scholarly journals Identifying drivers of parallel evolution: A regression model approach

2017 ◽  
Author(s):  
Susan F. Bailey ◽  
Qianyun Guo ◽  
Thomas Bataillon
Keyword(s):  
Evolutionary Biology ◽  
Empirical Studies ◽  
Parallel Evolution ◽  
Published Data ◽  
Genetic Changes ◽  
Selective Pressures ◽  
Evolutionary Changes ◽  
Gene Level ◽  
Peer Community ◽  
Mutation And Selection

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100045). Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution, however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce several statistical models to examine the contributions of mutation and selection heterogeneity to shaping parallel evolutionary changes at the gene-level. Using this framework we analyze published data from forty experimentally evolved Saccharomyces cerevisiae populations. We can partition the effects of a number of genomic variables into those affecting patterns of parallel evolution via effects on the rate of arising mutations, and those affecting the retention versus loss of the arising mutations (i.e. selection). Our results suggest that gene-to-gene heterogeneity in both mutation and selection, associated with gene length, recombination rate, and number of protein domains drive parallel evolution at both synonymous and nonsynonymous sites. While there are still a number of parallel changes that are not well described, we show that allowing for heterogeneous rates of mutation and selection can provide improved predictions of the prevalence and degree of parallel evolution.Data archival locationDryad, doi to be included later

scholarly journals Distribution of iridescent colours in hummingbird communities results from the interplay between selection for camouflage and communication

2019 ◽  
Author(s):  
Hugo Gruson ◽  
Marianne Elias ◽  
Juan L. Parra ◽  
Christine Andraud ◽  
Serge Berthier ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Species Recognition ◽  
Character Displacement ◽  
Specific Aspect ◽  
Community Level ◽  
Observation Angle ◽  
Evolutionary Mechanisms ◽  
Selective Pressures ◽  
Similar Appearance ◽  
Peer Community

AbstractIdentification errors between closely related, co-occurring, species may lead to misdirected social interactions such as costly interbreeding or misdirected aggression. This selects for divergence in traits involved in species identification among co-occurring species, resulting from character displacement. On the other hand, predation may select for crypsis, potentially leading co-occurring species that share the same environment and predators to have a similar appearance. However, few studies have explored how these antagonistic processes influence colour at the community level. Here, we assess colour clustering and overdispersion in 189 hummingbird communities, tallying 112 species, across Ecuador and suggest possible evolutionary mechanisms at stake by controlling for species phylogenetic relatedness. In hummingbirds, most colours are iridescent structural colours, defined as colours that change with the illumination or observation angle. Because small variations in the underlying structures can have dramatic effects on the resulting colours and because iridescent structures can produce virtually any hue and brightness, we expect iridescent colours to respond finely to selective pressures. Moreover, we predict that hue angular dependence – a specific aspect of iridescent colours – may be used as an additional channel for species recognition. In our hummingbird assemblages in Ecuador, we find support for colour overdispersion in ventral and facial patches at the community level even after controlling for the phylogeny, especially on iridescence-related traits, suggesting character displacement among co-occurring species. We also find colour clustering at the community level on dorsal patches, suspected to be involved in camouflage, suggesting that the same cryptic colours are selected among co-occurring species.This article has been peer-reviewed and recommended by Peer Community In Evolutionary Biology

scholarly journals Predicting the genetic loci of past evolution

2017 ◽  
Author(s):  
Virginie Courtier-Orgogozo ◽  
Arnaud Martin
Keyword(s):  
Genetic Evolution ◽  
Genetic Loci ◽  
Nucleotide Level ◽  
Genetic Changes ◽  
The Past ◽  
Independent Evolution ◽  
Evolutionary Changes ◽  
Gene Level ◽  
Regulatory Mutations

AbstractRepetitions in the mutations found to be responsible for independent evolution of similar phenotypes in various taxa have led some biologists to propose that for certain evolutionary changes the causal mutations are predictable. We examine here the nature of the predictions that have been made and their associated arguments. Predictions about the loci of past evolution are retrodictions, i.e. inferences about events that occurred in the past. They are not based on elaborate models and they derive mainly from the observation of repeated cases of genetic evolution. Predictions at the nucleotide level or at the gene level have a higher inference gain than those for broader categories of genetic changes such as cis-regulatory mutations.

scholarly journals Clownfishes evolution below and above the species level

2018 ◽  
Vol 285 (1873) ◽  
pp. 20171796 ◽  
Author(s):  
Jonathan Rolland ◽  
Daniele Silvestro ◽  
Glenn Litsios ◽  
Laurélène Faye ◽  
Nicolas Salamin
Keyword(s):  
Morphological Evolution ◽  
Empirical Studies ◽  
Evolutionary Process ◽  
Species Level ◽  
Receptor Protein ◽  
Effective Population ◽  
Selective Pressures ◽  
Rates Of Evolution ◽  
Evolutionary Changes ◽  
The Difference

The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro- and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1 , a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels.

