scholarly journals Phylogenomic conflict coincides with rapid morphological innovation

2020 ◽  
Author(s):  
Caroline Parins-Fukuchi ◽  
Gregory W. Stull ◽  
Stephen A. Smith
Keyword(s):  
Biological Significance ◽  
Population Level ◽  
Tree Of Life ◽  
Genomic Evolution ◽  
High Conflict ◽  
Complex Population ◽  
Population Processes ◽  
Morphological Innovation ◽  
Direct Correspondence

AbstractEvolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that phylogenomic conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between areas of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.

scholarly journals Phylogenomic conflict coincides with rapid morphological innovation

2021 ◽  
Vol 118 (19) ◽  
pp. e2023058118
Author(s):  
Caroline Parins-Fukuchi ◽  
Gregory W. Stull ◽  
Stephen A. Smith
Keyword(s):  
Gene Tree ◽  
Biological Significance ◽  
Population Level ◽  
Tree Of Life ◽  
Genomic Evolution ◽  
High Conflict ◽  
Complex Population ◽  
Population Processes ◽  
Morphological Innovation ◽  
Direct Correspondence

Evolutionary biologists have long been fascinated with the episodes of rapid phenotypic innovation that underlie the emergence of major lineages. Although our understanding of the environmental and ecological contexts of such episodes has steadily increased, it has remained unclear how population processes contribute to emergent macroevolutionary patterns. One insight gleaned from phylogenomics is that gene-tree conflict, frequently caused by population-level processes, is often rampant during the origin of major lineages. With the understanding that phylogenomic conflict is often driven by complex population processes, we hypothesized that there may be a direct correspondence between instances of high conflict and elevated rates of phenotypic innovation if both patterns result from the same processes. We evaluated this hypothesis in six clades spanning vertebrates and plants. We found that the most conflict-rich regions of these six clades also tended to experience the highest rates of phenotypic innovation, suggesting that population processes shaping both phenotypic and genomic evolution may leave signatures at deep timescales. Closer examination of the biological significance of phylogenomic conflict may yield improved connections between micro- and macroevolution and increase our understanding of the processes that shape the origin of major lineages across the Tree of Life.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Vol 3 (5) ◽  
Author(s):  
Y Miles Zhang ◽  
Jason L Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Abstract Targeted enrichment of ultraconserved elements (UCEs) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and biogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCEs in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

scholarly journals Noise-driven growth rate gain in clonal cellular populations

2016 ◽  
Vol 113 (12) ◽  
pp. 3251-3256 ◽  
Author(s):  
Mikihiro Hashimoto ◽  
Takashi Nozoe ◽  
Hidenori Nakaoka ◽  
Reiko Okura ◽  
Sayo Akiyoshi ◽  
...  
Keyword(s):  
Growth Rate ◽  
Population Growth ◽  
Single Cell ◽  
Single Cells ◽  
Population Level ◽  
Growth Conditions ◽  
Cell Dynamics ◽  
Generation Times ◽  
Complex Population ◽  
The Mean

Cellular populations in both nature and the laboratory are composed of phenotypically heterogeneous individuals that compete with each other resulting in complex population dynamics. Predicting population growth characteristics based on knowledge of heterogeneous single-cell dynamics remains challenging. By observing groups of cells for hundreds of generations at single-cell resolution, we reveal that growth noise causes clonal populations of Escherichia coli to double faster than the mean doubling time of their constituent single cells across a broad set of balanced-growth conditions. We show that the population-level growth rate gain as well as age structures of populations and of cell lineages in competition are predictable. Furthermore, we theoretically reveal that the growth rate gain can be linked with the relative entropy of lineage generation time distributions. Unexpectedly, we find an empirical linear relation between the means and the variances of generation times across conditions, which provides a general constraint on maximal growth rates. Together, these results demonstrate a fundamental benefit of noise for population growth, and identify a growth law that sets a “speed limit” for proliferation.

scholarly journals Understanding UCEs: A Comprehensive Primer on Using Ultraconserved Elements for Arthropod Phylogenomics

