scholarly journals Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps

2019 ◽  
Author(s):  
Lisandro Milocco ◽  
Isaac Salazar-Ciudad
Keyword(s):  
Natural Selection ◽  
Quantitative Genetics ◽  
Evolutionary Biology ◽  
Linear Models ◽  
Response To Selection ◽  
Multiple Traits ◽  
Highly Nonlinear ◽  
Nonlinear Maps ◽  
Evo Devo ◽  
Nonlinear Nature

AbstractA fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation (1). Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a population (2, 3). The other major field of research concerned with the GPM, developmental evolutionary biology or evo-devo (1, 4–6), has found the GPM to be highly nonlinear and complex (4, 7). Here we quantify how the predictions of quantitative genetics are affected by the complex, nonlinear maps found in developmental biology. We combine a realistic development-based GPM model and a population genetics model of recombination, mutation and natural selection. Each individual in the population consists of a genotype and a multi-trait phenotype that arises through the development model. We simulate evolution by applying natural selection on multiple traits per individual. In addition, we estimate the quantitative genetics parameters required to predict the response to selection. We found that the disagreements between predicted and observed responses to selection are common, roughly in a third of generations, and are highly dependent on the traits being selected. These disagreements are systematic and related to the nonlinear nature of the genotype-phenotype map. Our results are a step towards integrating the fields studying the GPM.

Multivariate Mixed Models in Ecology and Evolutionary biology: Inferences and implementation in R

2019 ◽  
Author(s):  
Jon Brommer ◽  
Barbara Class ◽  
Giovanny Covarrubias-Pazaran
Keyword(s):  
Mixed Models ◽  
Evolutionary Biology ◽  
Linear Models ◽  
Random Effect ◽  
Covariance Structures ◽  
Multiple Traits ◽  
Bayesian Monte Carlo ◽  
Software Implementations ◽  
R Packages ◽  
Multi Level

Multivariate mixed models (MMM) are generalized linear models with both fixed and random effect having multiple response variables. MMM allow partitioning of total (phenotypic) (co)variances for multiple traits into (co)variances on hierarchically lower levels. We outline why ecologists and evolutionary biologists should be interested in such partitioning as well as the levels of analyses that arise when making inferences on multi-level covariance structures. We consider biological levels of interest to be genes (e.g. GWAS, genomic selection), genotypes (genetic (co)variances), individual or other subject (e.g. between-individual (co)variances) and phylogenetic taxa (phylogenetic (co)variances). All of these biological levels can be modelled in a MMM and we distinguish several demand levels of using MMM of increasing complexity. We present an overview of current open-access software implementations of MMM in the open software R with respect to these demand levels, and present example scripts aimed at getting started with MMM on all biological levels. We describe four freely available R packages for MMM, two using Bayesian (Monte Carlo and Hamiltonian Markov Chains) and two using a likelihood framework. Depending on the need of the analyst, there are a number of freely available R-based MMM implementations of relevance to the field of ecology and evolution.

Evolution and Selection of Quantitative Traits

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Mathematical Models ◽  
Quantitative Genetics ◽  
Complex Traits ◽  
Evolutionary Biology ◽  
Quantitative Traits ◽  
Specific Gene ◽  
Real World Data ◽  
Holistic Treatment ◽  
Genetics And Genomics ◽  
Selection Of

Quantitative traits—be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene—usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences. This extensive work of reference is suitable for graduate level students as well as professional researchers (both empiricists and theoreticians) in the fields of evolutionary biology, genetics, and genomics. It will also be of particular relevance and use to plant and animal breeders, human geneticists, and statisticians.

