Temporal Flexibility of Gene Regulatory Network Underlies a Novel Wing Pattern in Flies
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Conceptual Barriers to Progress Within Evolutionary Biology
Found Sci (2009) 14:195–216 DOI 10.1007/s10699-008-9153-8 Conceptual Barriers to Progress Within Evolutionary Biology Kevin N. Laland · John Odling-Smee · Marcus W. Feldman · Jeremy Kendal Published online: 26 November 2008 © Springer Science+Business Media B.V. 2008 Abstract In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo- Darwinism fails to recognize a fundamental cause of evolutionary change, “niche construc- tion”. This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, includ- ing ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory. Keywords Niche construction · Evolutionary biology · Ecological inheritance · Ecosystem ecology · Developmental biology 1 Introduction On the face of it, evolutionary biology is a thriving discipline: It is built on the solid theoret- ical foundations of mathematical population biology; it has a rich and productive empirical K. N. Laland (B) School of Biology, University of St. Andrews, Bute Building, Queens Terrace, St. Andrews, Fife KY16 9TS, UK e-mail: [email protected] J. Odling-Smee Mansfield College, University of Oxford, Oxford OX1 3TF, UK M. -
Dynamical Gene Regulatory Networks Are Tuned by Transcriptional Autoregulation with Microrna Feedback Thomas G
www.nature.com/scientificreports OPEN Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback Thomas G. Minchington1, Sam Grifths‑Jones2* & Nancy Papalopulu1* Concepts from dynamical systems theory, including multi‑stability, oscillations, robustness and stochasticity, are critical for understanding gene regulation during cell fate decisions, infammation and stem cell heterogeneity. However, the prevalence of the structures within gene networks that drive these dynamical behaviours, such as autoregulation or feedback by microRNAs, is unknown. We integrate transcription factor binding site (TFBS) and microRNA target data to generate a gene interaction network across 28 human tissues. This network was analysed for motifs capable of driving dynamical gene expression, including oscillations. Identifed autoregulatory motifs involve 56% of transcription factors (TFs) studied. TFs that autoregulate have more interactions with microRNAs than non‑autoregulatory genes and 89% of autoregulatory TFs were found in dual feedback motifs with a microRNA. Both autoregulatory and dual feedback motifs were enriched in the network. TFs that autoregulate were highly conserved between tissues. Dual feedback motifs with microRNAs were also conserved between tissues, but less so, and TFs regulate diferent combinations of microRNAs in a tissue‑dependent manner. The study of these motifs highlights ever more genes that have complex regulatory dynamics. These data provide a resource for the identifcation of TFs which regulate the dynamical properties of human gene expression. Cell fate changes are a key feature of development, regeneration and cancer, and are ofen thought of as a “land- scape” that cells move through1,2. Cell fate changes are driven by changes in gene expression: turning genes on or of, or changing their levels above or below a threshold where a cell fate change occurs. -
Systematic Comparison of Sea Urchin and Sea Star Developmental Gene Regulatory Networks Explains How Novelty Is Incorporated in Early Development
ARTICLE https://doi.org/10.1038/s41467-020-20023-4 OPEN Systematic comparison of sea urchin and sea star developmental gene regulatory networks explains how novelty is incorporated in early development Gregory A. Cary 1,3,5, Brenna S. McCauley1,4,5, Olga Zueva1, Joseph Pattinato1, William Longabaugh2 & ✉ Veronica F. Hinman 1 1234567890():,; The extensive array of morphological diversity among animal taxa represents the product of millions of years of evolution. Morphology is the output of development, therefore phenotypic evolution arises from changes to the topology of the gene regulatory networks (GRNs) that control the highly coordinated process of embryogenesis. A particular challenge in under- standing the origins of animal diversity lies in determining how GRNs incorporate novelty while preserving the