evolutionary_biology   268

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Population Genetics: Why structure matters | eLife
"Berg et al. and Sohail et al. demonstrate the potential for population structure to create spurious results, especially when using methods that rely on large numbers of small effects, such as polygenic scores. Caution is clearly needed when interpreting and using the results of such studies. For clinical predictions, risks must be weighed against benefits (Rosenberg et al., 2019). In some cases, such as recommendations for more frequent medical checkups for patients found at higher ‘genetic’ risk of a condition, it may not matter greatly whether predictors are confounded as long as they work. By contrast, the results of behavioral studies of traits such as IQ and educational attainment (Plomin and von Stumm, 2018) must be presented carefully, because while the benefits are far from obvious, the risks of such results being misinterpreted and misused are quite clear. The problem is worsened by the tendency of popular media to ignore caveats and uncertainties of estimates."

"Finally, although quantitative genetics has proved highly successful in plant and animal breeding, it should be remembered that this success has been based on large pedigrees, well-controlled environments, and short-term prediction. When these methods have been applied to natural populations, even the most basic predictions fail, in large part due to poorly understood environmental factors (Charmantier et al., 2014). Natural populations are never homogeneous, and it is therefore misleading to imply there is a qualitative difference between ‘within-population’ and ‘between-population’ comparisons – as was recently done in connection with James Watson’s statements about race and IQ (Harmon, 2019). With respect to confounding by population structure, the key qualitative difference is between controlling the environment experimentally, and not doing so. Once we leave an experimental setting, we are effectively skating on thin ice, and whether the ice will hold depends on how far out we skate."
population_biology  genetics  evolutionary_biology  nature-nurture  debates  latent_variables  via:gelman 
9 weeks ago by rvenkat
[1907.09551] Cell differentiation: what have we learned in 50 years?
"I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network (MGRN) model, in light of newer knowledge of mechanisms of gene regulation in the metazoans (animals). The two models continue to inform hypotheses and computational studies of differentiation of lineage-adjacent cell types. However, their shared notion (based on bacterial regulatory systems) of gene switches and networks built from them, have constrained progress in understanding the dynamics and evolution of differentiation. Recent work has described unique write-read-rewrite chromatin-based expression encoding in eukaryotes, as well metazoan-specific processes of gene activation and silencing in condensed-phase, enhancer-recruiting regulatory hubs, employing disordered proteins, including transcription factors, with context-dependent identities. These findings suggest an evolutionary scenario in which the origination of differentiation in animals, rather than depending exclusively on adaptive natural selection, emerged as a consequence of a type of multicellularity in which the novel metazoan gene regulatory apparatus was readily mobilized to amplify and exaggerate inherent cell functions of unicellular ancestors. The plausibility of this hypothesis is illustrated by the evolution of the developmental role of Grainyhead-like in the formation of epithelium."
to:NB  developmental_biology  evolutionary_biology  gene_regulation  biochemical_networks 
12 weeks ago by cshalizi
[1908.06241] Graphon-valued stochastic processes from population genetics
"The goal of this paper is to develop a theory of graphon-valued stochastic processes, and to construct and analyse a natural class of such processes arising from population genetics. We consider finite populations where individuals change type according to Wright-Fisher resampling. At any time, each pair of individuals is linked by an edge with a probability that is given by a type-connection matrix, whose entries depend on the current empirical type distribution of the entire population via a fitness function. We show that, in the large-population-size limit and with an appropriate scaling of time, the evolution of the associated adjacency matrix converges to a random process in the space of graphons, driven by the type-connection matrix and the underlying Wright-Fisher diffusion on the multi-type simplex. In the limit as the number of types tends to infinity, the limiting process is driven by the type-connection kernel and the underlying Fleming-Viot diffusion."
