Feng; Yu Fang; Olav Rueppell; Jianke Li
Behavioral specialization is key to the success of social insects and often compartmentalized among colony members leading to division of labor. Response thresholds to task-specific stimuli proximally regulate behavioral specialization but their neurobiological regulation is not understood. Here, we show that response thresholds to task-relevant stimuli correspond to the specialization of three behavioral
-
Glacial connectivity and current population fragmentation in sky-islands explain the contemporary distribution of genomic variation in two narrow-endemic montane grasshoppers from a biodiversity hotspot bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Vanina Tonzo; Joaquín Ortego
Aim: Cold-adapted biotas from mid-latitudes often show small population sizes, harbor low levels of local genetic diversity, and are highly vulnerable to extinction due to ongoing climate warming and the progressive shrink of montane and alpine ecosystems. In this study, we use a suite of analytical approaches to infer the demographic processes that have shaped contemporary patterns of genomic variation
-
Using image-based haplotype alignments to map global adaptation of SARS-CoV-2 bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Tom W Ouellette; Jim Shaw; Philip Awadalla
Quantifying evolutionary change among viral genomes is an important clinical device to track critical adaptations geographically and temporally. We built image-based haplotype-guided evolutionary inference (ImHapE) to quantify adaptations in expanding populations of non-recombining SARS-CoV-2 genomes. By combining classic population genetic summaries with image-based deep learning methods, we show
-
An ancient viral epidemic involving host coronavirus interacting genes more than 20,000 years ago in East Asia bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Yassine Souilmi; M. Elise Lauterbur; Ray Tobler; Christian D. Huber; Angad S. Johar; David Enard
The current SARS-CoV-2 pandemic has emphasized the vulnerability of human populations to novel viral pressures, despite the vast array of epidemiological and biomedical tools now available. Notably, modern human genomes contain evolutionary information tracing back tens of thousands of years, which may help identify the viruses that have impacted our ancestors -- pointing to which viruses have future
-
Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Bram Vrancken; Simon Dellicour; Davey M Smith; Antoine Chaillon
The emergence of new variants of SARS-CoV-2 herald a new phase of the pandemic. This study used state-of-the-art phylodynamic methods to ascertain that the rapid rise of B.1.1.7 'Variant of Concern' most likely occurred by global dispersal rather than convergent evolution from multiple sources.
-
Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Evan Witt; Nicolas Svetec; Sigi Benjamin; Li Zhao
Evolutionarily young genes are usually preferentially expressed in the testis across species. While it is known that older genes are generally more broadly expressed than younger genes, the properties that shaped this pattern are unknown. Older genes may gain expression across other tissues uniformly, or faster in certain tissues than others. Using Drosophila gene expression data, we confirmed previous
-
Population genomic evidence for a repeated introduction and rapid expansion in Europe of a maize fungal pathogen bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Mireia Vidal-Villarejo; Fabian Freund; Hendrik Hanekamp; Andreas von Tiedemann; Karl J Schmid
Modern agricultural practices and the climate change foster the rapid spread of plant pathogens like the maize fungal pathogen Setosphaeria turcica, which causes Northern corn leaf blight and expanded into Central Europe since the 1980s. To investigate the rapid expansion of S. turcica we sequenced 121 isolates from Europe and Kenya. Population genomic inference revealed a single genetically diverse
-
Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life bioRxiv. Evol. Biol. Pub Date : 2021-01-13 Luiz Thiberio Rangel; Shannon M. Soucy; Joao Carlos Setubal; Johann Peter Gogarten; Gregory P. Fournier
Assessing the phylogenetic compatibility between individual gene families is a crucial and often computationally demanding step in many phylogenomics analyses. Here we describe the Evolutionary Similarity Index (IES) to assess shared evolution between gene families using a weighted Orthogonal Distance Regression applied to sequence distances. This approach allows for straightforward pairing of paralogs