overall stability of the network, and hence, embryonic viability. Here we assemble a comprehensive GRN for endomesoderm specification in the sea star from zygote through gastrulation that corresponds to the GRN for sea urchin development of equivalent territories and stages. Comparison of the GRNs identifies how novelty is incorporated in early development. We show how the GRN is resilient to the introduction of a transcription factor, pmar1, the inclusion of which leads to a switch between two stable modes of Delta-Notch signaling. Signaling pathways can function in multiple modes and we propose that GRN changes that lead to switches between modes may be a common evolutionary mechanism for changes in embryogenesis. Our data additionally proposes a model in which evolutionarily conserved network motifs, or kernels, may function throughout development to stabilize these signaling transitions. 1 Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA. -
An Automatic Design Framework of Swarm Pattern Formation Based on Multi-Objective Genetic Programming
JOURNAL OF LATEX CLASS FILES, VOL. 14, NO. 8, AUGUST 2015 1 An Automatic Design Framework of Swarm Pattern Formation based on Multi-objective Genetic Programming Zhun Fan, Senior Member, IEEE, Zhaojun Wang, Xiaomin Zhu, Bingliang Hu, Anmin Zou, and Dongwei Bao Abstract—Most existing swarm pattern formation methods predetermined trajectory and maintain a specific swarm pattern depend on a predefined gene regulatory network (GRN) structure in the execution of tasks. For example, Jin [11] proposed a that requires designers’ priori knowledge, which is difficult to hierarchical gene regulatory network for adaptive multi-robot adapt to complex and changeable environments. To dynamically adapt to the complex and changeable environments, we propose pattern formation. In this work, the swarm pattern is designed an automatic design framework of swarm pattern formation as a band of circle, which encircles targets in a dynamic based on multi-objective genetic programming. The proposed environments. In the latter case of using adaptive formation, framework does not need to define the structure of the GRN- swarm robots follow an adaptive pattern to encircle targets in based model in advance, and it applies some basic network motifs the environment. For example, Oh et al. [12] have introduced to automatically structure the GRN-based model. In addition, a multi-objective genetic programming (MOGP) combines with an evolving hierarchical gene regulatory network for morpho- NSGA-II, namely MOGP-NSGA-II, to balance the complexity genetic pattern formation in order to generate adaptive patterns and accuracy of the GRN-based model. In evolutionary process, which are adaptable to dynamic environments. an MOGP-NSGA-II and differential evolution (DE) are applied to In addition, swarm pattern formation has been widely ex- optimize the structures and parameters of the GRN-based model plored in recent years, which can be divided into four cate- in parallel. -
Wingless Is a Positive Regulator of Eyespot Color Patterns in Bicyclus Anynana Butterflies
bioRxiv preprint doi: https://doi.org/10.1101/154500; this version posted June 23, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. wingless is a positive regulator of eyespot color patterns in Bicyclus anynana butterflies 1,* 1 2 1 1,3,* Nesibe Özsu , Qian Yi Chan , Bin Chen , Mainak Das Gupta , and Antónia Monteiro 1 Biological Sciences, National University of Singapore, Singapore 117543; 2 Institute of Entomology and Molecular Biology, Chongqing Normal University, Shapingba, 400047 Chongqing, China 3 Yale-NUS College, Singapore 138614 * Corresponding authors: Nesibe Özsu5or Antónia Monteiro Department of Biological Sciences, 14 Science Drive 4 Singapore, 117543 Tel: +65 97551591 [email protected] or [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/154500; this version posted June 23, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Summary 2 Eyespot patterns of nymphalid butterflies are an example of a novel trait yet, the 3 developmental origin of eyespots is still not well understood. Several genes have been 4 associated with eyespot development but few have been tested for function. One of these 5 genes is the signaling ligand, wingless, which is expressed in the eyespot centers during early 6 pupation and may function in eyespot signaling and color ring differentiation. Here we 7 tested the function of wingless in wing and eyespot development by down-regulating it in 8 transgenic Bicyclus anynana butterflies via RNAi driven by an inducible heat-shock promoter. -