2019 ◽  
Author(s):  
Yuanmeng Zhang ◽  
Jason Williams ◽  
Andrea Lucky
Keyword(s):  
Time Scales ◽  
Evolutionary History ◽  
Population Level ◽  
Tree Of Life ◽  
Deep Time ◽  
Ultraconserved Elements ◽  
Background Theory ◽  
Promising Tool ◽  
Recent Advances ◽  
Targeted Enrichment

Targeted enrichment of ultraconserved elements (UCE) has emerged as a promising tool for inferring evolutionary history in many taxa, with utility ranging from phylogenetic and phylogeographic questions at deep time scales to population level studies at shallow time scales. However, the methodology can be daunting for beginners. Our goal is to introduce UCE phylogenomics to a wider audience by summarizing recent advances in arthropod research, and to familiarize readers with background theory and steps involved. We define terminology used in association with the UCE approach, evaluate current laboratory and bioinformatic methods and limitations, and, finally, provide a roadmap of steps in the UCE pipeline to assist phylogeneticists in making informed decisions as they employ this powerful tool. By facilitating increased adoption of UCE in phylogenomics studies that deepen our comprehension of the function of these markers across widely divergent taxa, we aim to ultimately improve understanding of the arthropod tree of life.

scholarly journals Positive Autoregulation of an Acyl-Homoserine Lactone Quorum-Sensing Circuit Synchronizes the Population Response

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Rebecca L. Scholz ◽  
E. Peter Greenberg
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Biological Significance ◽  
Population Level ◽  
Homoserine Lactone ◽  
Acyl Homoserine Lactone ◽  
Wild Type ◽  
Positive Signal ◽  
Signal Production ◽  
Engineered Strain

ABSTRACTMany proteobacteria utilize acyl-homoserine lactone quorum-sensing signals. At low population densities, cells produce a basal level of signal, and when sufficient signal has accumulated in the surrounding environment, it binds to its receptor, and quorum-sensing-dependent genes can be activated. A common characteristic of acyl-homoserine lactone quorum sensing is that signal production is positively autoregulated. We have examined the role of positive signal autoregulation inPseudomonas aeruginosa. We compared population responses and individual cell responses in populations of wild-typeP. aeruginosato responses in a strain with the signal synthase gene controlled by an arabinose-inducible promoter so that signal was produced at a constant rate per cell regardless of cell population density. At a population level, responses of the wild type and the engineered strain were indistinguishable, but the responses of individual cells in a population of the wild type showed greater synchrony than the responses of the engineered strain. Although sufficient signal is required to activate expression of quorum-sensing-regulated genes, it is not sufficient for activation of certain genes, the late genes, and their expression is delayed until other conditions are met. We found that late gene responses were reduced in the engineered strain. We conclude that positive signal autoregulation is not a required element in acyl-homoserine lactone quorum sensing, but it functions to enhance synchrony of the responses of individuals in a population. Synchrony might be advantageous in some situations, whereas a less coordinated quorum-sensing response might allow bet hedging and be advantageous in other situations.IMPORTANCEThere are many quorum-sensing systems that involve a transcriptional activator, which responds to an acyl-homoserine lactone signal. In all of the examples studied, the gene coding for signal production is positively autoregulated by the signal, and it has even been described as essential for a quorum-sensing response. We have used the opportunistic pathogenPseudomonas aeruginosaas a model to show that positive autoregulation is not required for a robust quorum-sensing response. We also show that positive autoregulation of signal production enhances the synchrony of the response. This information enhances our general understanding of the biological significance of how acyl-homoserine lactone quorum-sensing circuits are arranged.

