Evolutionary Biology for the 21st Century

Losos, Jonathan B.; Arnold, Stevan J.; Bejerano, Gill; Brodie, Edmund D.; Hibbett, David S.; Hoekstra, Hopi E.; Mindell, David P.; Monteiro, Antónia; Moritz, Craig; Orr, H. Allen; Petrov, Dmitri A.; Renner, Susanne S.; Ricklefs, Robert E.; Soltis, Pamela S.; Turner, Thomas L.

doi:10.1371/journal.pbio.1001466

Cited by 128 publications

(101 citation statements)

References 84 publications

(62 reference statements)

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“…In parallel, a large body of theory models the spread and fixation of mutations (Orr 2005), their distribution for various population sizes and fitness effects (Eyre-Walker and Keightley 2007), and whether selection or drift dominates their fate (Nei 2007). However, without a practical measure of the action of mutations on fitness, the theory cannot be applied to the massive inflow of genetic information (Orr 2005;Losos et al 2013).…”

Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

Katsonis¹,

2014

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The relationship between genotype mutations and phenotype variations determines health in the short term and evolution over the long term, and it hinges on the action of mutations on fitness. A fundamental difficulty in determining this action, however, is that it depends on the unique context of each mutation, which is complex and often cryptic. As a result, the effect of most genome variations on molecular function and overall fitness remains unknown and stands apart from population genetics theories linking fitness effect to polymorphism frequency. Here, we hypothesize that evolution is a continuous and differentiable physical process coupling genotype to phenotype. This leads to a formal equation for the action of coding mutations on fitness that can be interpreted as a product of the evolutionary importance of the mutated site with the difference in amino acid similarity. Approximations for these terms are readily computable from phylogenetic sequence analysis, and we show mutational, clinical, and population genetic evidence that this action equation predicts the effect of point mutations in vivo and in vitro in diverse proteins, correlates disease-causing gene mutations with morbidity, and determines the frequency of human coding polymorphisms, respectively. Thus, elementary calculus and phylogenetics can be integrated into a perturbation analysis of the evolutionary relationship between genotype and phenotype that quantitatively links point mutations to function and fitness and that opens a new analytic framework for equations of biology. In practice, this work explicitly bridges molecular evolution with population genetics with applications from protein redesign to the clinical assessment of human genetic variations.

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Section: [Supplemental Materials Is Available For This Article]mentioning

confidence: 99%

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

Katsonis¹,

2014

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“…Although the number of animal species considered to be accepted as biomedical model systems is decreasing [91], this trend is both paradoxical and misguided given that the very notion of a model system is undergoing rapid change and might soon be obsolete [92], at last liberating us to (again) use the species that are best suited for the problem in question (i.e., Krogh's Principle [93]). Innovative research programs in diverse species are now possible thanks to advances in behavioral ecology, genomics, and neuroscience together with numerous technological breakthroughs that facilitate the collection of ever-larger and more detailed datasets than were imaginable even a few years ago.…”