-
The biogeographic history of eelpouts and related fishes: linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group bioRxiv. Evol. Biol. Pub Date : 2021-01-12 Scott Hotaling; Marek L Borowiec; Luana S. F. Lins; Thomas Desvignes; Joanna L. Kelley
Modern genetic data sets present unprecedented opportunities to understand the evolutionary origins of taxonomic groups comprising hundreds to thousands of species. When the timing of key events are known, it is also possible to investigate biogeographic history in the context of major phenomena (e.g., continental drift). In this study, we investigated the biogeographic history of the suborder Zoarcoidei
-
Reconstructing the history of variation in effective population size along phylogenies. bioRxiv. Evol. Biol. Pub Date : 2021-01-12 Mathieu Brevet; Nicolas Lartillot
The nearly-neutral theory predicts specific relations between effective population size (Ne), and patterns of divergence and polymorphism, which depend on the shape of the distribution of fitness effects (DFE) of new mutations. However, testing these relations is not straightforward since Ne is difficult to estimate in practice. For that reason, indirect proxies for Ne have often been used to test
-
Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish. bioRxiv. Evol. Biol. Pub Date : 2021-01-11 gunjan Katyal; Brad Ebanks; Magnus Lucassen; Chiara Papetti; Lisa Chakrabarti
The Channichthyidae family (icefish) are the only known vertebrate species to be devoid of haemoglobin. Mitochondrial changes such as tight coupling of the mitochondria have facilitated sustained oxygen and respiratory activity in the fish. This makes it important to appreciate features in the sequence and structure of the proteins directly involved in proton transport, which could have physiological
-
Spatial Congruence Analysis (SCAN): An objective method for detecting biogeographical patterns based on species’ range congruences bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Cassiano AFR Gatto; Mario Cohn-Haft
Similar species ranges may represent outcomes of common biological processes and so form the basis for biogeographical concepts such as areas of endemism and ecoregions. Nevertheless, spatial range congruence is rarely quantified, much less incorporated in bioregionalization methods as an explicit parameter. Furthermore, most available methods suffer from limitations related to the loss, or the excess
-
Evolution of Mendelian dominance in gene regulatory networks associated with phenotypic robustness bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Kenji Okubo; Kunihiko Kaneko
Mendelian inheritance is a fundamental law of genetics. Considering two alleles in a diploid, a phenotype of a heterotype is dominated by a particular homotype according to the law of dominance. This picture is usually based on simple genotype-phenotype mapping in which one gene regulates one phenotype. However, in reality, some interactions between genes can result in deviation from Mendelian dominance
-
Gradual evolution of allopolyploidy in Arabidopsis suecica bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Robin Burns; Terezie Mandakova; Joanna Jagoda; Luz Mayela Soto-Jimenez; Chang Liu; Martin A. Lysak; Polina Yu. Novikova; Magnus Nordborg
The majority of diploid organisms have polyploid ancestors. The evolutionary process of polyploidization (and subsequent re-diploidization) is poorly understood, but has frequently been conjectured to involve some form of "genome shock" --- partly inspired by studies in crops, where polyploidy has been linked to major genomic changes such as genome reorganization and subgenome expression dominance
-
Extreme parallel evolution of flagellar motility facilitated by silent mutations bioRxiv. Evol. Biol. Pub Date : 2021-01-11 James S Horton; Louise M Flanagan; Robert W Jackson; Nicholas K Priest; Tiffany B Taylor
There is a growing need for accurate evolutionary forecasting, but we must first understand how possible evolutionary paths can be constrained by silent genetic features. Here we show that synonymous sequence variation determines extreme parallel evolution during the evolutionary rescue of flagellar motility. An immotile variant of the soil microbe, Pseudomonas fluorescens, swiftly recovers flagellum-dependent
-
A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Pengyao Jiang; Anja R. Ollodart; Vidha Sudhesh; Alan J. Herr; Maitreya J. Dunham; Kelley Harris
