A Lesson in Homology
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Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
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. -
Many but Not All Lineage-Specific Genes Can Be Explained by Homology Detection Failure
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.27.968420; this version posted April 14, 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 4.0 International license. Many but not all lineage-specific genes can be explained by homology detection failure Caroline M. Weisman1, Andrew W. Murray1, Sean R. Eddy1,2,3 1 Department of Molecular & Cellular Biology, 2 Howard Hughes Medical Institute, 3 John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge MA, USA Abstract Genes for which homologs can be detected only in a limited group of evolutionarily related species, called “lineage-specific genes,” are pervasive: essentially every lineage has them, and they often comprise a sizable fraction of the group’s total genes. Lineage-specific genes are often interpreted as “novel” genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well-explained by this novelty- free model. -
Amphibious Fishes: Terrestrial Locomotion, Performance, Orientation, and Behaviors from an Applied Perspective by Noah R
AMPHIBIOUS FISHES: TERRESTRIAL LOCOMOTION, PERFORMANCE, ORIENTATION, AND BEHAVIORS FROM AN APPLIED PERSPECTIVE BY NOAH R. BRESSMAN A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVESITY GRADUATE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Biology May 2020 Winston-Salem, North Carolina Approved By: Miriam A. Ashley-Ross, Ph.D., Advisor Alice C. Gibb, Ph.D., Chair T. Michael Anderson, Ph.D. Bill Conner, Ph.D. Glen Mars, Ph.D. ACKNOWLEDGEMENTS I would like to thank my adviser Dr. Miriam Ashley-Ross for mentoring me and providing all of her support throughout my doctoral program. I would also like to thank the rest of my committee – Drs. T. Michael Anderson, Glen Marrs, Alice Gibb, and Bill Conner – for teaching me new skills and supporting me along the way. My dissertation research would not have been possible without the help of my collaborators, Drs. Jeff Hill, Joe Love, and Ben Perlman. Additionally, I am very appreciative of the many undergraduate and high school students who helped me collect and analyze data – Mark Simms, Tyler King, Caroline Horne, John Crumpler, John S. Gallen, Emily Lovern, Samir Lalani, Rob Sheppard, Cal Morrison, Imoh Udoh, Harrison McCamy, Laura Miron, and Amaya Pitts. I would like to thank my fellow graduate student labmates – Francesca Giammona, Dan O’Donnell, MC Regan, and Christine Vega – for their support and helping me flesh out ideas. I am appreciative of Dr. Ryan Earley, Dr. Bruce Turner, Allison Durland Donahou, Mary Groves, Tim Groves, Maryland Department of Natural Resources, UF Tropical Aquaculture Lab for providing fish, animal care, and lab space throughout my doctoral research. -
Convergent Evolution
Exploring the KU Natural History Museum Convergent Evolution Target Audience: Middle school and above Differentiated Instruction Summary Strategy Levels Content/Process/Product Grouping(s) Learning modalities Whole group • Level 1 – Visual (spatial) Small groups Process Cubing Level 2 – Kinesthetic (physical) Peer partners • Product • Level 3 – Verbal (linguistic) Homogeneous Heterogeneous * Varied grouping options can be used for this activity, depending on student needs and chaperone ability. Objectives: Explore examples of convergent evolution in vertebrates. Pre-assessment/Prior Knowledge: Prior to their visit, students should be familiar with the idea of convergent evolution, overall evolutionary relationships/classification of vertebrate groups and basic anatomy of those groups. Activity Description: Students explore the idea of convergent evolution through museum exhibits through different learning modalities. Materials Needed: • Student o Cubes (three levels, see attached) o Paper and pencils (alternatively you could use flipchart paper and markers, whiteboards and dry erase markers) o Optional (cell phones or other recording device for visual or kinesthetic levels) Note: Format to record/present findings determined by individual teacher. Provide clear instructions about expectations for documenting participation, particularly for verbal/spatial and body/kinesthetic levels (e.g. stage direction, audio/video recording). • Teacher o Content Outline o Cube labels o Cube template Content: Convergence Overview Convergent evolution refers to the similarities in biological traits that arise independently in organisms that are not closely related, e.g. wings in birds, bats and insects. Similarity among organisms and their structures that was not inherited from a common ancestor is considered to be homoplasy. This can be contrasted with homology, which refers to similarity of traits due to common ancestry. -
Systematic Morphology of Fishes in the Early 21St Century