Development, Plasticity and Evolution of Butterfly Eyespot Patterns" (1996), by Paul M
Published on The Embryo Project Encyclopedia (https://embryo.asu.edu) "Development, Plasticity and Evolution of Butterfly Eyespot Patterns" (1996), by Paul M. Brakefield et al. [1] By: Zou, Yawen Keywords: Butterfly eyespots [2] Paul M. Brakefield experiment [3] Bush-brown butterfly [4] eyespot patterns [5] Paul M. Brakefield and his research team in Leiden, the Netherlands, examined the development, plasticity, ande volution [6] of butterfly [7] eyespot patterns, and published their findings in Nature in 1996. Eyespots are eye-shaped color patterns that appear on the wings of some butterflies and birds [8] as well as on the skin of some fish [9] and reptiles. In butterflies, such as the peacock butterfly [7] (Aglais io [10]), the eyespots resemble the eyes of birds [8] and help butterflies deter potential predators. Brakefield's research team described the stages through which eyespots develop, identified the genes [11] and environmental signals that affect eye-spot appearance in some species, and demonstrated that small genetic variations can change butterfly [7] eyespot color and shape. The research focused on a few butterfly [7] species, but it contributed to more general claims of how the environment may affect the development of coloration and how specific color patterns may have evolved. At the time of experiment, Brakefield was a Chair in Evolutionary Biology at the University of Leiden [12], in Leiden, the Netherlands, though in 2010 he moved to Cambridge, UK to direct the University Museum of Zoology. While in Leiden, he persued a research program in evolutionary developmental biology [13] and had started working on butterfly [7] eyespots in collaboration with Vernon French, who was at the University of Edinburgh [14] in Edinburgh, Scotland. -
Cellular Asymmetry in Chlamydomonas Reinhardtii
Cellular asymmetry in Chlamydomonas reinhardtii JEFFREY A. HOLMES and SUSAN K. DUTCHER* Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309-0347, USA •Author for correspondence Summary Although largely bilaterally symmetric, the two asymmetric. As a result of asymmetric, but differ- sides of the unicellular alga Chlamydomonas rein- ent, locations of the plus and minus mating struc- hardtii can be distinguished by the location of the tures, mating preferentially results in quadriflagel- single eyespot. When viewed from the anterior end, late dikaryons with parallel flagellar pairs and both the eyespot is always closer to one flagellum than eyespots on the same side of the cell. This asymmet- the other, and located at an angle of approximately ric fusion, as well as all the other asymmetries 45° clockwise of the flagellar plane. This location described, may be necessary for the proper photo- correlates with the position of one of four acetylated tactic behavior of these cells. The invariant handed- microtubule bundles connected to the flagellar ap- ness of the spindle pole, eyespot position, and paratus. Each basal body is attached to two of these mating structure position appears to be based on microtubule rootlets. The rootlet that positions the the inherent asymmetry of the basal body pair, eyespot is always attached to the same basal body, providing an example of how an intracellular pat- which is the daugher of the parental/daughter basal tern can be determined and maintained. body pair. At mitosis, the replicated basal body pairs segregate in a precise orientation that main- tains the asymmetry of the cell and results in mitotic poles that have an invariant handedness. -
Gene Regulatory Networks