to:NB  evolutionary_biology  graphons  stochastic_processes  den_hollander.frank 
august 2019 by cshalizi
[1908.05996] Turbulent coherent structures and early life below the Kolmogorov scale
"A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. While the chemical aspects of the role of water in biology are well-studied, the effects of water's physical characteristics on evolutionary events, such as the control of population structure via its rich transport properties, are less clear. Evolutionary transitions such as the emergence of the first cells and of multicellularity, require cooperation among groups of individuals. However, evolution of cooperation faces challenges in unstructured "well-mixed" populations, as parasites quickly overwhelm cooperators. Models that assume population structure to promote cooperation envision such structure to arise from spatial "lattice" models (e.g. surface bound individuals) or compartmentalization models, often realized as protocells. Here we study the effect of turbulent motions in spatial models, and propose that coherent structures, i.e. flow patterns which trap fluid and arise naturally in turbulent flows, may serve many of the properties associated with compartments--collocalization, division, and merging--and thought to play a key role in the origins of life and other evolutionary transitions. These results suggest that group selection models may be applicable with fewer physical and chemical constraints than previously thought, and apply much more widely in aqueous environments."
to:NB  evolutionary_biology  turbulence 
august 2019 by cshalizi
Adaptive colour change and background choice behaviour in peppered moth caterpillars is mediated by extraocular photoreception | Communications Biology
Light sensing by tissues distinct from the eye occurs in diverse animal groups, enabling circadian control and phototactic behaviour. Extraocular photoreceptors may also facilitate rapid colour change in cephalopods and lizards, but little is known about the sensory system that mediates slow colour change in arthropods. We previously reported that slow colour change in twig-mimicking caterpillars of the peppered moth (Biston betularia) is a response to achromatic and chromatic visual cues. Here we show that the perception of these cues, and the resulting phenotypic responses, does not require ocular vision. Caterpillars with completely obscured ocelli remained capable of enhancing their crypsis by changing colour and choosing to rest on colour-matching twigs. A suite of visual genes, expressed across the larval integument, likely plays a key role in the mechanism. To our knowledge, this is the first evidence that extraocular colour sensing can mediate pigment-based colour change and behaviour in an arthropod.

-- partially answers a lot of the questions I have had forever about mechanisms behind rapid color changes in animals.

Related
https://link.springer.com/article/10.1007/s12052-008-0107-y
ethology  evolutionary_biology  via:coyne 
august 2019 by rvenkat
Rev. Mod. Phys. 91, 031001 (2019) - Colloquium: Proteins: The physics of amorphous evolving matter
"Protein is matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with diverse biochemistry. But it is also a point along an evolutionary trajectory determined by the function performed by the protein within a hierarchy of interwoven interaction networks of the cell, the organism, and the population. A physical theory of proteins therefore needs to unify both aspects, the biophysical and the evolutionary. Specifically, it should provide a model of how the DNA gene is mapped into the functional phenotype of the protein. Several physical approaches to the protein problem are reviewed, focusing on a mechanical framework which treats proteins as evolvable condensed matter: Mutations introduce localized perturbations in the gene, which are translated to localized perturbations in the protein matter. A natural tool to examine how mutations shape the phenotype are Green’s functions. They map the evolutionary linkage among mutations in the gene (termed epistasis) to cooperative physical interactions among the amino acids in the protein. The mechanistic view can be applied to examine basic questions of protein evolution and design."

--- Ungated: https://arxiv.org/abs/1907.13371
to:NB  biophysics  evolutionary_biology  eckmann.jean-pierre 
july 2019 by cshalizi
Cryptic genetic variation accelerates evolution by opening access to diverse adaptive peaks | Science
"Cryptic genetic variation can facilitate adaptation in evolving populations. To elucidate the underlying genetic mechanisms, we used directed evolution in Escherichia coli to accumulate variation in populations of yellow fluorescent proteins and then evolved these proteins toward the new phenotype of green fluorescence. Populations with cryptic variation evolved adaptive genotypes with greater diversity and higher fitness than populations without cryptic variation, which converged on similar genotypes. Populations with cryptic variation accumulated neutral or deleterious mutations that break the constraints on the order in which adaptive mutations arise. In doing so, cryptic variation opens paths to adaptive genotypes, creates historical contingency, and reduces the predictability of evolution by allowing different replicate populations to climb different adaptive peaks and explore otherwise-inaccessible regions of an adaptive landscape."