Section: Revisiting Tinbergen's Visionmentioning

confidence: 99%

An evolutionary framework for studying mechanisms of social behavior

Hofmann

Beery

Blumstein³

et al. 2014

Trends in Ecology & Evolution

168

133

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Social interactions are central to most animals and have a fundamental impact upon the phenotype of an individual. Social behavior (social interactions among conspecifics) represents a central challenge to the integration of the functional and mechanistic bases of complex behavior. Traditionally, studies of proximate and ultimate elements of social behavior have been conducted by distinct groups of researchers, with little communication across perceived disciplinary boundaries. However, recent technological advances, coupled with increased recognition of the substantial variation in mechanisms underlying social interactions, should compel investigators from divergent disciplines to pursue more integrative analyses of social behavior. We propose an integrative conceptual framework intended to guide researchers towards a comprehensive understanding of the evolution and maintenance of mechanisms governing variation in sociality.The study of social behavior in the 21st century All animals interact with conspecifics at some point in their lives. Members of the same species tend to be each other's fiercest competitors and strongest allies, as evidenced by the intense cooperation and conflict that characterize many intraspecific interactions [1]. These interactions are the products of genetic, epigenetic, endocrine, and neural mechanisms that -in conjunction with environmental conditions -affect Darwinian fitness and evolve via natural selection. Building upon Aristotle's four questions, Tinbergen [2] posited that understanding behavior requires the integration of studies of mechanism and function. Only by asking questions both from a proximate perspective (i.e., focusing on causation and development) and an ultimate perspective (i.e., focusing on adaptive value and evolutionary descent) can behavior be fully understood. Social behavior in particular lends itself to such an integrative approach not only because it commands the attention of many disciplines [3] but also because even many behaviors commonly considered nonsocial often occur in a social context (e.g., mating, fighting, parental care). Social behavior is also special because the selective agents are other members of the same species, and this results in intriguing evolutionary dynamics. Nevertheless, in the intervening decades since Tinbergen's

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“…As a result, data gathered during collection serve as the only available source of information. Those limitations to sample and observe specimens in the field are among the main reasons for our little PrePrints knowledge about the biology or ecology of a significant proportion of the described biodiversity (Costello et al, 2013b;Losos et al, 2013). Collectors usually keep detailed records in personal field books (Beidleman, 2004), but these data are often not linked to the specimens through labels or database access codes and may therefore be easily lost or inaccessible.…”

Section: Animal Behavior and Ecology Data In Museumsmentioning

confidence: 99%

Forgotten treasures: the fate of data in animal behavior studies

Caetano

Aisenberg

2014

Preprint

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PrePrints AbstractPublished discussions on data stewardship often focus on standardized datasets whose reuse patterns are known. Improvements in stewardship of animal behavior data are virtually absent and lag behind other disciplines such as molecular biology and systematics. In this essay, we discuss best practices of three key aspects related to the collection and archival of behavioral data: data supporting published results; data collected from field observations; and the potential of museum specimens as source of data to animal behavior and ecology. To quantify how much data is shared in publications we reviewed selected journals in animal behavior and behavioral ecology. We found that only an extremely small proportion of the articles published in 2013 made even part of their data available. We discuss about the benefits of making data available, review resources available for data archiving and provide practical guidance for ethologists. We discuss and provide examples of the amount of ethological and ecological data that can be recorded during field observations. To investigate the potential of museum specimens as source of data, we surveyed researchers working in areas related to ecology, animal behavior, and systematics. Both ethologists and systematists agreed that natural history information stored in collections would be a valuable source of data. We make recommendations to enhance data collection and stewardship from the point of view of researchers in animal behavior sciences, considering the special characteristics of the discipline and the type of data that is often produced. We suggest that there is a large amount of crucial data about natural history, ecology and behavior that investigators could glean from collections. Although it is difficult to appreciate the relevance of data for future studies at the time of publication, such data may inspire fruitful opportunities that we cannot afford to lose. PrePrintsData collection is a fundamental step of research and often the most expensive with respect to both time and money, yet the fate of data after publication is often neglected (Heidorn, 2008).Despite willingness to populate digital repositories with data, the fact that many researchers have reservations about doing so (Tenopir et al., 2011;Wolkovich et al., 2012) seems to explain the general lack of data available for publications in the biological sciences (Hartter et al. 2013;Zamir, 2013 -but see Wallis et al., 2013. There are a few exceptions, such as molecular journals that require sequence data archival in publicly accessible repositories among other examples such as the journals Evolution and the Public Library of Science (PLoS). The main reasons why authors opt to avoid storing data in digital repositories are related to concerns about lack of time and appropriate tools to prepare and upload datasets, the potential for data misuse (Whitlock, 2011), and lack of personal benefits (Arzberger et al., 2004). In this essay, we surveyed and evaluated how much data from animal behavior is ...

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Evolutionary Biology for the 21st Century

Abstract: New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.

Cited by 128 publications

References 84 publications

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

An evolutionary framework for studying mechanisms of social behavior

Forgotten treasures: the fate of data in animal behavior studies

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