scholarly journals Mosaic evolution, preadaptation, and the evolution of evolvability in apes

2019 ◽  
Author(s):  
Caroline Parins-Fukuchi
Keyword(s):  
Evolutionary Biology ◽  
Evolutionary Rate ◽  
Anatomical Structure ◽  
Major Goal ◽  
Complex Interactions ◽  
Evolutionary Changes ◽  
Character Matrix ◽  
Post Synthesis ◽  
Ape Evolution ◽  
Multiple Character

AbstractA major goal in post-synthesis evolutionary biology has been to better understand how complex interactions between traits drive movement along and facilitate the formation of distinct evolutionary pathways. I present analyses of a character matrix sampled across the haplorrhine skeleton that revealed several modules of characters displaying distinct patterns in macroevolutionary disparity. Comparison of these patterns to those in neurological development showed that early ape evolution was characterized by an intense regime of evolutionary and developmental flexibility. Shifting and reduced constraint in apes was met with episodic bursts in phenotypic innovation that built a wide array of functional diversity over a foundation of shared developmental and anatomical structure. Shifts in modularity drove dramatic evolutionary changes across the ape body plan in two distinct ways: 1) an episode of relaxed integration early in hominoid evolution coincided with bursts in evolutionary rate across multiple character suites; 2) the formation of two new trait modules along the branch leading to chimps and humans preceded rapid and dramatic evolutionary shifts in the carpus and pelvis. Changes to the structure of evolutionary mosaicism may correspond to enhanced evolvability that has a ‘preadaptive’ effect by catalyzing later episodes of dramatic morphological remodeling.

scholarly journals On the feasibility of saltational evolution

2018 ◽  
Author(s):  
Mikhail I. Katsnelson ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Evolutionary Biology ◽  
Fitness Landscape ◽  
Evolutionary Process ◽  
Analytic Solutions ◽  
Population Bottlenecks ◽  
Effective Population ◽  
Evolutionary Transitions ◽  
Evolutionary Changes ◽  
Saltational Evolution ◽  
As Stress

One of the key tenets of Darwin’s theory that was inherited by the Modern Synthesis of evolutionary biology is gradualism, that is, the notion that evolution proceeds gradually, via accumulation of “infinitesimally small” heritable changes 1,2. However, some of the most consequential evolutionary changes, such as, for example, the emergence of major taxa, seem to occur abruptly rather than gradually, as captured in the concepts of punctuated equilibrium 3,4 and evolutionary transitions 5,6. We examine a mathematical model of an evolutionary process on a rugged fitness landscape 7,8 and obtain analytic solutions for the probability of multi-mutational leaps, that is, several mutations occurring simultaneously, within a single generation in one genome, and being fixed all together in the evolving population. The results indicate that, for typical, empirically observed combinations of the parameters of the evolutionary process, namely, effective population size, mutation rate, and distribution of selection coefficients of mutations, the probability of a multi-mutational leap is low, and accordingly, their contribution to the evolutionary process is minor at best. However, such leaps could become an important factor of evolution in situations of population bottlenecks and elevated mutation rates, such as stress-induced mutagenesis in microbes or tumor progression, as well as major evolutionary transitions and evolution of primordial replicators.

scholarly journals A meta-analysis of the activity, stability, and mutational characteristics of temperature-adapted enzymes

2021 ◽  
Author(s):  
Stewart Gault ◽  
Peter Higgins ◽  
Charles S Cockell ◽  
Kaitlyn Gillies
Keyword(s):  
Protein Stability ◽  
Enzyme Catalysis ◽  
Evolutionary Rate ◽  
Meta Analysis ◽  
Amino Acid Substitutions ◽  
Major Goal ◽  
Thermophilic Enzymes ◽  
Melting Temperatures ◽  
Psychrophilic Enzyme ◽  
Existing Data

Understanding the characteristics that define temperature-adapted enzymes has been a major goal of extremophile enzymology in recent decades. In this study, we explore these characteristics by comparing psychrophilic, mesophilic, and thermophilic enzymes. Through a meta-analysis of existing data, we show that psychrophilic enzymes exhibit a significantly larger gap (Tg) between their optimum and melting temperatures compared to mesophilic and thermophilic enzymes. These results suggest that Tg may be a useful indicator as to whether an enzyme is psychrophilic or not and that models of psychrophilic enzyme catalysis need to account for this gap. Additionally, by using predictive protein stability software, HoTMuSiC and PoPMuSiC, we show that the deleterious nature of amino acid substitutions to protein stability increases from psychrophiles to thermophiles. How this ultimately affects the mutational tolerance and evolutionary rate of temperature adapted organisms is currently unknown.