The Expansion of Life

2021 ◽  
pp. 99-118
Author(s):  
Franklin M. Harold
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Atmospheric Oxygen ◽  
Gene Level ◽  
Chance Events ◽  
Eukaryotic Microbes ◽  
Multicellular Organisms ◽  
And Behavior ◽  
New Phase ◽  
Recurrent Theme

The story of life tells of relentless expansion from obscure beginnings to smother the earth in organized biochemistry. First came the prokaryotes, Bacteria and Archaea, followed some two billion years later by eukaryotic microbes. The latter pattern of organization underpins the rise of multicellular organisms, and their spectacular proliferation over the past 600 million years. There have been no fundamentally new kinds of organisms since, but the rise of mind culminating in humanity may signal a new phase in life’s history. Life has expanded in both quantity and quality, a gyre of mounting size, complexity, and functional capacity; in some elusive sense evolution is progressive. Multicellularity, the key invention, is not singular but happened multiple times in several eukaryotic lineages. The proliferation of higher organisms was probably enabled by increased energy flow, and dependent on the increase in atmospheric oxygen. It is studded with innovations in structure, physiology, and behavior, whose origin is a recurrent theme in evolutionary biology. Novelty is rooted in mutational events at the gene level, supplemented by the acquisition of genes from the outside by both gene transfer and symbiosis, and possibly by other avenues. Chance events were scrutinized and culled by natural selection. There appears to be no intrinsic progressive drive, but natural selection generally favors the more functional and better organized.

scholarly journals Threat of plastic pollution to seabirds is global, pervasive, and increasing

2015 ◽  
Vol 112 (38) ◽  
pp. 11899-11904 ◽  
Author(s):  
Chris Wilcox ◽  
Erik Van Sebille ◽  
Britta Denise Hardesty
Keyword(s):  
Risk Model ◽  
Ingestion Rate ◽  
Empirical Studies ◽  
Global Scale ◽  
Marine Debris ◽  
Published Data ◽  
Plastic Pollution ◽  
Anthropogenic Pressures ◽  
Seabird Species ◽  
Spatial Risk

Plastic pollution in the ocean is a global concern; concentrations reach 580,000 pieces per km2 and production is increasing exponentially. Although a large number of empirical studies provide emerging evidence of impacts to wildlife, there has been little systematic assessment of risk. We performed a spatial risk analysis using predicted debris distributions and ranges for 186 seabird species to model debris exposure. We adjusted the model using published data on plastic ingestion by seabirds. Eighty of 135 (59%) species with studies reported in the literature between 1962 and 2012 had ingested plastic, and, within those studies, on average 29% of individuals had plastic in their gut. Standardizing the data for time and species, we estimate the ingestion rate would reach 90% of individuals if these studies were conducted today. Using these results from the literature, we tuned our risk model and were able to capture 71% of the variation in plastic ingestion based on a model including exposure, time, study method, and body size. We used this tuned model to predict risk across seabird species at the global scale. The highest area of expected impact occurs at the Southern Ocean boundary in the Tasman Sea between Australia and New Zealand, which contrasts with previous work identifying this area as having low anthropogenic pressures and concentrations of marine debris. We predict that plastics ingestion is increasing in seabirds, that it will reach 99% of all species by 2050, and that effective waste management can reduce this threat.

scholarly journals Range-wide spatial mapping reveals convergent character displacement of bird song

2019 ◽  
Vol 286 (1902) ◽  
pp. 20190443 ◽  
Author(s):  
Alexander N. G. Kirschel ◽  
Nathalie Seddon ◽  
Joseph A. Tobias
Keyword(s):  
Spatial Patterns ◽  
Evolutionary Biology ◽  
Environmental Gradients ◽  
Empirical Studies ◽  
Remote Sensing Data ◽  
Character Displacement ◽  
Similar Species ◽  
Interspecific Territoriality ◽  
Coexisting Species

A long-held view in evolutionary biology is that character displacement generates divergent phenotypes in closely related coexisting species to avoid the costs of hybridization or ecological competition, whereas an alternative possibility is that signals of dominance or aggression may instead converge to facilitate coexistence among ecological competitors. Although this counterintuitive process—termed convergent agonistic character displacement—is supported by recent theoretical and empirical studies, the extent to which it drives spatial patterns of trait evolution at continental scales remains unclear. By modelling the variation in song structure of two ecologically similar species of Hypocnemis antbird across western Amazonia, we show that their territorial signals converge such that trait similarity peaks in the sympatric zone, where intense interspecific territoriality between these taxa has previously been demonstrated. We also use remote sensing data to show that signal convergence is not explained by environmental gradients and is thus unlikely to evolve by sensory drive (i.e. acoustic adaptation to the sound transmission properties of habitats). Our results suggest that agonistic character displacement driven by interspecific competition can generate spatial patterns opposite to those predicted by classic character displacement theory, and highlight the potential role of social selection in shaping geographical variation in signal phenotypes of ecological competitors.