Gene Regulatory Networks 02-710 Computaonal Genomics Seyoung Kim Transcrip6on Factor Binding Transcrip6on Control • Gene transcrip.on is influenced by – Transcrip.on factor binding affinity for the regulatory regions of target genes – Transcrip.on factor concentraon – Nucleosome posi.oning and chroman states – Enhancer ac.vity Gene Transcrip6onal Regulatory Network • The expression of a gene is controlled by cis and trans regulatory elements – Cis regulatory elements: DNA sequences in the regulatory region of the gene (e.g., TF binding sites) – Trans regulatory elements: RNAs and proteins that interact with the cis regulatory elements Gene Transcrip6onal Regulatory Network • Consider the following regulatory relaonships: Target gene1 Target TF gene2 Target gene3 Cis/Trans Regulatory Elements Binding site: cis Target TF regulatory element TF binding affinity gene1 can influence the TF target gene Target gene2 expression Target TF gene3 TF: trans regulatory element TF concentra6on TF can influence the target gene TF expression Gene Transcrip6onal Regulatory Network • Cis and trans regulatory elements form a complex transcrip.onal regulatory network – Each trans regulatory element (proteins/RNAs) can regulate mul.ple target genes – Cis regulatory modules (CRMs) • Mul.ple different regulators need to be recruited to ini.ate the transcrip.on of a gene • The DNA binding sites of those regulators are clustered in the regulatory region of a gene and form a CRM How Can We Learn Transcriponal Networks? • Leverage allele specific expressions – In diploid organisms, the transcript levels from the two copies of the genes may be different – RNA-seq can capture allele- specific transcript levels How Can We Learn Transcriponal Networks? • Leverage allele specific gene expressions – Teasing out cis/trans regulatory divergence between two species (WiZkopp et al. -
Functional Genetic Approaches to Provide Evidence for the Role of Toolkit Genes in the Evolution of Complex Color Patterns in Drosophila Guttifera
Michigan Technological University Digital Commons @ Michigan Tech Dissertations, Master's Theses and Master's Reports 2021 FUNCTIONAL GENETIC APPROACHES TO PROVIDE EVIDENCE FOR THE ROLE OF TOOLKIT GENES IN THE EVOLUTION OF COMPLEX COLOR PATTERNS IN DROSOPHILA GUTTIFERA Mujeeb Olushola Shittu Michigan Technological University, [email protected] Copyright 2021 Mujeeb Olushola Shittu Recommended Citation Shittu, Mujeeb Olushola, "FUNCTIONAL GENETIC APPROACHES TO PROVIDE EVIDENCE FOR THE ROLE OF TOOLKIT GENES IN THE EVOLUTION OF COMPLEX COLOR PATTERNS IN DROSOPHILA GUTTIFERA", Open Access Dissertation, Michigan Technological University, 2021. https://doi.org/10.37099/mtu.dc.etdr/1174 Follow this and additional works at: https://digitalcommons.mtu.edu/etdr Part of the Biology Commons, Developmental Biology Commons, Evolution Commons, Molecular Genetics Commons, and the Other Cell and Developmental Biology Commons FUNCTIONAL GENETIC APPROACHES TO PROVIDE EVIDENCE FOR THE ROLE OF TOOLKIT GENES IN THE EVOLUTION OF COMPLEX COLOR PATTERNS IN DROSOPHILA GUTTIFERA By Mujeeb Olushola Shittu A DISSERTATION Submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY In Biochemistry and Molecular Biology MICHIGAN TECHNOLOGICAL UNIVERSITY 2021 ©2021 Mujeeb Olushola Shittu This dissertation has been approved in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY in Biochemistry and Molecular Biology. Department of Biological Sciences Dissertation Advisor: Dr. Thomas Werner Committee Member: Dr. Chandrashekhar -
Wonderful Wacky Water Critters
Wonderful, Wacky, Water Critters WONDERFUL WACKY WATER CRITTERS HOW TO USE THIS BOOK 1. The “KEY TO MACROINVERTEBRATE LIFE IN THE RIVER” or “KEY TO LIFE IN THE POND” identification sheets will help you ‘unlock’ the name of your animal. 2. Look up the animal’s name in the index in the back of this book and turn to the appropriate page. 3. Try to find out: a. What your animal eats. b. What tools it has to get food. c. How it is adapted to the water current or how it gets oxygen. d. How it protects itself. 