Urban Evolutionary Biology

2020 ◽  
Keyword(s):  
Urban Space ◽  
Evolutionary Biology ◽  
Current Knowledge ◽  
Social Characteristics ◽  
Urban Habitat ◽  
Evolutionary Processes ◽  
Urban Neighbourhoods ◽  
Evolutionary Changes ◽  
Research Themes ◽  
New Research

Cities occupy about 3 per cent of the Earth’s habitable land area and are home to one out of two humans worldwide; both estimates are predicted to grow. Urban space is thus becoming an important, novel ecological niche for humans and wildlife alike. Building on knowledge gathered by urban ecologists during the last half century, evidence of evolutionary responses to urbanization has rapidly emerged. Urban evolutionary biology is a nascent yet fast-growing field of research—and a fascinating testing ground for evolutionary biologists worldwide. Urbanization offers a great range of opportunities to examine evolutionary processes because of the radically altered and easily quantifiable urban habitat, and the large number of cities worldwide, enabling rigorous, replicated tests of evolutionary hypotheses. Urban populations are increasingly exhibiting both neutral and adaptive evolutionary changes at levels ranging from genotypes to phenotypes. The novelty of urban evolutionary biology is that these changes are driven by the cities we have built, including effects of infrastructure, pollution, and social characteristics of our urban neighbourhoods. It will thereby enrich the field of evolutionary biology with emergent yet incredibly potent new research themes where the urban habitat is key. In a series of sixteen chapters written by leading evolutionary biologists working on urban drivers of evolution, Urban Evolutionary Biology is the first academic book in the field. It synthesizes current knowledge on evolutionary processes occurring literally on our doorstep, across the globe, and in each city independently.

scholarly journals Life History Divergence in Livebearing Fishes in Response to Predation: Is There a Microevolution to Macroevolution Barrier?

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 179 ◽  
Author(s):  
Mark C. Belk ◽  
Spencer J. Ingley ◽  
Jerald B. Johnson
Keyword(s):  
Life History ◽  
Evolutionary Biology ◽  
Offspring Size ◽  
Population Divergence ◽  
Female Size ◽  
Trait Variation ◽  
Closely Related Species ◽  
Trait Divergence ◽  
Evolutionary Changes ◽  
Established Species

A central problem in evolutionary biology is to determine whether adaptive phenotypic variation within species (microevolution) ultimately gives rise to new species (macroevolution). Predation environment can select for trait divergence among populations within species. The implied hypothesis is that the selection resulting from predation environment that creates population divergence within species would continue across the speciation boundary such that patterns of divergence after speciation would be a magnified accumulation of the trait variation observed before speciation. In this paper, we test for congruence in the mechanisms of microevolution and macroevolution by comparing the patterns of life history divergence among three closely related species of the livebearer genus Brachyrhaphis (Poeciliidae), namely B. rhabdophora, B. roseni, and B. terrabensis. Within B. rhabdophora, populations occur in either predator or predator-free environments, and have been considered to be at a nascent stage of speciation. Sister species B. roseni and B. terrabensis are segregated into predator and predator-free environments, respectively, and represent a post-speciation comparison. Male and female size at maturity, clutch size, and offspring size (and to a lesser extent reproductive allocation) all diverged according to predation environment and differences were amplified through evolutionary time, i.e., across the speciation boundary. Variation observed among nascent species differentiated by predation environment is a good predictor of variation among established species differentiated by predation environment. We found no evidence for different processes or different levels of selection acting across the speciation boundary, suggesting that macroevolution in these species can be understood as an accumulation of micro-evolutionary changes.