The Analysis of Complex Population Processes

1964 ◽  
Vol 96 (1-2) ◽  
pp. 335-347 ◽  
Author(s):  
C. S. Holling
Keyword(s):  
Mathematical Models ◽  
Population Ecology ◽  
Population Models ◽  
Biological Processes ◽  
Complex Population ◽  
Distinctive Type ◽  
Population Processes ◽  
Whole Systems ◽  
Considerable Complexity ◽  
Digital Computers

AbstractPopulation ecology requires realistic and precise analyses of whole systems, or processes, and not just fragments of them. This poses some difficult problems because of the distinctive complexity of these processes. Recent studies of predation have shown, however, that it is possible to achieve great analytical depth and to simulate whole systems in the form of realistic and precise mathematical models. This is accomplished by ignoring the degree of simplicity traditionally required of population models and by emphasizing the need for reality. Extensive experimentation is required to suggest and test possible explanations for the action of each component of the process so that the explanation evolves in gradual steps to include one component after another. The form of the explanation and the resulting equations is hence dictated by the process itself and not by the need for mathematical neatness. The considerable complexity of the predation model arose from features common to many biological processes i.e. the prevalence of limits and thresholds, the presence of important discontinuities and the historical character of biological events. These features can be analyzed effectively only by establishing an intimate feed-back between experiment and theory. Mathematical models incorporating these features are admirably solved using digital computers. Computers, and the languages used to program them, seem to be ideally suited to handle the distinctive type of complexity shown by population processes.

scholarly journals Comparative analysis of continuum angiogenesis models

2021 ◽  
Vol 82 (4) ◽  
Author(s):  
W. Duncan Martinson ◽  
Hirokazu Ninomiya ◽  
Helen M. Byrne ◽  
Philip K. Maini
Keyword(s):  
Mean Field ◽  
Cell Movement ◽  
Coarse Graining ◽  
Population Level ◽  
Coarse Grained ◽  
Continuum Models ◽  
Biological Phenomena ◽  
Complex Population ◽  
The Mean ◽  
Work Done

AbstractAlthough discrete approaches are increasingly employed to model biological phenomena, it remains unclear how complex, population-level behaviours in such frameworks arise from the rules used to represent interactions between individuals. Discrete-to-continuum approaches, which are used to derive systems of coarse-grained equations describing the mean-field dynamics of a microscopic model, can provide insight into such emergent behaviour. Coarse-grained models often contain nonlinear terms that depend on the microscopic rules of the discrete framework, however, and such nonlinearities can make a model difficult to mathematically analyse. By contrast, models developed using phenomenological approaches are typically easier to investigate but have a more obscure connection to the underlying microscopic system. To our knowledge, there has been little work done to compare solutions of phenomenological and coarse-grained models. Here we address this problem in the context of angiogenesis (the creation of new blood vessels from existing vasculature). We compare asymptotic solutions of a classical, phenomenological “snail-trail” model for angiogenesis to solutions of a nonlinear system of partial differential equations (PDEs) derived via a systematic coarse-graining procedure (Pillay et al. in Phys Rev E 95(1):012410, 2017. https://doi.org/10.1103/PhysRevE.95.012410). For distinguished parameter regimes corresponding to chemotaxis-dominated cell movement and low branching rates, both continuum models reduce at leading order to identical PDEs within the domain interior. Numerical and analytical results confirm that pointwise differences between solutions to the two continuum models are small if these conditions hold, and demonstrate how perturbation methods can be used to determine when a phenomenological model provides a good approximation to a more detailed coarse-grained system for the same biological process.

scholarly journals Tour boats affect the activity patterns of bottlenose dolphins (Tursiops truncatus) in Bocas del Toro, Panama

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8804 ◽  
Author(s):  
Ayshah Kassamali-Fox ◽  
Fredrik Christiansen ◽  
Laura J. May-Collado ◽  
Eric A. Ramos ◽  
Beth A. Kaplin
Keyword(s):  
Markov Chain ◽  
Tursiops Truncatus ◽  
Transition Probabilities ◽  
Bottlenose Dolphins ◽  
Activity Patterns ◽  
Biological Significance ◽  
Population Level ◽  
Tourism Industry ◽  
Activity Budgets ◽  
Bocas Del Toro