Mutations are the source of genetic variation and a prerequisite for evolution. Despite their fundamental importance, however, their rarity makes them expensive and difficult to detect, which has limited our ability to measure the extent to which mutational processes vary within and between species. Here, we use the 1011 Saccharomyces cerevisiae collection to measure variation of mutation rates and
-
Continuous cis-regulatory changes in an advantageous gene are linked with adaptive radiation in cichlid fishes bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Langyu Gu; Chenzheng Li; Xiaobing Mao; Zongfang Wei; Youkui Huang; Ximin He; Wenjun Zhou; Li Li; Deshou Wang
Deciphering why some lineages produce spectacular radiations while others do not provides important insights into biodiversity, but the molecular basis underlying this process remains largely unknown. Here, we identified a lineage-restricted gene, which we named lg. Combined omics analyses showed that lg is under positive selection in the most species-rich lineage of cichlid fishes, the modern haplochromine
-
Optimal evolutionary control for artificial selection on molecular phenotypes bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Armita Nourmohammad; Ceyhun Eksin
Controlling an evolving population is an important task in modern molecular genetics, including directed evolution for improving the activity of molecules and enzymes, in breeding experiments in animals and in plants, and in devising public health strategies to suppress evolving pathogens. An optimal intervention to direct evolution should be designed by considering its impact over an entire stochastic
-
Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Tyler K Chafin; Zachery D. Zbinden; Marlis R. Douglas; Bradley T. Martin; Christopher R. Middaugh; M. Cory Gray; Jennifer R. Ballard; Michael E. Douglas
Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural
-
Relaxation of purifying selection suggests low effective population size in eusocial Hymenoptera and solitary pollinating bees bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Jonathan Romiguier; Arthur Weyna
With one of the highest number of parasite, eusocial and pollinator species among all insect orders, Hymenoptera features a great diversity of specific lifestyles. At the population genetic level, such life-history strategies are expected to decrease effective population size and efficiency of purifying selection. In this study, we tested this hypothesis by estimating the relative rate of non-synonymous
-
Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Kathryn Kistler; Trevor Bedford
Seasonal coronaviruses (OC43, 229E, NL63 and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here, we address the influence of antigenic drift on immune evasion of seasonal
-
Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Ekaterina D Badaeva; Fedor A Konovalov; Helmut Knuepffer; Agostino Fricano; Alevtina S Ruban; Zakaria Kehel; Svyatoslav A Zoshchuk; Sergei A Surzhikov; Kerstin Neumann; Andreas Graner; Karl Hammer; Anna A Filatenko; Amy Bogaard; Glynis Jones; Hakan Ozkan; Benjamin Kilian
Background: Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite of its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native
-
Interhemispheric connectivity endures across species: An allometric exposé on the corpus callosum bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Ben Cipollini; Garrison W Cottrell
Rilling & Insel have argued that in primates, bigger brains have proportionally fewer anatomical interhemispheric connections, leading to reduced functional connectivity between the hemispheres. They based this on a comparison between surface areas of the corpus callosum and cortex rather than estimating connection counts, while leaving out other quantities also dependent on brain size such as callosal
-
Late Pleistocene palaeoecology and phylogeography of woolly rhinoceroses bioRxiv. Evol. Biol. Pub Date : 2021-01-11 Alba Rey-Iglesia; Adrian M. Lister; Anthony J. Stuart; Hervé Bocherens; Paul Szpak; Eske Willerslev; Eline D. Lorenzen
The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted herbivore, widely distributed from western Europe to north-east Siberia during the Late Pleistocene. Previous studies associate the extinction of the species ~14,000 years before present to climatic and vegetational changes, and suggest that later survival of populations in north-east Siberia may relate to the later persistence of open
-
Evolutionary processes driving the rise and fall of Staphylococcus aureus ST239, a dominant hybrid pathogen bioRxiv. Evol. Biol. Pub Date : 2021-01-10 Jacqueline L Gill; Jessica Hedge; Daniel J Wilson; Craig MacLean
