scholarly journals The effect of autopolyploidy on population genetic signals of hard sweeps

2019 ◽  
Author(s):  
Patrick Monnahan ◽  
Yaniv Brandvain
Keyword(s):  
Evolutionary Biology ◽  
Fundamental Parameter ◽  
Ploidy Levels ◽  
Natural Systems ◽  
Left Behind ◽  
Sequencing Technologies ◽  
Coalescent Simulations ◽  
Outstanding Question ◽  
Genomic Signals ◽  
Systems Studies

AbstractSearching for population genomic signals left behind by positive selection is a major focus of evolutionary biology, particularly as sequencing technologies develop and costs decline. The effect of the number of chromosome copies (i.e. ploidy) on the manifestation of these signals remains an outstanding question, despite a wide appreciation of ploidy being a fundamental parameter governing numerous biological processes. We clarify the principal forces governing the differential manifestation and persistence of the signal of selection by separating the effects of polyploidy on rates of fixation versus rates of diversity (i.e. mutation and recombination) with a set of coalescent simulations. We explore what the major consequences of polyploidy, such as a more localized signal, greater dependence on dominance, and longer persistence of the signal following fixation, mean for within- and across-ploidy inference on the strength and prevalence of selective sweeps. As genomic advances continue to open doors for interrogating natural systems, studies such as this aid our ability to anticipate, interpret, and compare data across ploidy levels.

scholarly journals The effect of autopolyploidy on population genetic signals of hard sweeps

2020 ◽  
Vol 16 (2) ◽  
pp. 20190796 ◽  
Author(s):  
Patrick Monnahan ◽  
Yaniv Brandvain
Keyword(s):  
Evolutionary Biology ◽  
Fundamental Parameter ◽  
Ploidy Levels ◽  
Natural Systems ◽  
Left Behind ◽  
Sequencing Technologies ◽  
Coalescent Simulations ◽  
Outstanding Question ◽  
Genomic Signals ◽  
Selection Signal

Searching for population genomic signals left behind by positive selection is a major focus of evolutionary biology, particularly as sequencing technologies develop and costs decline. The effect of the number of chromosome copies (i.e. ploidy) on the manifestation of these signals remains an outstanding question, despite a wide appreciation of ploidy being a fundamental parameter governing numerous biological processes. We clarify the principal forces governing the differential manifestation and persistence of the selection signal by separating the effects of polyploidy on the rates of fixation versus rates of diversity (i.e. mutation and recombination) using coalescent simulations. We explore the major consequences of polyploidy, finding a more localized signal, greater dependence on dominance and longer persistence of the signal following fixation, and discuss what this means for within- and across ploidy inference on the strength and prevalence of selective sweeps. As genomic advances continue to open doors for interrogating natural systems, simulations such as this aid our ability to interpret and compare data across ploidy levels.

A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

2021 ◽  
Author(s):  
Aniket Sengupta ◽  
Lena C. Hileman
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Tomato Fruit ◽  
Regulatory Interaction ◽  
En Bloc ◽  
Regulatory Interactions ◽  
Developmental Program ◽  
Novel Traits ◽  
Carpel Development ◽  
Outstanding Question

Abstract BackgroundAn outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype—Lamiales flower monosymmetry—defined by a developmental program that relies on regulatory interaction among CYCLOIDEA , RADIALIS , DIVARICATA , and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. ResultsWe found that RADIALIS , DIVARICATA , and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. Additionally, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. ConclusionOur results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.

scholarly journals Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

2017 ◽  
Author(s):  
Raúl Amado Cattáneo ◽  
Luis Diambra ◽  
Andrés Norman McCarthy
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Low Frequency ◽  
Genomic Data ◽  
Data Sets ◽  
High Coverage ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Alignment Free ◽  
Chloroplast Phylogeny

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

scholarly journals Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

2017 ◽  
Author(s):  
Raúl Amado Cattáneo ◽  
Luis Diambra ◽  
Andrés Norman McCarthy
Keyword(s):  
Dna Sequences ◽  
Evolutionary Biology ◽  
Low Frequency ◽  
Genomic Data ◽  
Data Sets ◽  
High Coverage ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Alignment Free ◽  
Chloroplast Phylogeny

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

scholarly journals Polynomial Phylogenetic Analysis of Tree Shapes

2020 ◽  
Author(s):  
Pengyu Liu ◽  
Priscila Biller ◽  
Matthew Gould ◽  
Caroline Colijn
Keyword(s):  
Phylogenetic Analysis ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Rooted Trees ◽  
Evolutionary Patterns ◽  
Sequencing Technologies ◽  
Branch Lengths ◽  
Discrete Structures ◽  
Best Fit ◽  
Central Tool

