Perspectives on the Genetic Architecture of Divergence in Body
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From Developmental Constraint to Evolvability
From Developmental Constraint to Evolvability How Concepts Figure in Explanation and Disciplinary Identity Ingo Brigandt Department of Philosophy, University of Alberta 2-40 Assiniboia Hall, Edmonton, AB T6G2E7, Canada [email protected] Abstract The concept of developmental constraint was at the heart of develop- mental approaches to evolution of the 1980s. While this idea was widely used to criticize neo-Darwinian evolutionary theory, critique does not yield an alternative framework that offers evolutionary explanations. In current Evo-devo the concept of constraint is of minor importance, whereas notions as evolvability are at the center of attention. The latter clearly defines an explanatory agenda for evolution- ary research, so that one could view the historical shift from ‘developmental con- straint’ towards ‘evolvability’ as the move from a concept that is a mere tool of criticism to a concept that establishes a positive explanatory project. However, by taking a look at how the concept of constraint was employed in the 1980s, I argue that developmental constraint was not just seen as restricting possibilities (‘con- straining’), but also as facilitating morphological change in several ways. Ac- counting for macroevolutionary transformation and the origin of novel form was an aim of these developmental approaches to evolution. Thus, the concept of de- velopmental constraint was part of a positive explanatory agenda long before the advent of Evo-devo as a genuine scientific discipline. In the 1980s, despite the lack of a clear disciplinary identity, this concept coordinated research among pale- ontologists, morphologists, and developmentally inclined evolutionary biologists. I discuss the different functions that scientific concepts can have, highlighting that instead of classifying or explaining natural phenomena, concepts such as ‘devel- opmental constraint’ and ‘evolvability’ are more important in setting explanatory agendas so as to provide intellectual coherence to scientific approaches. -
Variation in Marine Threespine Stickleback (Gasterosteus Aculeatus) and Its Implications for Adaptive Divergence
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2017 Contemporary ancestor? Variation in marine threespine stickleback (Gasterosteus aculeatus) and its implications for adaptive divergence Morris, Matthew Morris, M. (2017). Contemporary ancestor? Variation in marine threespine stickleback (Gasterosteus aculeatus) and its implications for adaptive divergence (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/25434 http://hdl.handle.net/11023/3910 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Contemporary ancestor? Variation in marine threespine stickleback (Gasterosteus aculeatus) and its implications for adaptive divergence by Matthew Richard John Morris A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA JUNE, 2017 © Matthew Richard John Morris 2017 Abstract Standing genetic variation (SGV) can affect the incidence and pace of adaptation and parallel evolution. The role of SGV versus de novo mutation can be tested in ancestral-derived comparisons when the “contemporary ancestor” is extant. Assumptions about SGV in these contemporary ancestors require formal testing. The threespine stickleback is an icon of adaptive divergence, with multiple freshwater forms having evolved in parallel from a presumably panmictic, evolutionarily static marine population – in part from SGV at Ectodysplasin. -
A Comprehensive Study of Metabolite Genetics Reveals Strong Pleiotropy and Heterogeneity Across Time and Context
ARTICLE https://doi.org/10.1038/s41467-019-12703-7 OPEN A comprehensive study of metabolite genetics reveals strong pleiotropy and heterogeneity across time and context Apolline Gallois1,12, Joel Mefford2,12, Arthur Ko 3, Amaury Vaysse 1, Hanna Julienne1, Mika Ala-Korpela4,5,6,7,8,9, Markku Laakso 10, Noah Zaitlen2,12*, Päivi Pajukanta 3,12*& Hugues Aschard 1,11,12* 1234567890():,; Genetic studies of metabolites have identified thousands of variants, many of which are associated with downstream metabolic and obesogenic disorders. However, these studies have relied on univariate analyses, reducing power and limiting context-specific under- standing. Here we aim to provide an integrated perspective of the genetic basis of meta- bolites by leveraging the Finnish Metabolic Syndrome In Men (METSIM) cohort, a unique genetic resource which contains metabolic measurements, mostly lipids, across distinct time points as well as information on statin usage. We increase effective sample size by an average of two-fold by applying the Covariates for Multi-phenotype Studies (CMS) approach, identifying 588 significant SNP-metabolite associations, including 228 new associations. Our analysis pinpoints a small number of master metabolic regulator genes, balancing the relative proportion of dozens of metabolite levels. We further identify associations to changes in metabolic levels across time as well as genetic interactions with statin at both the master metabolic regulator and genome-wide level. 1 Department of Computational Biology - USR 3756 CNRS, Institut Pasteur, Paris, France. 2 Department of Medicine, University of California, San Francisco, CA, USA. 3 Department of Human Genetics, University of California, Los Angeles, CA, USA. -