Bottlenose dolphins (Tursiops truncatus) of the Bocas del Toro archipelago are targeted by the largest boat-based cetacean watching operation in Panama. Tourism is concentrated in Dolphin Bay, home to a population of resident dolphins. Previous studies have shown that tour boats elicit short-term changes in dolphin behavior and communication; however, the relationship of these responses to the local population’s biology and ecology is unclear. Studying the effects of tour boats on dolphin activity patterns and behavior can provide information about the biological significance of these responses. Here, we investigated the effects of tour boat activity on bottlenose dolphin activity patterns in Bocas del Toro, Panama over 10 weeks in 2014. Markov chain models were used to assess the effect of tour boats on dolphin behavioral transition probabilities in both control and impact scenarios. Effect of tour boat interactions was quantified by comparing transition probabilities of control and impact chains. Data were also used to construct dolphin activity budgets. Markov chain analysis revealed that in the presence of tour boats, dolphins were less likely to stay socializing and were more likely to begin traveling, and less likely to begin foraging while traveling. Additionally, activity budgets for foraging decreased and traveling increased as an effect of tour boat presence. These behavioral responses are likely to have energetic costs for individuals which may ultimately result in population-level impacts. Boat operator compliance with Panamanian whale watching regulations is urgently needed to minimize potential long-term impacts on this small, genetically distinct population and to ensure the future viability of the local tourism industry.

scholarly journals Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jing Xu ◽  
Guo Chen ◽  
Peter J. Hermanson ◽  
Qiang Xu ◽  
Changshuo Sun ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genetic Variation ◽  
Association Analysis ◽  
Phenotypic Variation ◽  
Biological Significance ◽  
Population Level ◽  
Unique Information ◽  
Genome Wide ◽  
Methylation Profiling ◽  
Methylation Variation

Abstract Background DNA methylation can provide a source of heritable information that is sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling and the roles of DNA methylation in shaping diversity of both gene expression and phenotypes are hotly debated. Here, we investigate the genetic basis and biological functions of DNA methylation at a population scale in maize. Results We perform targeted DNA methylation profiling for a diverse panel of 263 maize inbred genotypes. All genotypes show similar levels of DNA methylation globally, highlighting the importance of DNA methylation in maize development. Nevertheless, we identify more than 16,000 differentially methylated regions (DMRs) that are distributed across the 10 maize chromosomes. Genome-wide association analysis with high-density genetic markers reveals that over 60% of the DMRs are not tagged by SNPs, suggesting the presence of unique information in DMRs. Strong associations between DMRs and the expression of many genes are identified in both the leaf and kernel tissues, pointing to the biological significance of methylation variation. Association analysis with 986 metabolic traits suggests that DNA methylation is associated with phenotypic variation of 156 traits. There are some traits that only show significant associations with DMRs and not with SNPs. Conclusions These results suggest that DNA methylation can provide unique information to explain phenotypic variation in maize.

scholarly journals There and back again: metagenome-assembled genomes provide new insights into two thermal pools in Kamchatka, Russia

2018 ◽  
Author(s):  
Laetitia G. E. Wilkins ◽  
Cassandra L. Ettinger ◽  
Guillaume Jospin ◽  
Jonathan A. Eisen
Keyword(s):  
Microbial Diversity ◽  
Hot Springs ◽  
Environmental Dna ◽  
Population Level ◽  
Kamchatka Peninsula ◽  
Tree Of Life ◽  
Rrna Gene ◽  
Shotgun Metagenomics ◽  
Microbial Isolation ◽  
Culture Independent

AbstractCulture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. Using a shotgun metagenomics approach, we assembled population-level genomes of bacteria and archaea from two pools using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and placed them in the context of the current microbial tree of life. We highlight MAGs representing previously underrepresented archaeal phyla (Korarchaeota, BathyarchaeotaandAciduliprofundum) and one potentially new species within the bacterial genusSulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study can be considered complementary to foregoing studies in the same ecosystem as it adds more comprehensive information about phylogenetic diversity and functional potential within this highly selective habitat.

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