scholarly journals Ilkka Aulis Hanski. 14 February 1953—10 May 2016

2020 ◽  
Vol 68 ◽  
pp. 231-250
Author(s):  
Daniel Simberloff ◽  
Otso Ovaskainen
Keyword(s):  
Evolutionary Biology ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Empirical Work ◽  
Dung Beetle ◽  
Research Centre ◽  
University Of Oxford ◽  
Evolutionary Changes ◽  
Ecological Aspects ◽  
Research Findings

Professor Ilkka Hanski made seminal contributions to both empirical and theoretical ecology and evolutionary biology, in particular metapopulation biology, throughout his scientific career. He started his career with dung beetle ecology, earning his doctorate at University of Oxford in 1979. He developed the rest of his career at University of Helsinki, where he was appointed professor in ecology in 1993 and academy professor in 2006. Hanski's most influential research was based on empirical work on the Glanville fritillary metapopulation in the Åland Islands, started in 1991, and continued until his death. His early research focused on ecological aspects of metapopulation biology, such as how the spatial structure of a landscape influences extinction thresholds, whereas his later work focused on genetic and evolutionary processes, such as maintenance of genetic variation by selection pressures varying with landscape structure. During the last years of his career, Hanski was a pioneer in the field of eco-evolutionary dynamics, showing how molecular-level underpinnings of trait variation can explain rapid evolutionary changes in natural populations. Hanski actively applied his research findings to conservation biology, involving himself in debates ranging from forest conservation in Finland to the links between human health and biodiversity. He was an exceptionally devoted group leader and mentor of younger researchers. His Metapopulation Research Centre grew gradually from a group consisting of Hanski and a few PhD students into a centre of 70 researchers.

scholarly journals Ecology and Evolution of Marine Fungi With Their Adaptation to Climate Change

2021 ◽  
Vol 12 ◽  
Author(s):  
Vinit Kumar ◽  
V. Venkateswara Sarma ◽  
Kasun M. Thambugala ◽  
Jun-Jie Huang ◽  
Xiang-Yang Li ◽  
...  
Keyword(s):  
Climate Change ◽  
Evolutionary Biology ◽  
Marine Fungi ◽  
Climate Change Impacts ◽  
Marine Environments ◽  
Adaptation To Climate Change ◽  
Ecological Functions ◽  
Adaptation Mechanism ◽  
Complex Interactions ◽  
Marine Habitats

Climate change agitates interactions between organisms and the environment and forces them to adapt, migrate, get replaced by others, or extinct. Marine environments are extremely sensitive to climate change that influences their ecological functions and microbial community including fungi. Fungi from marine habitats are engaged and adapted to perform diverse ecological functions in marine environments. Several studies focus on how complex interactions with the surrounding environment affect fungal evolution and their adaptation. However, a review addressing the adaptation of marine fungi to climate change is still lacking. Here we have discussed the adaptations of fungi in the marine environment with an example of Hortaea werneckii and Aspergillus terreus which may help to reduce the risk of climate change impacts on marine environments and organisms. We address the ecology and evolution of marine fungi and the effects of climate change on them to explain the adaptation mechanism. A review of marine fungal adaptations will show widespread effects on evolutionary biology and the mechanism responsible for it.

scholarly journals Evolutionary rate coevolution between mitochondria and mitochondria-associated nuclear-encoded proteins in insects

2018 ◽  
Author(s):  
Zhichao Yan ◽  
Gongyin Ye ◽  
John H. Werren
Keyword(s):  
Mitochondrial Function ◽  
Evolutionary Biology ◽  
Evolutionary Rate ◽  
Strong Predictor ◽  
Nuclear Proteins ◽  
Sequence Evolution ◽  
Minichromosome Maintenance ◽  
Encoded Proteins ◽  
Associated Proteins ◽  
Protein Conservation