Staphylococcus aureus ST239 has been one of the most successful epidemic MRSA strains, and one of the leading causes of healthcare-associated MRSA infections. Here we investigate the evolution of ST239 using a combination of computational and experimental approaches. ST239 is thought to have emerged by a large scale chromosomal replacement event in which an ST8 clone acquired approximately 600 kb of
-
Molecular population genetics of Sex-lethal (Sxl) in the D. melanogaster species group - a locus that genetically interacts with Wolbachia pipientis in Drosophila melanogaster bioRxiv. Evol. Biol. Pub Date : 2021-01-10 Vanessa L Bauer DuMont; Simone L White; Daniel Zinshteyn; Charles F Aquadro
Sex-lethal (Sxl) is the sex determination switch in Drosophila, and also plays a critical role in germ-line stem cell (GSC) daughter differentiation in Drosophila melanogaster. Three female-sterile alleles at Sxl in Drosophila melanogaster were previously shown to genetically interact to varying degrees with the maternally inherited endosymbiont Wolbachia pipientis. Given this genetic interaction and
-
Competition and environmental gradients structure Canidae assemblages across the planet bioRxiv. Evol. Biol. Pub Date : 2021-01-10 Lucas Marafina Vieira Porto; Rampal S Etienne; Renan Maestri
Aim: The phylogenetic information of assemblages carries the signature of ecological and evolutionary processes that assembled these communities. Closely related species, under similar environmental conditions, are likely to present similar traits due to environmental filtering. However, if species are too similar, it is unlikely that they will co-occur because of competitive exclusion. Identifying
-
Evolution of Crassulacean Acid Metabolism (CAM) as an escape from ecological niche conservatism in Malagasy Bulbophyllum (Orchidaceae) bioRxiv. Evol. Biol. Pub Date : 2021-01-09 Alexander Gamisch; Klaus Winter; Gunter Alexander Fischer; Hans Peter Comes
Despite growing evidence that niche shifts are more common in flowering plants than previously thought, still little is known about the key physiological (e.g. photosynthesis) traits underlying such niche shifts. To address this question, we here combine a comprehensively sampled phylogeny for mostly epiphytic Malagasy Bulbophyllum orchids (c. 210 spp.) with climatic niche and carbon isotope-derived
-
Signatures of Mutational Processes in Human DNA Evolution bioRxiv. Evol. Biol. Pub Date : 2021-01-09 Hamid Hamidi; Hamid Alinejad-Rokny; Tim Coorens; Rashesh Sanghvi; Sarah J Lindsay; Raheleh Rahbari; Diako Ebrahimi
The human genome contains over 100 million SNPs, most of which are C/T (G/A) variations. The type and sequence context of these SNPs are not random, suggesting that they are caused by distinct mutational processes. Deciphering the mutational signatures is a crucial step to discovering the molecular processes responsible for DNA variations across human populations, and potentially for causing genetic
-
Cancer risk and sexual conflict as constraints to body size evolution bioRxiv. Evol. Biol. Pub Date : 2021-01-09 E. Yagmur Erten; Hanna Kokko
Selection often favours large bodies, visible as Cope's rule over macroevolutionary time − but size increases are not inevitable. One understudied cost of large bodies is the high number of cell divisions and the associated risk of oncogenic mutations. Our elasticity analysis shows that selection against a proportional increase in size becomes ever more intense with increasing body size if cancer is
-
Explosive diversification following continental colonizations by canids bioRxiv. Evol. Biol. Pub Date : 2021-01-09 Lucas Marafina Vieira Porto; Rampal S Etienne; Renan Maestri
Colonization of a new environment may trigger an explosive radiation process, defined as an accelerated accumulation of species in a short period of time. However, how often colonization events trigger explosive radiations is still an open question. We studied the worldwide dispersal of the subfamily Caninae, to investigate whether the invasion of new continents resulted in explosive radiations. We
-
The collapse of genetic incompatibilities in a hybridizing population bioRxiv. Evol. Biol. Pub Date : 2021-01-09 Tianzhu Xiong; James L MALLET
Genetic incompatibility has long been considered to be a hallmark of speciation due to its role in reproductive isolation. Previous analyses of the stability of epistatic incompatibility show that it is subject to collapse upon hybridization. In the present work, we derive explicitly the distribution of the lifespan of two-locus incompatibilities, and show that genetic drift, along with recombination