Deconstructing and reconstructing joint hypermobility on an evo-devo perspective

Rheumatology ◽  
2021 ◽  
Author(s):  
Marco Castori
Keyword(s):  
Evolutionary Biology ◽  
Phenotypic Variability ◽  
Morphological Variability ◽  
Complex Trait ◽  
Joint Hypermobility ◽  
Integration Model ◽  
Ehlers Danlos Syndrome ◽  
Evo Devo ◽  
Derivatives Of ◽  
Continuous Traits

Abstract Joint hypermobility is a common characteristic in humans. Its non-casual association with various musculoskeletal complaints is known and currently defined “the spectrum”. It includes hypermobile Ehlers–Danlos syndrome (hEDS) and hypermobility spectrum disorders (HSD). hEDS is recognized by a set of descriptive criteria, while HSD is the background diagnosis for individuals not fulfilling these criteria. Little is known about the aetiopathogenesis of the spectrum. It may be interpreted as a complex trait according to the integration model. Particularly, the spectrum is common in the general population, affects morphology, presents extreme clinical variability and is characterized by marked sex bias without a clear Mendelian or hormonal explanation. Joint hypermobility and the other hEDS systemic criteria are intended as qualitative derivatives of continuous traits of normal morphological variability. The need for a minimum set of criteria for hEDS diagnosis implies a tendency to co-vary of these underlying continuous traits. In evolutionary biology, such a co-variation (i.e. integration) is driven by multiple forces, including genetic, developmental, functional and environmental/acquired interactors. The aetiopathogenesis of the spectrum may be resolved by a deeper understanding of phenotypic variability, which superimposes on normal morphological variability.

scholarly journals Genome size correlates with reproductive fitness in seed beetles

2015 ◽  
Vol 282 (1815) ◽  
pp. 20151421 ◽  
Author(s):  
Göran Arnqvist ◽  
Ahmed Sayadi ◽  
Elina Immonen ◽  
Cosima Hotzy ◽  
Daniel Rankin ◽  
...  
Keyword(s):  
Life History ◽  
Natural Selection ◽  
Genome Size ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Life History Traits ◽  
Single Species ◽  
Reproductive Fitness ◽  
Correlated Evolution ◽  
Seed Beetles

The ultimate cause of genome size (GS) evolution in eukaryotes remains a major and unresolved puzzle in evolutionary biology. Large-scale comparative studies have failed to find consistent correlations between GS and organismal properties, resulting in the ‘ C -value paradox’. Current hypotheses for the evolution of GS are based either on the balance between mutational events and drift or on natural selection acting upon standing genetic variation in GS. It is, however, currently very difficult to evaluate the role of selection because within-species studies that relate variation in life-history traits to variation in GS are very rare. Here, we report phylogenetic comparative analyses of GS evolution in seed beetles at two distinct taxonomic scales, which combines replicated estimation of GS with experimental assays of life-history traits and reproductive fitness. GS showed rapid and bidirectional evolution across species, but did not show correlated evolution with any of several indices of the relative importance of genetic drift. Within a single species, GS varied by 4–5% across populations and showed positive correlated evolution with independent estimates of male and female reproductive fitness. Collectively, the phylogenetic pattern of GS diversification across and within species in conjunction with the pattern of correlated evolution between GS and fitness provide novel support for the tenet that natural selection plays a key role in shaping GS evolution.

scholarly journals Evolutionary biology today and the call for an extended synthesis

2017 ◽  
Vol 7 (5) ◽  
pp. 20160145 ◽  
Author(s):  
Douglas J. Futuyma
Keyword(s):  
Natural Selection ◽  
Evolutionary Theory ◽  
Evolutionary Biology ◽  
Epigenetic Inheritance ◽  
Reaction Norm ◽  
Evolutionary Synthesis ◽  
Historical Background ◽  
Extended Evolutionary Synthesis ◽  
Extended Synthesis ◽  
Proximate Causation

Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an ‘extended evolutionary synthesis’. ‘Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected ‘process’ of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation. Evolutionary theory will continue to be extended, but there is no sign that it requires emendation.

scholarly journals The evolution of superstitious and superstition-like behaviour

2008 ◽  
Vol 276 (1654) ◽  
pp. 31-37 ◽  
Author(s):  
Kevin R Foster ◽  
Hanna Kokko
Keyword(s):  
Popular Culture ◽  
Natural Selection ◽  
Simple Model ◽  
Correct Response ◽  
Evolutionary Biology ◽  
Adaptive Behaviour ◽  
Multiple Events ◽  
Cause And Effect ◽  
Pascal’S Wager ◽  
Hamilton's Rule