AbstractThe mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. How these two genomes coevolve is a long-standing question in evolutionary biology. Here we initially investigate the evolutionary rates of mitochondrial components (oxidative phosphorylation (OXPHOS) proteins and ribosomal RNAs) and nuclear-encoded proteins associated with mitochondria, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondria and mitochondria-associated nuclear-encoded proteins, which is likely driven by different rates of mitochondrial sequence evolution and compensatory changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for nuclear-encoded OXPHOS proteins in contact with mitochondrial-encoded OXPHOS proteins and nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNA. Mitochondrial-associated proteins show apparent rate acceleration over evolutionary time, but we suspect this pattern to be due to artifacts (e.g. rate estimation or calibration bias). We find that ERC between mitochondrial and nuclear proteins is a strong predictor of nuclear proteins known to interact with mitochondria, and therefore ERCs can be used to predict new candidate nuclear proteins with mitochondrial function. Using this approach, we detect proteins with high ERCs but not with known mitochondrial function based on gene ontology (GO). Manual screening of the literature revealed potential mitochondrial function for some of these proteins in humans or yeast. Their holometabolous ERCs therefore indicate these proteins may have phylogenetically conserved mitochondrial function. Twenty three additional candidates warrant further study for mitochondrial function based on this approach, including ERC evidence that proteins in the minichromosome maintenance helicase (MCM) complex interact with mitochondria. We conclude that the ERC method shows promise for identifying new candidate proteins with mitochondrial function.

Why Sociology Should Incorporate Biology

2018 ◽  
Author(s):  
Rosemary L. Hopcroft
Keyword(s):  
Evolutionary Biology ◽  
Biological Theory ◽  
Sociological Theory ◽  
Social Phenomenon ◽  
Complex Interactions ◽  
The Social ◽  
Central Paradigm ◽  
Limited Scope

Sociology has long been dominated by descriptive studies of social phenomenon, and theory in sociology has been characterized by myriad small theories of limited scope. Incorporation of method and theory from biology can change that. Theory from evolutionary biology has the potential to unify much sociological theory and become the central paradigm of sociology, much as it has unified biology, and to unify all the disparate threads of the current discipline of sociology into a fully fledged science. This chapter explains why sociologists should be doing more research that incorporates biology and biological theory into sociology. Although disentangling the social and biological is difficult because of the complex interactions between them, the fact that the interactions exist is indisputable, and sociology can benefit from examining them.

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 The missing expression level-evolutionary rate anticorrelation in viruses does not support protein function as a main constraint on sequence evolution

2021 ◽  
Author(s):  
Changshuo Wei ◽  
Yan-Ming Chen ◽  
Ying Chen ◽  
Wenfeng Qian
Keyword(s):  
Protein Function ◽  
Viral Protein ◽  
Evolutionary Biology ◽  
Evolutionary Rate ◽  
Purifying Selection ◽  
Endogenous Retroviruses ◽  
Expression Level ◽  
Sequence Evolution ◽  
Virus Species ◽  
Selective Constraints

Abstract One of the central goals in molecular evolutionary biology is to determine the sources of variation in the rate of sequence evolution among proteins. Gene expression level is widely accepted as the primary determinant of protein evolutionary rate, because it scales with the extent of selective constraints imposed on a protein, leading to the well-known negative correlation between expression level and protein evolutionary rate (the E-R anticorrelation). Selective constraints have been hypothesized to entail the maintenance of protein function, the avoidance of cytotoxicity caused by protein misfolding or nonspecific protein-protein interactions, or both. However, empirical tests evaluating the relative importance of these hypotheses remain scarce, likely due to the non-trivial difficulties in distinguishing the effect of a deleterious mutation on a protein’s function vs. its cytotoxicity. We realized that examining the sequence evolution of viral proteins could overcome this hurdle. It is because purifying selection against mutations in a viral protein that result in cytotoxicity per se is likely relaxed, while purifying selection against mutations that impair viral protein function persists. Multiple analyses of SARS-CoV-2 and nine other virus species revealed a complete absence of any E-R anticorrelation. As a control, the E-R anticorrelation does exist in human endogenous retroviruses where purifying selection against cytotoxicity is present. Taken together, these observations do not support the maintenance of protein function as the main constraint on protein sequence evolution in cellular organisms.

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