4. Draw your animal’s adaptations in the circles on your adaptation worksheet on the following page. GWQ023 Wonderful Wacky Water Critters DNR: WT-513-98 This publication is available from county UW-Extension offices or from Extension Publications, 45 N. Charter St., Madison, WI 53715. (608) 262-3346, or toll-free 877-947-7827 Lead author: Suzanne Wade, University of Wisconsin–Extension Contributing scientists: Phil Emmling, Stan Nichols, Kris Stepenuck (University of Wisconsin–Extension) and Mike Miller, Mike Sorge (Wisconsin Department of Natural Resources) Adapted with permission from a booklet originally published by Riveredge Nature Center, Newburg, WI, Phone 414/675-6888 Printed on Recycled Paper Illustrations by Carolyn Pochert and Lynne Bergschultz Page 1 CRITTER ADAPTATION CHART How does it get its food? How does it get away What is its food? from enemies? Draw your “critter” here NAME OF “CRITTER” How does it get oxygen? Other unique adaptations. Page 2 TWO COMMON LIFE CYCLES: WHICH METHOD OF GROWING UP DOES YOUR ANIMAL HAVE? egg larva adult larva - older (mayfly) WITHOUT A PUPAL STAGE? THESE ANIMALS GROW GRADUALLY, CHANGING ONLY SLIGHTLY AS THEY GROW UP. -
A Combined RAD-Seq and WGS Approach Reveals the Genomic
www.nature.com/scientificreports OPEN A combined RAD‑Seq and WGS approach reveals the genomic basis of yellow color variation in bumble bee Bombus terrestris Sarthok Rasique Rahman1,2, Jonathan Cnaani3, Lisa N. Kinch4, Nick V. Grishin4 & Heather M. Hines1,5* Bumble bees exhibit exceptional diversity in their segmental body coloration largely as a result of mimicry. In this study we sought to discover genes involved in this variation through studying a lab‑generated mutant in bumble bee Bombus terrestris, in which the typical black coloration of the pleuron, scutellum, and frst metasomal tergite is replaced by yellow, a color variant also found in sister lineages to B. terrestris. Utilizing a combination of RAD‑Seq and whole‑genome re‑sequencing, we localized the color‑generating variant to a single SNP in the protein‑coding sequence of transcription factor cut. This mutation generates an amino acid change that modifes the conformation of a coiled‑coil structure outside DNA‑binding domains. We found that all sequenced Hymenoptera, including sister lineages, possess the non‑mutant allele, indicating diferent mechanisms are involved in the same color transition in nature. Cut is important for multiple facets of development, yet this mutation generated no noticeable external phenotypic efects outside of setal characteristics. Reproductive capacity was reduced, however, as queens were less likely to mate and produce female ofspring, exhibiting behavior similar to that of workers. Our research implicates a novel developmental player in pigmentation, and potentially caste, thus contributing to a better understanding of the evolution of diversity in both of these processes. Understanding the genetic architecture underlying phenotypic diversifcation has been a long-standing goal of evolutionary biology. -
A Computational Model Inspired by Gene Regulatory Networks
Rui Miguel Lourenço Lopes A Computational Model Inspired by Gene Regulatory Networks Doctoral thesis submitted to the Doctoral Program in Information Science and Technology, supervised by Full Professor Doutor Ernesto Jorge Fernandes Costa, and presented to the Department of Informatics Engineering of the Faculty of Sciences and Technology of the University of Coimbra. January 2015 A Computational Model Inspired by Gene Regulatory Networks A thesis submitted to the University of Coimbra in partial fulfillment of the requirements for the Doctoral Program in Information Science and Technology by Rui Miguel Lourenço Lopes [email protected] Department of Informatics Engineering Faculty of Sciences and Technology University of Coimbra Coimbra, January 2015 Financial support by Fundação para a Ciência e a Tecnologia, through the PhD grant SFRH/BD/69106/2010. A Computational Model Inspired by Gene Regulatory Networks ©2015 Rui L. Lopes ISBN 978-989-20-5460-5 Cover image: Composition of a Santa Fe trail program evolved by ReNCoDe overlaid on the ancestors, with a 3D model of the DNA crystal structure (by Paul Hakimata). This dissertation was prepared under the supervision of Ernesto J. F. Costa Full Professor of the Department of Informatics Engineering of the Faculty of Sciences and Tecnology of the University of Coimbra In loving memory of my father. Acknowledgements Thank you very much to Prof. Ernesto Costa, for his vision on research and education, for all the support and contributions to my ideas, and for the many life stories that always lighten the mood. Thank you also to Nuno Lourenço for the many discussions, shared books, and his constant helpfulness.