AbstractPhylogenetic trees are a central tool in evolutionary biology. They demonstrate evolutionary patterns among species, genes, and with modern sequencing technologies, patterns of ancestry among sets of individuals. Phylogenetic trees usually consist of tree shapes, branch lengths and partial labels. Comparing tree shapes is a challenging aspect of comparing phylogenetic trees as there are few tools to describe tree shapes in a quantitative, accurate, comprehensive and easy-to-interpret way. Current methods to compare tree shapes are often based on scalar indices reflecting tree imbalance, and on frequencies of small subtrees. In this paper, we present tree comparisons and applications based on a polynomial that fully characterizes trees. Polynomials are important tools to describe discrete structures and have been used to study various objects including graphs and knots. There are also polynomials that describe rooted trees. We use tree-defining polynomials to compare tree shapes randomly generated by simulations and tree shapes reconstructed from data. Moreover, we show that the comparisons can be used to estimate parameters and to select the best-fit model that generates specific tree shapes.

scholarly journals Introduction

2010 ◽  
Vol 38 (1/4) ◽  
pp. 9-17
Author(s):  
Timo Maran ◽  
Ester Võsu
Keyword(s):  
Evolutionary Biology ◽  
Literary Studies ◽  
Sign Systems ◽  
Iconic Signs ◽  
Systems Studies

This issue of Sign Systems Studies includes twelve papers on semiotics of resemblance. Readers competent in semiotics may argue that there is no such field as semiotics of resemblance and they would indeed be right. In this case, resemblance should be considered to be an umbrella term that covers various concepts, such as iconicity, iconic signs, similarity, analogy, categorization, metaphors, mimesis, mimicry, onomatopoeia, and others. These terms are used in different fields within and outside of semiotics. Accordingly, semiotics of resemblance should be treated as a possibility for establishing commonalities between different paradigms, from aesthetics to evolutionary biology and from theoretical semiotics to literary studies.

scholarly journals Developing Chloroplast Genomic Resources from 25 Avena Species for the Characterization of Oat Wild Relative Germplasm

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 438
Author(s):  
Yong-Bi Fu ◽  
Pingchuan Li ◽  
Bill Biligetu
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Genome Structure ◽  
Single Copy ◽  
Gene Arrangement ◽  
Wild Relative ◽  
Ploidy Levels ◽  
Avena Species ◽  
Genomic Resources

Chloroplast (cp) genomics will play an important role in the characterization of crop wild relative germplasm conserved in worldwide gene banks, thanks to the advances in genome sequencing. We applied a multiplexed shotgun sequencing procedure to sequence the cp genomes of 25 Avena species with variable ploidy levels. Bioinformatics analysis of the acquired sequences generated 25 de novo genome assemblies ranging from 135,557 to 136,006 bp. The gene annotations revealed 130 genes and their duplications, along with four to six pseudogenes, for each genome. Little differences in genome structure and gene arrangement were observed across the 25 species. Polymorphism analyses identified 1313 polymorphic sites and revealed an average of 277 microsatellites per genome. Greater nucleotide diversity was observed in the short single-copy region. Genome-wide scanning of selection signals suggested that six cp genes were under positive selection on some amino acids. These research outputs allow for a better understanding of oat cp genomes and evolution, and they form an essential set of cp genomic resources for the studies of oat evolutionary biology and for oat wild relative germplasm characterization.

scholarly journals Allan Charles Wilson. 18 October 1934 — 21 July 1991

2014 ◽  
Vol 60 ◽  
pp. 455-473 ◽  
Author(s):  
Rebecca L. Cann
Keyword(s):  
New Zealand ◽  
Molecular Evolution ◽  
Doctoral Students ◽  
Molecular Clock ◽  
Evolutionary Biology ◽  
Evolutionary Change ◽  
Left Behind ◽  
The Usa ◽  
Living Species ◽  
The University

