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Developmental system drift

Kushal Suryamohan, Casey Hanson, Emily Andrews, Saurabh Sinha, Molly Duman Scheel, Marc S Halfon
Changes in gene regulatory networks (GRNs) underlie the evolution of morphological novelty and developmental system drift. The fruitfly Drosophila melanogaster and the dengue and Zika vector mosquito Aedes aegypti have substantially similar nervous system morphology. Nevertheless, they show significant divergence in a set of genes co-expressed in the midline of the Drosophila central nervous system, including the master regulator single minded and downstream genes including short gastrulation, Star, and NetrinA...
August 15, 2016: Developmental Biology
Annalise B Paaby, Greg Gibson
Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution...
2016: Biology
Emiliano Trucchi, Anna B Mazzarella, Gregor D Gilfillan, Maria T Lorenzo, Peter Schönswetter, Ovidiu Paun
Epigenetic modifications are expected to occur at a much faster rate than genetic mutations, potentially causing isolated populations to stochastically drift apart, or if they are subjected to different selective regimes, to directionally diverge. A high level of genome-wide epigenetic divergence between individuals occupying distinct habitats is therefore predicted. Here, we introduce bisulfite-converted restriction site associated DNA sequencing (bsRADseq), an approach to quantify the level of DNA methylation differentiation across multiple individuals...
April 2016: Molecular Ecology
Anton Crombach, Karl R Wotton, Eva Jiménez-Guri, Johannes Jaeger
Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as "system drift." System drift is illustrated by the gap gene network-involved in segmental patterning-in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species...
May 2016: Molecular Biology and Evolution
Patrick Lemaire, Jacques Piette
This review is a tribute to the remarkable contributions of Thomas Huxley to the biology of tunicates, the likely sister group of vertebrates. In 1851, the great biologist and philosopher published two landmark papers on pelagic tunicates in the Philosophical Transactions of the Royal Society. They were dedicated to the description of the adult anatomy and life cycle of thaliaceans and appendicularians, the pelagic relatives of ascidians. In the first part of this review, we discuss the novel anatomical observations and evolutionary hypotheses made by Huxley, which would have a lasting influence on tunicate biology...
June 2015: Open Biology
Liliana Milani, Fabrizio Ghiselli
BACKGROUND: The retention of a genome in mitochondria (mtDNA) has several consequences, among which the problem of ensuring a faithful transmission of its genetic information through generations despite the accumulation of oxidative damage by reactive oxygen species (ROS) predicted by the free radical theory of ageing. A division of labour between male and female germ line mitochondria was proposed: since mtDNA is maternally inherited, female gametes would prevent damages by repressing oxidative phosphorylation, thus being quiescent genetic templates...
2015: Biology Direct
Jo Cooke, Steven Ariss, Christine Smith, Jennifer Read
BACKGROUND: International policy suggests that collaborative priority setting (CPS) between researchers and end users of research should shape the research agenda, and can increase capacity to address the research-practice translational gap. There is limited research evidence to guide how this should be done to meet the needs of dynamic healthcare systems. One-off priority setting events and time-lag between decision and action prove problematic. This study illustrates the use of CPS in a UK research collaboration called Collaboration and Leadership in Applied Health Research and Care (CLAHRC)...
2015: Health Research Policy and Systems
Ehud Lamm
This article describes how empirical discoveries in the 1930s-1950s regarding population variation for chromosomal inversions affected Theodosius Dobzhansky and Richard Goldschmidt. A significant fraction of the empirical work I discuss was done by Dobzhansky and his coworkers; Goldschmidt was an astute interpreter, with strong and unusual commitments. I argue that both belong to a mechanistic tradition in genetics, concerned with the effects of chromosomal organization and systems on the inheritance patterns of species...
November 2015: Journal of the History of Biology
Karl R Wotton, Eva Jiménez-Guri, Anton Crombach, Hilde Janssens, Anna Alcaine-Colet, Steffen Lemke, Urs Schmidt-Ott, Johannes Jaeger
The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M...
2015: ELife
Nadine Piekarski, Joshua B Gross, James Hanken
Development of the vertebrate skull has been studied intensively for more than 150 years, yet many essential features remain unresolved. One such feature is the extent to which embryonic derivation of individual bones is evolutionarily conserved or labile. We perform long-term fate mapping using GFP-transgenic axolotl and Xenopus laevis to document the contribution of individual cranial neural crest streams to the osteocranium in these amphibians. Here we show that the axolotl pattern is strikingly similar to that in amniotes; it likely represents the ancestral condition for tetrapods...
2014: Nature Communications
Alexander Y Tulchinsky, Norman A Johnson, Adam H Porter
Hybrid incompatibility can result from gene misregulation produced by divergence in trans-acting regulatory factors and their cis-regulatory targets. However, change in trans-acting factors may be constrained by pleiotropy, which would in turn limit the evolution of incompatibility. We employed a mechanistically explicit bioenergetic model of gene expression wherein parameter combinations (number of transcription factor molecules, energetic properties of binding to the regulatory site, and genomic background size) determine the shape of the genotype-phenotype (G-P) map, and interacting allelic variants of mutable cis and trans sites determine the phenotype along that map...