Evolution by Natural Selection, Formulated Independently by Charles Darwin and Alfred Russel Wallace
UNIT 4 EVOLUTIONARY PATT EVOLUTIONARY E RNS AND PROC E SS E Evolution by Natural S 22 Selection Natural selection In this chapter you will learn that explains how Evolution is one of the most populations become important ideas in modern biology well suited to their environments over time. The shape and by reviewing by asking by applying coloration of leafy sea The rise of What is the evidence for evolution? Evolution in action: dragons (a fish closely evolutionary thought two case studies related to seahorses) 22.1 22.4 are heritable traits that with regard to help them to hide from predators. The pattern of evolution: The process of species have changed evolution by natural and are related 22.2 selection 22.3 keeping in mind Common myths about natural selection and adaptation 22.5 his chapter is about one of the great ideas in science: the theory of evolution by natural selection, formulated independently by Charles Darwin and Alfred Russel Wallace. The theory explains how T populations—individuals of the same species that live in the same area at the same time—have come to be adapted to environments ranging from arctic tundra to tropical wet forest. It revealed one of the five key attributes of life: Populations of organisms evolve. In other words, the heritable characteris- This chapter is part of the tics of populations change over time (Chapter 1). Big Picture. See how on Evolution by natural selection is one of the best supported and most important theories in the history pages 516–517. of scientific research. -
Why Call It Developmental Bias When It Is Just Development? Isaac Salazar-Ciudad1,2,3
Salazar-Ciudad Biology Direct (2021) 16:3 https://doi.org/10.1186/s13062-020-00289-w OPINION Open Access Why call it developmental bias when it is just development? Isaac Salazar-Ciudad1,2,3 Abstract The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation. This opinion article argues that the concepts of developmental constraints and developmental biases do not accurately represent the role of development in evolution. The concept of developmental constraints was coined to oppose the view that natural selection is all-capable and to highlight the importance of development for understanding evolution. In the modern synthesis, natural selection was seen as the main factor determining the direction of morphological evolution. For that to be the case, morphological variation needs to be isotropic (i.e. equally possible in all directions). The proponents of the developmental constraint concept argued that development makes that some morphological variation is more likely than other (i.e. variation is not isotropic), and that, thus, development constraints evolution by precluding natural selection from being all-capable. This article adds to the idea that development is not compatible with the isotropic expectation by arguing that, in fact, it could not be otherwise: there is no actual reason to expect that development could lead to isotropic morphological variation. It is then argued that, since the isotropic expectation is untenable, the role of development in evolution should not be understood as a departure from such an expectation. -
Contrasting Tempos of Sex Chromosome Degeneration In
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.17.300236; this version posted September 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Contrasting tempos of sex chromosome 2 degeneration in sticklebacks 3 4 5 Jason M. Sardell1*, Matthew P. Josephson2, Anne C. Dalziel3, 6 Catherine L. Peichel2, and Mark Kirkpatrick1 7 8 1 Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 9 2 Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland 10 3 Department of Biology, Saint Mary’s University, Halifax, NS, Canada B3H 3C3 11 * Corresponding author: [email protected] 12 13 RUNNING TITLE: Blackspotted stickleback sex chromosomes 14 KEY WORDS: Sex chromosomes, stickleback, Gasterosteus, neo-Y chromosome, 15 recombination, fish 16 17 Revised version submitted 16 July 2020; original version submitted 3 April 2020 18 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.17.300236; this version posted September 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 19 20 Abstract 21 The steps of sex chromosome evolution are often thought to follow a predictable pattern and tempo, but 22 few studies have examined how the outcomes of this process differ between closely related species with 23 homologous sex chromosomes. -
Appendix B Wells Harbor Ecology (Materials from the Wells NERR)