Allan Charles Wilson was born on 18 October 1934 at Ngaruawahia, New Zealand. He died in Seattle, Washington, on 21 July 1991 while undergoing treatment for leukaemia. Allan was known as a pioneering and highly innovative biochemist, helping to define the field of molecular evolution and establish the use of a molecular clock to measure evolutionary change between living species. The molecular clock, a method of measuring the timescale of evolutionary change between two organisms on the basis of the number of mutations that they have accumulated since last sharing a common genetic ancestor, was an idea initially championed by Émile Zuckerkandl and Linus Pauling (Zuckerkandl & Pauling 1962), on the basis of their observations that the number of changes in an amino acid sequence was roughly linear with time in the aligned haemoglobin proteins of animals. Although it is now not unusual to see the words ‘molecular evolution’ and ‘molecular phylogeny’ together, when Allan formed his own biochemistry laboratory in 1964 at the University of California, Berkeley, many scientists in the field of evolutionary biology considered these ideas complete heresy. Allan’s death at the relatively young age of 56 years left behind his wife, Leona (deceased in 2009), a daughter, Ruth (b. 1961), and a son, David (b. 1964), as well his as mother, Eunice (deceased in 2002), a younger brother, Gary Wilson, and a sister, Colleen Macmillan, along with numerous nieces, nephews and cousins in New Zealand, Australia and the USA. In this short span of time, he trained more than 55 doctoral students and helped launch the careers of numerous postdoctoral fellows.

scholarly journals Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play

2009 ◽  
Vol 364 (1523) ◽  
pp. 1629-1640 ◽  
Author(s):  
David M. Post ◽  
Eric P. Palkovacs
Keyword(s):  
Evolutionary Biology ◽  
Niche Construction ◽  
Biological Diversity ◽  
Life History Evolution ◽  
Habitat Modification ◽  
Ecological Change ◽  
Contemporary Evolution ◽  
Nutrient Excretion ◽  
Natural Systems ◽  
Tree Leaf

Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer–algae chemostats; alewife–zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife–zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.

scholarly journals Symbiont-mediated protection varies with wasp genotype in the Drosophila melanogaster-Spiroplasma interaction

2019 ◽  
Author(s):  
Jordan E Jones ◽  
Gregory D D Hurst
Keyword(s):  
Drosophila Melanogaster ◽  
Natural Enemies ◽  
Evolutionary Biology ◽  
Model System ◽  
Common Source ◽  
Parasitoid Wasps ◽  
Composite Measure ◽  
Natural Systems ◽  
Microbial Symbionts ◽  
Positive Effect

AbstractThe ability of an insect to survive attack by natural enemies can be modulated by the presence of defensive symbionts. Study of aphid-symbiont-enemy interactions has indicated that protection may depend on the interplay of symbiont, host and attacking parasite genotypes. However, the importance of these interactions are poorly understood outside of this model system. Here, we study interactions within a Drosophila model system, in which Spiroplasma protect their host against parasitoid wasps and nematode attack. We examine whether the strength of protection conferred by Spiroplasma to its host, Drosophila melanogaster varies with strain of attacking Leptopilina heterotoma wasp. We perform this analysis in the presence and absence of ethanol, an environmental factor that also impacts the outcome of parasitism. We observed that Spiroplasma killed all strains of wasp. However, the protection produced by Spiroplasma following wasp attack depended on attacking wasp strain. A composite measure of protection, including both the chance of the fly surviving attack and the relative fecundity/fertility of the survivors, varied from a <4% positive effect of the symbiont following attack of the fly host by the Lh14 strain of wasp to 21% for the Lh-Fr strain in the absence of ethanol. Variation in protection provided was not associated with differences in the oviposition behaviour of the different wasp strains. We observed that environmental ethanol altered the pattern of protection against wasp strains, with Spiroplasma being most protective against the Lh-Mad wasp strain in the presence of ethanol. These data indicate that the dynamics of the Spiroplasma-Drosophila-wasp tripartite interaction depend upon the genetic diversity within the attacking wasp population, and that prediction of symbiont dynamics in natural systems will thus require analysis across natural enemy genotypes and levels of environmental ethanol.Impact SummaryNatural enemies – predators, parasites and pathogens – are a common source of mortality in animals, and this has driven the evolution of an array of mechanisms for preventing and surviving attack. Recently it has been observed that microbial symbionts form a component of insect defence against attack by pathogens and parasites. Whether an individual fly dies or lives following wasp attack, for instance, is partly determined by the presence or absence of Spiroplasma bacteria in the fly blood. The evolutionary biology of these ‘protective symbioses’ will in part depend on the specificity of defence – does Spiroplasma defend against all wasp strains equally, or does defence vary between wasp strains? We investigated this in the model insect, Drosophila melanogaster. We observed that the defensive symbiont killed all strains of wasps tested. However, the capacity of the symbiont to rescue the fly varied – Spiroplasma rescued the flies for some attacking wasp strains, but not for others. These data mean that the degree to which symbionts protect their host will depend on the wasp strains circulating in nature. Our results are important in terms of understanding the forces that promote symbiont mediated protection and understanding the origins of diversity of circulating wasp strains. Further, these data indicate enemy diversity and their interaction with protective symbionts should be included in evaluation of the efficiency of biocontrol programmes involving natural enemies.

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