December 2014: Genetics
Naoki Morimoto, Marcia S Ponce de León, Christoph P E Zollikofer
Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development...
2014: PloS One
Ehud Lamm
This paper applies the conceptual toolkit of Evolutionary Developmental Biology (evo-devo) to the evolution of the genome and the role of the genome in organism development. This challenges both the Modern Evolutionary Synthesis, the dominant view in evolutionary theory for much of the 20th century, and the typically unreflective analysis of heredity by evo-devo. First, the history of the marginalization of applying system-thinking to the genome is described. Next, the suggested framework is presented. Finally, its application to the evolution of genome modularity, the evolution of induced mutations, the junk DNA versus ENCODE debate, the role of drift in genome evolution, and the relationship between genome dynamics and symbiosis with microorganisms are briefly discussed...
June 1, 2014: Journal of Physiology
Philipp H Schiffer, Ndifon A Nsah, Henny Grotehusmann, Michael Kroiher, Curtis Loer, Einhard Schierenberg
Comparative studies of nematode embryogenesis among different clades revealed considerable variations. However, to what extent developmental differences exist between closely related species has mostly remained nebulous. Here, we explore the correlation between phylogenetic neighborhood and developmental variation in a restricted and morphologically particularly uniform taxonomic group (Panagrolaimidae) to determine to what extent (1) morphological and developmental characters go along with molecular data and thus can serve as diagnostic tools for the definition of kinship and (2) developmental system drift (DSD; modifications of developmental patterns without corresponding morphological changes) can be found within a small taxonomic unit...
June 2014: Development Genes and Evolution
Helle K Falkenberg, William A Simpson, Gordon N Dutton
The aim of this study was to use an equivalent noise paradigm to investigate the development and maturation of motion perception, and how the underlying limitations of sampling efficiency and internal noise effect motion detection and direction discrimination in school-aged children (5-14 years) and adults. Contrast energy thresholds of a 2c/deg sinusoidal grating drifting at 1.0 or 6.0 Hz were measured as a function of added dynamic noise in three tasks: detection of a drifting grating; detection of the sum of two oppositely drifting gratings and direction discrimination of oppositely drifting gratings...
July 2014: Vision Research
Eric S Haag
No abstract text is available yet for this article.
February 2014: PLoS Genetics
Adrian J Verster, Arun K Ramani, Sheldon J McKay, Andrew G Fraser
Although two related species may have extremely similar phenotypes, the genetic networks underpinning this conserved biology may have diverged substantially since they last shared a common ancestor. This is termed Developmental System Drift (DSD) and reflects the plasticity of genetic networks. One consequence of DSD is that some orthologous genes will have evolved different in vivo functions in two such phenotypically similar, related species and will therefore have different loss of function phenotypes. Here we report an RNAi screen in C...
February 2014: PLoS Genetics
Christian A Yates
The incorporation of domain growth into stochastic models of biological processes is of increasing interest to mathematical modellers and biologists alike. In many situations, especially in developmental biology, the growth of the underlying tissue domain plays an important role in the redistribution of particles (be they cells or molecules) which may move and react atop the domain. Although such processes have largely been modelled using deterministic, continuum models there is an increasing appetite for individual-based stochastic models which can capture the fine details of the biological movement processes which are being elucidated by modern experimental techniques, and also incorporate the inherent stochasticity of such systems...
June 7, 2014: Journal of Theoretical Biology
Amar M Singh, James Chappell, Robert Trost, Li Lin, Tao Wang, Jie Tang, Brittany K Matlock, Kevin P Weller, Hao Wu, Shaying Zhao, Peng Jin, Stephen Dalton
Heterogeneity within pluripotent stem cell (PSC) populations is indicative of dynamic changes that occur when cells drift between different states. Although the role of metastability in PSCs is unclear, it appears to reflect heterogeneity in cell signaling. Using the Fucci cell-cycle indicator system, we show that elevated expression of developmental regulators in G1 is a major determinant of heterogeneity in human embryonic stem cells. Although signaling pathways remain active throughout the cell cycle, their contribution to heterogeneous gene expression is restricted to G1...
2013: Stem Cell Reports
Qinwen Liu, Eric S Haag
Gene duplication and divergence has emerged as an important aspect of developmental evolution. The genomes of Caenorhabditis nematodes encode an ancient family of PUF RNA-binding proteins. Most have been implicated in germline development, and are often redundant with paralogs of the same sub-family. An exception is Cbr-puf-2 (one of three Caenorhabditis briggsae PUF-2 sub-family paralogs), which is required for development past the second larval stage. Here, we provide a detailed functional characterization of Cbr-puf-2...
May 2014: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
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