-
Widespread introgression across a phylogeny of 155 Drosophila genomes bioRxiv. Evol. Biol. Pub Date : 2021-01-09 Anton Suvorov; Bernard Y. Kim; Jeremy Wang; Ellie E. Armstrong; David Peede; Emmanuel R. R. D'Agostino; Donald K. Price; Peter Wadell; Michael Lang; Virginie Courtier-Orgogozo; Jean R. David; Dmitri Petrov; Daniel R. Matute; Daniel R. Schrider; Aaron A. Comeault
Genome-scale sequence data has invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across
-
A Phylogenetic Approach to Inferring the Order in Which Mutations Arise during Cancer Progression bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Yuan Gao; Jeff Gaither; Julia Chifman; Laura Kubatko
Although the role of evolutionary processes in cancer progression is widely accepted, increasing attention is being given to evolutionary mechanisms that can lead to differences in clinical outcome. Recent studies suggest that the temporal order in which somatic mutations accumulate during cancer progression is important. Single-cell sequencing provides a unique opportunity to examine the mutation
-
High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur). bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Tiange Lang; Pierre Abadie; Valérie Léger; Thibaut Decourcelle; Jean-Marc Frigerio; Christian Burban; Catherine Bodénès; Erwan Guichoux; Grégoire Le Provost; Cécile Robin; Naoki Tani; Patrick Léger; Camille Lepoittevin; Veronica A El Mujtar; François Hubert; Josquin Tibbits; Jorge Paiva; Alain Franc; Frédéric Raspail; Stéphanie Mariette; Marie-Pierre Reviron; Christophe Plomion; Antoine Kremer; Marie-Laure
In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. Sequence data were produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks, in a discovery panel of 25 individuals from western and central Europe (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted
-
Evolvability and constraint in the primate basicranium, shoulder, and hip and the importance of multi-trait evolution bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Elizabeth R Agosto; Benjamin M Auerbach
The scapula shares developmental and functional relationships with traits of the basicranium, vertebral column, humerus, and clavicle. As a limb girdle, it also shares analogous characteristics with the pelvis. Despite these relationships, studies of primate shoulder evolution often focus on traits of the scapula in isolation. Such analyses may lead to spurious conclusions, as they implicitly model
-
Evolution in salmon life-history induced by direct and indirect effects of fishing bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Yann Czorlich; Tutku Aykanat; Jaakko Erkinaro; Panu Orell; Craig R Primmer
Understanding the drivers of evolution is a fundamental aim in biology. However, identifying the evolutionary impacts of human activities, both direct and indirect, is challenging because of lack of temporal data and limited knowledge of the genetic basis of most traits1. Atlantic salmon is a species exposed to intense anthropogenic pressures during its anadromous life cycle. Previous research has
-
Sexually Transmitted Infections Select for Different Levels of Immunocompetence And Reproductive Efforts in The Two Sexes bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Lafi Aldakak; Frank Rühli; Nicole Bender
Sex differences in immunity have been described in humans and other mammal species. Females have a lower incidence of infections and non-reproductive malignancies and exhibit higher antibody levels after vaccination. Existing evolutionary explanations are based on differences in reproductive strategies and reaction to extrinsic differences in susceptibility and virulence between the sexes. Here, we
-
Is Palmer's elm leaf goldenrod real? The Angiosperms353 kit provides within-species signal in Solidago ulmifolia s.l. bioRxiv. Evol. Biol. Pub Date : 2021-01-08 James B Beck; Morgan L Markley; Mackenzie G Zielke; Justin R Thomas; Haley J Hale; Lindsay D Williams; Matthew G Johnson
The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri, a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri
-
Substantial intraspecific variation in energy budgets: biology or artefact? bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Tomos Potter; David N Reznick; Tim Coulson