Superstitious behaviours, which arise through the incorrect assignment of cause and effect, receive considerable attention in psychology and popular culture. Perhaps owing to their seeming irrationality, however, they receive little attention in evolutionary biology. Here we develop a simple model to define the condition under which natural selection will favour assigning causality between two events. This leads to an intuitive inequality—akin to an amalgam of Hamilton's rule and Pascal's wager—-that shows that natural selection can favour strategies that lead to frequent errors in assessment as long as the occasional correct response carries a large fitness benefit. It follows that incorrect responses are the most common when the probability that two events are really associated is low to moderate: very strong associations are rarely incorrect, while natural selection will rarely favour making very weak associations. Extending the model to include multiple events identifies conditions under which natural selection can favour associating events that are never causally related. Specifically, limitations on assigning causal probabilities to pairs of events can favour strategies that lump non-causal associations with causal ones. We conclude that behaviours which are, or appear, superstitious are an inevitable feature of adaptive behaviour in all organisms, including ourselves.

scholarly journals Genetic basis of phenotypic plasticity and genotype x environment interaction in a multi-parental population

2020 ◽  
Author(s):  
Isidore Diouf ◽  
Laurent Derivot ◽  
Shai Koussevitzky ◽  
Yolande Carretero ◽  
Frédérique Bitton ◽  
...  
Keyword(s):  
Phenotypic Plasticity ◽  
Genetic Architecture ◽  
Genetic Basis ◽  
Linear Models ◽  
Global Climate ◽  
Functional Characterization ◽  
Genotype X Environment Interaction ◽  
Environment Interaction ◽  
Multiple Traits ◽  
Genotype X Environment

AbstractDeciphering the genetic basis of phenotypic plasticity and genotype x environment interaction (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato is a widely cultivated crop that can grow in different geographical habitats and which evinces a great capacity of expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore GxE and plasticity for multiple traits measured in a multi-environment trial (MET) design comprising optimal cultural conditions and water deficit, salinity and heat stress over 12 environments. Substantial GxE was observed for all the traits measured. Different plasticity parameters were estimated through the Finlay-Wilkinson and factorial regression models and used together with the genotypic means for quantitative trait loci (QTL) mapping analyses. Mixed linear models were further used to investigate the presence of interactive QTLs (QEI). The results highlighted a complex genetic architecture of tomato plasticity and GxE. Candidate genes that might be involved in the occurrence of GxE were proposed, paving the way for functional characterization of stress response genes in tomato and breeding for climate-adapted crop.HighlightThe genetic architecture of tomato response to several abiotic stresses is deciphered. QTL for plasticity and QTL x Environment were identified in a highly recombinant MAGIC population.

scholarly journals Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise

2018 ◽  
Author(s):  
Russell A. Ligon ◽  
Christopher D. Diaz ◽  
Janelle L. Morano ◽  
Jolyon Troscianko ◽  
Martin Stevens ◽  
...  
Keyword(s):  
Sexual Selection ◽  
Natural Selection ◽  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Functional Integration ◽  
Empirical Support ◽  
Evolutionary Patterns ◽  
Evolutionary Innovation ◽  
Birds Of Paradise ◽  
Analytical Approaches