scholarly journals Global, regional and national estimates ofToxoplasma gondiiseroprevalence in pregnant women: a protocol for a systematic review and modelling analysis

BMJ Open ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. e030472 ◽  
Author(s):  
Jean Joel Bigna ◽  
Joel Noutakdie Tochie ◽  
Dahlia Noelle Tounouga ◽  
Anne Olive Bekolo ◽  
Nadia S Ymele ◽  
...  
Keyword(s):  
Public Health ◽  
Toxoplasma Gondii ◽  
Pregnant Women ◽  
Data Extraction ◽  
Meta Analysis ◽  
Empirical Studies ◽  
Published Data ◽  
Representative Study ◽  
Nationally Representative ◽  
Meta Analyses

IntroductionTo set priorities for public health policy, funding for public health interventions, and healthcare planning which will ultimately contribute in bending the burden of toxoplasmosis towards maternal and neonatal health, it is necessary to have accurate data on the prevalence of toxoplasmosis in pregnancy. Therefore, we aimed to estimate the seroprevalence ofToxoplasma gondiiinfection in pregnant women by countries, WHO regions and globally.Methods and analysisWe will search multiple databases to identify studies that reported the prevalence (or enough data to compute this estimate) ofToxoplasma gondiiin the global population of pregnant women up till December 31, 2018 without any language restrictions. Study selection, data extraction and risk of bias assessment will be conducted independently by three pairs of investigators. For each country, we will estimate the prevalence based on empirical studies if there is either one nationally representative study, or two or more not nationally representative studies. Then, we will perform a country-specific random-effects meta-analyses. The heterogeneity will be evaluated using the χ² test on Cochrane’s Q statistic and quantified with H and I² statistics. For countries with one or no empirical studies or where the meta-analysis will result in a wide CI of 0%–100%, we will predict the country’s prevalence by using a Bayesian generalised non-linear multilevel model. The model will have a hierarchical structure in which estimates for each country will be informed by its own data, if available, or by data from other countries in the same WHO region.Ethics and disseminationSince this study will be based on published data, it does not require any ethical approval. Its findings will be published in a scientific peer-reviewed journal. They will also be presented at scientific conferences and to relevant public health sectors.PROSPERO registration numberCRD42019125572.

scholarly journals IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations

2019 ◽  
Vol 47 (W1) ◽  
pp. W151-W157
Author(s):  
Camilo Andres Perez-Romero ◽  
Bram Weytjens ◽  
Dries Decap ◽  
Toon Swings ◽  
Jan Michiels ◽  
...  
Keyword(s):  
Web Service ◽  
Parallel Evolution ◽  
Specific Interaction ◽  
Web Server ◽  
Interaction Network ◽  
Genetic Changes ◽  
Adaptive Mutations ◽  
Additional Information ◽  
Genotype Information ◽  
Passenger Mutations

Abstract IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adaptive from passenger mutations, IAMBEE searches for neighborhoods in an organism-specific interaction network that are recurrently mutated in the adapted populations. This search for recurrently mutated network neighborhoods, as proxies for pathways is driven by additional information on the functional impact of the observed genetic changes and their dynamics during adaptive evolution. In addition, the search explicitly accounts for the differences in mutation rate between the independently evolved populations. Using this approach, IAMBEE allows exploiting parallel evolution to identify adaptive pathways. The web-server is freely available at http://bioinformatics.intec.ugent.be/iambee/ with no login requirement.

scholarly journals Evolutionary Changes of the flhDC Flagellar Master Operon in Shigella Strains

2005 ◽  
Vol 187 (12) ◽  
pp. 4295-4302 ◽  
Author(s):  
Akira Tominaga ◽  
Ruiting Lan ◽  
Peter R. Reeves
Keyword(s):  
Dna Sequences ◽  
Gene Clusters ◽  
Housekeeping Gene ◽  
Genetic Damage ◽  
Flagellar Motility ◽  
Genetic Changes ◽  
Mutational Change ◽  
E Coli ◽  
Evolutionary Changes ◽  
Cluster 2

ABSTRACT Shigella strains are nonmotile. The master operon of flagellar synthesis, flhDC, was analyzed for genetic damage in 46 Shigella strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the flhDC operon was completely deleted. PCR and sequence analysis of the flhDC region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their flhDC genes. As these genes also play a role in regulation of nonflagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that Shigella strains fall mostly into three clusters within Escherichia coli, with five outlier strains, four of which are also within E. coli (G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the flhDC region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the flhDC locus. Two cluster 2 strains were found to have unique flhDC sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.

Sign in / Sign up

Export Citation Format

Share Document