to:NB  evolutionary_biology  wagner.andreas 
july 2019 by cshalizi
Evolutionary Genetics - Hardcover - Glenn-Peter Saetre; Mark Ravinet - Oxford University Press
"With recent technological advances, vast quantities of genetic and genomic data are being generated at an ever-increasing pace. The explosion in access to data has transformed the field of evolutionary genetics. A thorough understanding of evolutionary principles is essential for making sense of this, but new skill sets are also needed to handle and analyze big data. This contemporary textbook covers all the major components of modern evolutionary genetics, carefully explaining fundamental processes such as mutation, natural selection, genetic drift, and speciation. It also draws on a rich literature of exciting and inspiring examples to demonstrate the diversity of evolutionary research, including an emphasis on how evolution and selection has shaped our own species.
"Practical experience is essential for developing an understanding of how to use genetic and genomic data to analyze and interpret results in meaningful ways. In addition to the main text, a series of online tutorials using the R language serves as an introduction to programming, statistics, and analysis. Indeed the R environment stands out as an ideal all-purpose source platform to handle and analyze such data. The book and its online materials take full advantage of the authors' own experience in working in a post-genomic revolution world, and introduces readers to the plethora of molecular and analytical methods that have only recently become available.
"Evolutionary Genetics is an advanced but accessible textbook aimed principally at students of various levels (from undergraduate to postgraduate) but also for researchers looking for an updated introduction to modern evolutionary biology and genetics. "
to:NB  genetics  evolutionary_biology  statistics  R  books:noted 
july 2019 by cshalizi
[1907.01681] Gradient flow formulations of discrete and continuous evolutionary models: a unifying perspective
"We consider three classical models of biological evolution: (i) the Moran process, an example of a reducible Markov Chain; (ii) the Kimura Equation, a particular case of a degenerated Fokker-Planck Diffusion; (iii) the Replicator Equation, a paradigm in Evolutionary Game Theory. While these approaches are not completely equivalent, they are intimately connected, since (ii) is the diffusion approximation of (i), and (iii) is obtained from (ii) in an appropriate limit. It is well known that the Replicator Dynamics for two strategies is a gradient flow with respect to the celebrated Shahshahani distance. We reformulate the Moran process and the Kimura Equation as gradient flows and in the sequel we discuss conditions such that the associated gradient structures converge: (i) to (ii) and (ii) to (iii). This provides a geometric characterisation of these evolutionary processes and provides a reformulation of the above examples as time minimization of free energy functionals."
to:NB  replicator_dynamics  evolutionary_biology  dynamical_systems 
july 2019 by cshalizi
Development and Evolutionary Constraints in Animals | Annual Review of Ecology, Evolution, and Systematics
"We review the evolutionary importance of developmental mechanisms in constraining evolutionary changes in animals—in other words, developmental constraints. We focus on hard constraints that can act on macroevolutionary timescales. In particular, we discuss the causes and evolutionary consequences of the ancient metazoan constraint that differentiated cells cannot divide and constraints against changes of phylotypic stages in vertebrates and other higher taxa. We conclude that in all cases these constraints are caused by complex and highly controlled global interactivity of development, the disturbance of which has grave consequences. Mutations that affect such global interactivity almost unavoidably have many deleterious pleiotropic effects, which will be strongly selected against and will lead to long-term evolutionary stasis. The discussed developmental constraints have pervasive consequences for evolution and critically restrict regeneration capacity and body plan evolution."
evolutionary_biology  developmental_biology  via:cshalizi 
june 2019 by rvenkat
Development and Evolutionary Constraints in Animals | Annual Review of Ecology, Evolution, and Systematics
"We review the evolutionary importance of developmental mechanisms in constraining evolutionary changes in animals—in other words, developmental constraints. We focus on hard constraints that can act on macroevolutionary timescales. In particular, we discuss the causes and evolutionary consequences of the ancient metazoan constraint that differentiated cells cannot divide and constraints against changes of phylotypic stages in vertebrates and other higher taxa. We conclude that in all cases these constraints are caused by complex and highly controlled global interactivity of development, the disturbance of which has grave consequences. Mutations that affect such global interactivity almost unavoidably have many deleterious pleiotropic effects, which will be strongly selected against and will lead to long-term evolutionary stasis. The discussed developmental constraints have pervasive consequences for evolution and critically restrict regeneration capacity and body plan evolution."