APPENDICES Appendix B Wells Harbor Ecology (materials from the Wells NERR) CHAPTER 8 Vegetation Caitlin Mullan Crain lants are primary producers that use photosynthesis ter). In this chapter, we will describe what these vegeta- to convert light energy into carbon. Plants thus form tive communities look like, special plant adaptations for Pthe base of all food webs and provide essential nutrition living in coastal habitats, and important services these to animals. In coastal “biogenic” habitats, the vegetation vegetative communities perform. We will then review also engineers the environment, and actually creates important research conducted in or affiliated with Wells the habitat on which other organisms depend. This is NERR on the various vegetative community types, giving particularly apparent in coastal marshes where the plants a unique view of what is known about coastal vegetative themselves, by trapping sediments and binding the communities of southern Maine. sediment with their roots, create the peat base and above- ground structure that defines the salt marsh. The plants OASTAL EGETATION thus function as foundation species, dominant C V organisms that modify the physical environ- Macroalgae ment and create habitat for numerous dependent Algae, commonly known as seaweeds, are a group of organisms. Other vegetation types in coastal non-vascular plants that depend on water for nutrient systems function in similar ways, particularly acquisition, physical support, and seagrass beds or dune plants. Vegetation is reproduction. Algae are therefore therefore important for numerous reasons restricted to living in environ- including transforming energy to food ments that are at least occasionally sources, increasing biodiversity, and inundated by water. -
Investigations Into Roles for Endocytosis in LIN-12/Notch
Investigations into roles for endocytosis in LIN-12/Notch signaling and its regulation Jessica Chan Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2020 © 2020 Jessica Chan All Rights Reserved Abstract The LIN-12/Notch signaling pathway is highly conserved in all animals, and is crucial for proper development. It is a key pathway in specifying cell fate in many cellular contexts, and dysregulation of the pathway can have deleterious consequences. Therefore, understanding how LIN-12/Notch signaling is regulated in different contexts has been a main area of interest in the field. Previous studies in different model organisms have identified many modes of regulation of the signaling pathway, one of which is endocytosis of the ligand and receptor. Here, I further investigated the role of endocytosis in LIN-12/Notch signaling in multiple developmental contexts in Caenorhabditis elegans. Work in Drosophila and vertebrates had previously established that ligand-mediated activation of Notch requires ubiquitination of the intracellular domain of the transmembrane ligand and the activity of the endocytic adaptor Epsin in the signaling cell. The consensus in the field is that Epsin-mediated endocytosis of mono-ubiquitinated ligand generates a pulling force that exposes a cleavage site in Notch for an ADAM protease, a critical step in signal transduction. In contrast, in this thesis, I examined two different transmembrane ligands in several different cell contexts and found that activation of LIN-12/Notch and the paralogous GLP-1/Notch in C. -
Nicotinic Receptor Alpha7 Expression During Tooth Morphogenesis Reveals Functional Pleiotropy
Nicotinic Receptor Alpha7 Expression during Tooth Morphogenesis Reveals Functional Pleiotropy Scott W. Rogers1,2*, Lorise C. Gahring1,3 1 Geriatric Research, Education and Clinical Center, Veteran’s Administration, Salt Lake City, Utah, United States of America, 2 Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah, United States of America, 3 Division of Geriatrics, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America Abstract The expression of nicotinic acetylcholine receptor (nAChR) subtype, alpha7, was investigated in the developing teeth of mice that were modified through homologous recombination to express a bi-cistronic IRES-driven tau-enhanced green fluorescent protein (GFP); alpha7GFP) or IRES-Cre (alpha7Cre). The expression of alpha7GFP was detected first in cells of the condensing mesenchyme at embryonic (E) day E13.5 where it intensifies through E14.5. This expression ends abruptly at E15.5, but was again observed in ameloblasts of incisors at E16.5 or molar ameloblasts by E17.5–E18.5. This expression remains detectable until molar enamel deposition is completed or throughout life as in the constantly erupting mouse incisors. The expression of alpha7GFP also identifies all stages of innervation of the tooth organ. Ablation of the alpha7-cell lineage using a conditional alpha7Cre6ROSA26-LoxP(diphtheria toxin A) strategy substantially reduced the mesenchyme and this corresponded with excessive epithelium overgrowth consistent with an instructive role by these cells during ectoderm patterning. However, alpha7knock-out (KO) mice exhibited normal tooth size and shape indicating that under normal conditions alpha7 expression is dispensable to this process. -