Ornaments used in courtship often vary wildly among species, reflecting the evolutionary interplay between mate preference functions and the constraints imposed by natural selection. Consequently, understanding the evolutionary dynamics responsible for ornament diversification has been a longstanding challenge in evolutionary biology. However, comparing radically different ornaments across species, as well as different classes of ornaments within species, is a profound challenge to understanding diversification of sexual signals. Using novel methods and a unique natural history dataset, we explore evolutionary patterns of ornament evolution in a group - the birds-of-paradise - exhibiting dramatic phenotypic diversification widely assumed to be driven by sexual selection. Rather than the tradeoff between ornament types originally envisioned by Darwin and Wallace, we found positive correlations among cross-modal (visual/acoustic) signals indicating functional integration of ornamental traits into a composite unit - the courtship phenotype. Furthermore, given the broad theoretical and empirical support for the idea that systemic robustness - functional overlap and interdependency - promotes evolutionary innovation, we posit that birds-of-paradise have radiated extensively through ornamental phenotype space as a consequence of the robustness in the courtship phenotype that we document at a phylogenetic scale. We suggest that the degree of robustness in courtship phenotypes among taxa can provide new insights into the relative influence of sexual and natural selection on phenotypic radiations.Author SummaryAnimals frequently vary widely in ornamentation, even among closely related species. Understanding the patterns that underlie this variation is a significant challenge, requiring comparisons among drastically different traits - like comparing apples to oranges. Here, we use novel analytical approaches to quantify variation in ornamental diversity and richness across the wildly divergent birds-of-paradise, a textbook example of how sexual selection can profoundly shape organismal phenotypes. We find that color and acoustic complexity, along with behavior and acoustic complexity, are positively correlated across evolutionary time-scales. Positive covariation among ornament classes suggests that selection is acting on correlated suites of traits - a composite courtship phenotype - and that this integration may be partially responsible for the extreme variation we see in birds-of-paradise.

scholarly journals Natural Selection at an Exceptionally Long GGC Repeat in the Human RASGEF1C and Divergent Genotypes in Late-onset Neurocognitive Disorder

2021 ◽  
Author(s):  
Z Jafarian ◽  
S Khamse ◽  
H Afshar ◽  
Khorram Khorshid HR ◽  
A Delbari ◽  
...  
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Late Onset ◽  
Core Promoter ◽  
Human Subjects ◽  
Specific Gene ◽  
Protein Coding ◽  
Repeat Allele ◽  
Complex Disorders ◽  
Selection For

Abstract Across the human protein-coding genes, the neuron-specific gene, RASGEF1C, contains the longest (GGC)-repeat, spanning its core promoter and 5′ untranslated region (RASGEF1C-201 ENST00000361132.9). RASGEF1C expression dysregulation occurs in late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. Here we sequenced the GGC-repeat in a sample of human subjects (N = 269), consisting of late-onset NCDs (N = 115) and controls (N = 154). We also studied the status of this STR across vertebrates. The 6-repeat allele of this repeat was the predominant allele in the controls (frequency = 0.85) and NCD patients (frequency = 0.78). The NCD genotype compartment consisted of an excess of genotypes that lacked the 6-repeat (Mid-P exact = 0.004). We also detected divergent genotypes that were present in five NCD patients and not in the controls (Mid-P exact = 0.007). This STR expanded beyond 2-repeats specifically in primates, and was at maximum length in human. We conclude that there is natural selection for the 6-repeat allele of the RASGEF1C (GGC)-repeat in human, and significant divergence from that allele in late-onset NCDs. Indication of natural selection for predominantly abundant STR alleles and divergent genotypes enhance the perspective of evolutionary biology and disease pathogenesis in human complex disorders.

The naked ape as an evolutionary model, 50 years later

2018 ◽  
Vol 68 (3) ◽  
pp. 227-246
Author(s):  
Nico M. van Straalen
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Evolutionary Model ◽  
Developmental Constraints ◽  
Body Hair ◽  
Product Evolution ◽  
Adaptive Explanation ◽  
History Of ◽  
Popular Texts ◽  
The Brain

AbstractEvolution acts through a combination of four different drivers: (1) mutation, (2) selection, (3) genetic drift, and (4) developmental constraints. There is a tendency among some biologists to frame evolution as the sole result of natural selection, and this tendency is reinforced by many popular texts. “The Naked Ape” by Desmond Morris, published 50 years ago, is no exception. In this paper I argue that evolutionary biology is much richer than natural selection alone. I illustrate this by reconstructing the evolutionary history of five different organs of the human body: foot, pelvis, scrotum, hand and brain. Factors like developmental tinkering, by-product evolution, exaptation and heterochrony are powerful forces for body-plan innovations and the appearance of such innovations in human ancestors does not always require an adaptive explanation. While Morris explained the lack of body hair in the human species by sexual selection, I argue that molecular tinkering of regulatory genes expressed in the brain, followed by positive selection for neotenic features, may have been the driving factor, with loss of body hair as a secondary consequence.

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