to:NB  evolutionary_biology  developmental_biology 
may 2019 by cshalizi
Evaluating Model Performance in Evolutionary Biology | Annual Review of Ecology, Evolution, and Systematics
"Many fields of evolutionary biology now depend on stochastic mathematical models. These models are valuable for their ability to formalize predictions in the face of uncertainty and provide a quantitative framework for testing hypotheses. However, no mathematical model will fully capture biological complexity. Instead, these models attempt to capture the important features of biological systems using relatively simple mathematical principles. These simplifications can allow us to focus on differences that are meaningful, while ignoring those that are not. However, simplification also requires assumptions, and to the extent that these are wrong, so is our ability to predict or compare. Here, we discuss approaches for evaluating the performance of evolutionary models in light of their assumptions by comparing them against reality. We highlight general approaches, how they are applied, and remaining opportunities. Absolute tests of fit, even when not explicitly framed as such, are fundamental to progress in understanding evolution."
to:NB  evolutionary_biology  stochastic_models  modeling  model_checking  statistics 
may 2019 by cshalizi
Dinosaur Macroevolution and Macroecology | Annual Review of Ecology, Evolution, and Systematics
"Dinosaurs were large-bodied land animals of the Mesozoic that gave rise to birds. They played a fundamental role in structuring Jurassic–Cretaceous ecosystems and had physiology, growth, and reproductive biology unlike those of extant animals. These features have made them targets of theoretical macroecology. Dinosaurs achieved substantial structural diversity, and their fossil record documents the evolutionary assembly of the avian body plan. Phylogeny-based research has allowed new insights into dinosaur macroevolution, including the adaptive landscape of their body size evolution, patterns of species diversification, and the origins of birds and bird-like traits. Nevertheless, much remains unknown due to incompleteness of the fossil record at both local and global scales. This presents major challenges at the frontier of paleobiological research regarding tests of macroecological hypotheses and the effects of dinosaur biology, ecology, and life history on their macroevolution."
to:NB  evolutionary_biology  dinosaurs  ecology 
may 2019 by cshalizi
Variation and Evolution of Function-Valued Traits | Annual Review of Ecology, Evolution, and Systematics
"Function-valued traits—phenotypes whose expression depends on a continuous index (such as age, temperature, or space)—occur throughout biology and, like any trait, it is important to understand how they vary and evolve. Although methods for analyzing variation and evolution of function-valued traits are well developed, they have been underutilized by evolutionists, especially those who study natural populations. We seek to summarize advances in the study of function-valued traits and to make their analyses more approachable and accessible to biologists who could benefit greatly from their use. To that end, we explain how curve thinking benefits conceptual understanding and statistical analysis of functional data. We provide a detailed guide to the most flexible and statistically powerful methods and include worked examples (with R code) as supplemental material. We review ways to characterize variation in function-valued traits and analyze consequences for evolution, including constraint. We also discuss how selection on function-valued traits can be estimated and combined with estimates of heritable variation to project evolutionary dynamics."
to:NB  evolutionary_biology  functional_data_analysis  statistics 
may 2019 by cshalizi
The Contemporary Evolution of Fitness | Annual Review of Ecology, Evolution, and Systematics
"The rate of evolution of population mean fitness informs how selection acting in contemporary populations can counteract environmental change and genetic degradation (mutation, gene flow, drift, recombination). This rate influences population increases (e.g., range expansion), population stability (e.g., cryptic eco-evolutionary dynamics), and population recovery (i.e., evolutionary rescue). We review approaches for estimating such rates, especially in wild populations. We then review empirical estimates derived from two approaches: mutation accumulation (MA) and additive genetic variance in fitness (IAw). MA studies inform how selection counters genetic degradation arising from deleterious mutations, typically generating estimates of <1% per generation. IAw studies provide an integrated prediction of proportional change per generation, nearly always generating estimates of <20% and, more typically, <10%. Overall, considerable, but not unlimited, evolutionary potential exists in populations facing detrimental environmental or genetic change. However, further studies with diverse methods and species are required for more robust and general insights."