Inventory of Tidepool and Estuarine Fishes in Acadia National Park
INVENTORY OF TIDEPOOL AND ESTUARINE FISHES IN ACADIA NATIONAL PARK Edited by Linda J. Kling and Adrian Jordaan School of Marines Sciences University of Maine Orono, Maine 04469 Report to the National Park Service Acadia National Park February 2008 EXECUTIVE SUMMARY Acadia National Park (ANP) is part of the Northeast Temperate Network (NETN) of the National Park Service’s Inventory and Monitoring Program. Inventory and monitoring activities supported by the NETN are becoming increasingly important for setting and meeting long-term management goals. Detailed inventories of fishes of estuaries and intertidal areas of ANP are very limited, necessitating the collection of information within these habitats. The objectives of this project were to inventory fish species found in (1) tidepools and (2) estuaries at locations adjacent to park lands on Mount Desert Island and the Schoodic Peninsula over different seasons. The inventories were not intended to be part of a long-term monitoring effort. Rather, the objective was to sample as many diverse habitats as possible in the intertidal and estuarine zones to maximize the resultant species list. Beyond these original objectives, we evaluated the data for spatial and temporal patterns and trends as well as relationships with other biological and physical characteristics of the tidepools and estuaries. For the tidepool survey, eighteen intertidal sections with multiple pools were inventoried. The majority of the tidepool sampling took place in 2001 but a few tidepools were revisited during the spring/summer period of 2002 and 2003. Each tidepool was visited once during late spring (Period 1: June 6 – June 26), twice during the summer (Period 2: July 3 – August 2 and Period 3: August 3 – September 18) and once during early fall (Period 4: September 29 – October 21). -
Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt
Bryn Mawr College Scholarship, Research, and Creative Work at Bryn Mawr College Biology Faculty Research and Scholarship Biology 2013 Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt Gregory K. Davis Bryn Mawr College, [email protected] Caleb Trujillo Mark Terry Donald P. French See next page for additional authors Let us know how access to this document benefits ouy . Follow this and additional works at: http://repository.brynmawr.edu/bio_pubs Part of the Biology Commons Custom Citation Hiatt A, Davis GK, Trujillo C, Terry M, French DP, Price RM and Perez KE . "Getting to evo-devo: concepts and challenges for students learning evolutionary developmental biology". CBE-Life Sciences Education 12 (2013): 494-508. This paper is posted at Scholarship, Research, and Creative Work at Bryn Mawr College. http://repository.brynmawr.edu/bio_pubs/10 For more information, please contact [email protected]. Authors Anna Hiatt, Gregory K. Davis, Caleb Trujillo, Mark Terry, Donald P. French, Rebecca M. Price, and Kathryn E. Perez This article is available at Scholarship, Research, and Creative Work at Bryn Mawr College: http://repository.brynmawr.edu/ bio_pubs/10 CBE—Life Sciences Education Vol. 12, 494–508, Fall 2013 Article Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt,*† Gregory K. Davis,‡ Caleb Trujillo,§ Mark Terry, Donald P. French,* Rebecca M. Price,¶ and Kathryn E. Perez** *Department of Zoology, Oklahoma -
An Introduction to Quantitative Genetics I Heather a Lawson Advanced Genetics Spring2018 Outline
An Introduction to Quantitative Genetics I Heather A Lawson Advanced Genetics Spring2018 Outline • What is Quantitative Genetics? • Genotypic Values and Genetic Effects • Heritability • Linkage Disequilibrium and Genome-Wide Association Quantitative Genetics • The theory of the statistical relationship between genotypic variation and phenotypic variation. 1. What is the cause of phenotypic variation in natural populations? 2. What is the genetic architecture and molecular basis of phenotypic variation in natural populations? • Genotype • The genetic constitution of an organism or cell; also refers to the specific set of alleles inherited at a locus • Phenotype • Any measureable characteristic of an individual, such as height, arm length, test score, hair color, disease status, migration of proteins or DNA in a gel, etc. Nature Versus Nurture • Is a phenotype the result of genes or the environment? • False dichotomy • If NATURE: my genes made me do it! • If NURTURE: my mother made me do it! • The features of an organisms are due to an interaction of the individual’s genotype and environment Genetic Architecture: “sum” of the genetic effects upon a phenotype, including additive,dominance and parent-of-origin effects of several genes, pleiotropy and epistasis Different genetic architectures Different effects on the phenotype Types of Traits • Monogenic traits (rare) • Discrete binary characters • Modified by genetic and environmental background • Polygenic traits (common) • Discrete (e.g. bristle number on flies) or continuous (human height)