Dynamic energy budget (DEB) models provide a mechanistic description of life-histories in terms of fluxes of energy through biological processes. In these models, life-histories are a function of environmental conditions and of fundamental traits of the organism relating to the acquisition, allocation, and use of energy. These traits are described by the parameters of the DEB model, which have been
-
Allopatric divergence limits cheating range and alters genetic requirements for a cooperative trait bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Kaitlin A. Schaal; Yuen-Tsu Nicco Yu; Marie Vasse; Gregory J. Velicer
Social and genomic context may constrain the fates of mutations in cooperation genes. While some mechanisms limiting cheaters evolve in the presence of cheating, here we ask whether cheater resistance can evolve latently even in environments where cooperation is not expressed and cheaters are absent. The bacterium Myxococcus xanthus undergoes cooperative multicellular development upon starvation, but
-
The effects of chromosome fusions on genetic diversity and evolutionary turnover of functional loci consistently depends on chromosome size bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Francesco Cicconardi; James J Lewis; Simon Henry Martin; Robert D. Reed; Charles G Danko; Stephen H Montgomery
Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination
-
Using genomic prediction to detect microevolutionary change of a quantitative trait bioRxiv. Evol. Biol. Pub Date : 2021-01-08 DC Hunter; B Ashraf; C Bérénos; PA Ellis; SE Johnston; AJ Wilson; JG Pilkington; JM Pemberton; J Slate
Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply
-
In vivo deciduous dental eruption in LuiKotale bonobos and Gombe chimpanzees bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Sean M. Lee; L. J. Sutherland; Barbara Fruth; Carson M. Murray; Elizabeth V. Lonsdorf; Keely Arbenz-Smith; Rafael Augusto; Sean Brogan; Stephanie L. Canington; Kevin C. Lee; Kate McGrath; Shannon C. McFarlin; Gottfried Hohmann
Existing data on bonobo and chimpanzee dental eruption timing are derived predominantly from captive individuals or deceased wild individuals. However, recent advances in noninvasive photographic monitoring of living, wild apes have greatly expanded our knowledge of chimpanzee dental eruption in relatively healthy individuals under naturalistic conditions. We employ similar methods to expand on this
-
Serial Section-Based 3D Reconstruction of Anaxagorea (Annonaceae) Carpel Vasculature and Implications on Integrated Axial-Foliar Origin of Angiosperm Carpels bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Ya Li; Wei Du; Ye Chen; Shuai Wang; Xiao-Fan Wang
The carpel is the basic unit of the gynoecium in angiosperms and one of the most important morphological features distinguishing angiosperms from gymnosperms; therefore, carpel origin is of great significance in angiosperm phylogenetic origin. Recent consensus favors the interpretation that the carpel originates from the fusion of an ovule-bearing axis and the phyllome that subtends it. It has been
-
Social groups with diverse personalities mitigate physiological stress in a songbird bioRxiv. Evol. Biol. Pub Date : 2021-01-08 Csongor I. Vágási; Attila Fülöp; Gergely Osváth; Péter L. Pap; Janka Pénzes; Zoltán Benkő; Ádám Z. Lendvai; Zoltán Barta
Social groups often consist of diverse phenotypes, including personality types, and this diversity is known to affect the functioning of the group as a whole. Social selection theory proposes that group composition (i.e. social environment) also influences the performance of individual group members. However, the effect of group behavioural composition on group members remains largely unexplored, and
-
Phylogenetic inference of changes in amino acid propensities with single-position resolution bioRxiv. Evol. Biol. Pub Date : 2021-01-07 Galya V. Klink; Olga V. Kalinina; Georgii A. Bazykin
Fitness conferred by the same allele may differ between genotypes, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that
-
Nonadaptive radiation of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes with minor shifts for scale-eating bioRxiv. Evol. Biol. Pub Date : 2021-01-07 Joseph Heras; Christopher Martin
Adaptive radiations offer an excellent opportunity to understand the eco-evolutionary dynamics of gut microbiota and host niche specialization. In a laboratory common garden, we compared the gut microbiota of two novel trophic specialists, a scale-eater and a molluscivore, to a set of four outgroup generalist populations from which this adaptive radiation originated. We predicted an adaptive and highly
Contents have been reproduced by permission of the publishers.