to:NB  evolutionary_biology  statistics 
may 2019 by cshalizi
R. A. Fisher: a faith fit for eugenics. - PubMed - NCBI
In discussions of 'religion-and-science', faith is usually emphasized more than works, scientists' beliefs more than their deeds. By reversing the priority, a lingering puzzle in the life of Ronald Aylmer Fisher (1890-1962), statistician, eugenicist and founder of the neo-Darwinian synthesis, can be solved. Scholars have struggled to find coherence in Fisher's simultaneous commitment to Darwinism, Anglican Christianity and eugenics. The problem is addressed by asking what practical mode of faith or faithful mode of practice lent unity to his life? Families, it is argued, with their myriad practical, emotional and intellectual challenges, rendered a mathematically-based eugenic Darwinian Christianity not just possible for Fisher, but vital.
history_of_ideas  people  statistics  religion  evolutionary_biology  via:noahpinion 
february 2019 by rvenkat
[1506.03414] An evolutionary advantage of cooperation
Cooperation is a persistent behavioral pattern of entities pooling and sharing resources. Its ubiquity in nature poses a conundrum. Whenever two entities cooperate, one must willingly relinquish something of value to the other. Why is this apparent altruism favored in evolution? Classical solutions assume a net fitness gain in a cooperative transaction which, through reciprocity or relatedness, finds its way back from recipient to donor. We seek the source of this fitness gain. Our analysis rests on the insight that evolutionary processes are typically multiplicative and noisy. Fluctuations have a net negative effect on the long-time growth rate of resources but no effect on the growth rate of their expectation value. This is an example of non-ergodicity. By reducing the amplitude of fluctuations, pooling and sharing increases the long-time growth rate for cooperating entities, meaning that cooperators outgrow similar non-cooperators. We identify this increase in growth rate as the net fitness gain, consistent with the concept of geometric mean fitness in the biological literature. This constitutes a fundamental mechanism for the evolution of cooperation. Its minimal assumptions make it a candidate explanation of cooperation in settings too simple for other fitness gains, such as emergent function and specialization, to be probable. One such example is the transition from single cells to early multicellular life.
evolution_of_cooperation  evolutionary_biology  game_theory 
january 2019 by rvenkat
Massive increase in visual range preceded the origin of terrestrial vertebrates | PNAS
The evolution of terrestrial vertebrates, starting around 385 million years ago, is an iconic moment in evolution that brings to mind images of fish transforming into four-legged animals. Here, we show that this radical change in body shape was preceded by an equally dramatic change in sensory abilities akin to transitioning from seeing over short distances in a dense fog to seeing over long distances on a clear day. Measurements of eye sockets and simulations of their evolution show that eyes nearly tripled in size just before vertebrates began living on land. Computational simulations of these animal’s visual ecology show that for viewing objects through water, the increase in eye size provided a negligible increase in performance. However, when viewing objects through air, the increase in eye size provided a large increase in performance. The jump in eye size was, therefore, unlikely to have arisen for seeing through water and instead points to an unexpected hybrid of seeing through air while still primarily inhabiting water. Our results and several anatomical innovations arising at the same time suggest lifestyle similarity to crocodiles. The consequent combination of the increase in eye size and vision through air would have conferred a 1 million-fold increase in the amount of space within which objects could be seen. The “buena vista” hypothesis that our data suggest is that seeing opportunities from afar played a role in the subsequent evolution of fully terrestrial limbs as well as the emergence of elaborated action sequences through planning circuits in the nervous system.
evolutionary_biology  cognitive_science  neuroscience  information_theory  philosophy_of_biology 
december 2018 by rvenkat

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