Copeia 103, No. 4, 2015, 858–873 When Tradition Meets Technology: Systematic Morphology of Fishes in the Early 21st Century Eric J. Hilton1, Nalani K. Schnell2, and Peter Konstantinidis1 Many of the primary groups of fishes currently recognized have been established through an iterative process of anatomical study and comparison of fishes that has spanned a time period approaching 500 years. In this paper we give a brief history of the systematic morphology of fishes, focusing on some of the individuals and their works from which we derive our own inspiration. We further discuss what is possible at this point in history in the anatomical study of fishes and speculate on the future of morphology used in the systematics of fishes. Beyond the collection of facts about the anatomy of fishes, morphology remains extremely relevant in the age of molecular data for at least three broad reasons: 1) new techniques for the preparation of specimens allow new data sources to be broadly compared; 2) past morphological analyses, as well as new ideas about interrelationships of fishes (based on both morphological and molecular data) provide rich sources of hypotheses to test with new morphological investigations; and 3) the use of morphological data is not limited to understanding phylogeny and evolution of fishes, but rather is of broad utility to understanding the general biology (including phenotypic adaptation, evolution, ecology, and conservation biology) of fishes. Although in some ways morphology struggles to compete with the lure of molecular data for systematic research, we see the anatomical study of fishes entering into a new and exciting phase of its history because of recent technological and methodological innovations. -
Segmentation and Tagmosis in Chelicerata
Arthropod Structure & Development 46 (2017) 395e418 Contents lists available at ScienceDirect Arthropod Structure & Development journal homepage: www.elsevier.com/locate/asd Segmentation and tagmosis in Chelicerata * Jason A. Dunlop a, , James C. Lamsdell b a Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstrasse 43, D-10115 Berlin, Germany b American Museum of Natural History, Division of Paleontology, Central Park West at 79th St, New York, NY 10024, USA article info abstract Article history: Patterns of segmentation and tagmosis are reviewed for Chelicerata. Depending on the outgroup, che- Received 4 April 2016 licerate origins are either among taxa with an anterior tagma of six somites, or taxa in which the ap- Accepted 18 May 2016 pendages of somite I became increasingly raptorial. All Chelicerata have appendage I as a chelate or Available online 21 June 2016 clasp-knife chelicera. The basic trend has obviously been to consolidate food-gathering and walking limbs as a prosoma and respiratory appendages on the opisthosoma. However, the boundary of the Keywords: prosoma is debatable in that some taxa have functionally incorporated somite VII and/or its appendages Arthropoda into the prosoma. Euchelicerata can be defined on having plate-like opisthosomal appendages, further Chelicerata fi Tagmosis modi ed within Arachnida. Total somite counts for Chelicerata range from a maximum of nineteen in Prosoma groups like Scorpiones and the extinct Eurypterida down to seven in modern Pycnogonida. Mites may Opisthosoma also show reduced somite counts, but reconstructing segmentation in these animals remains chal- lenging. Several innovations relating to tagmosis or the appendages borne on particular somites are summarised here as putative apomorphies of individual higher taxa. -
Cooption of an Appendage-Patterning Gene Cassette in the Head
Cooption of an appendage-patterning gene cassette in PNAS PLUS the head segmentation of arachnids Emily V. W. Settona and Prashant P. Sharmaa,1 aDepartment of Integrative Biology, University of Wisconsin–Madison, Madison, WI 53706 Edited by Nipam H. Patel, University of California, Berkeley, CA, and accepted by Editorial Board Member David Jablonski February 28, 2018 (received for review November 20, 2017) The jointed appendages of arthropods have facilitated the spec- ventral tissue. Ectopic expression of both Dmel–Sp6-9 and Dmel- tacular diversity and success of this phylum. Key to the regulation btd can induce wing-to-leg transformations, but Dmel–Sp6-9 has of appendage outgrowth is the Krüppel-like factor (KLF)/specific- a more important role in D. melanogaster leg fate specification, ity protein (Sp) family of zinc finger transcription factors. In the as Dmel–Sp6-9 can rescue double-null mutants, whereas Dmel- fruit fly, Drosophila melanogaster, the Sp6-9 homolog is activated btd cannot. In later development, both Dmel–Sp6-9 and Dmel-btd by Wnt-1/wingless (wg) and establishes ventral appendage (leg) are required for proper leg growth in larval stages (27, 28). fate. Subsequently, Sp6-9 maintains expression of the axial pat- Beyond D. melanogaster, gene expression surveys of Sp6-9 have terning gene Distal-less (Dll), which promotes limb outgrowth. In- demonstrated conservation of expression domains across insects and triguingly, in spiders, Dll has been reported to have a derived role one crustacean [all members of the same clade, Pancrustacea (29)]; as a segmentation gap gene, but the evolutionary origin and reg- taxonomically broader surveys of wg have shown broadly conserved ulation of this function are not understood because functional in- expression patterns across Arthropoda. -
Geological History and Phylogeny of Chelicerata
Arthropod Structure & Development 39 (2010) 124–142 Contents lists available at ScienceDirect Arthropod Structure & Development journal homepage: www.elsevier.com/locate/asd Review Article Geological history and phylogeny of Chelicerata Jason A. Dunlop* Museum fu¨r Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Invalidenstraße 43, D-10115 Berlin, Germany article info abstract Article history: Chelicerata probably appeared during the Cambrian period. Their precise origins remain unclear, but may Received 1 December 2009 lie among the so-called great appendage arthropods. By the late Cambrian there is evidence for both Accepted 13 January 2010 Pycnogonida and Euchelicerata. Relationships between the principal euchelicerate lineages are unre- solved, but Xiphosura, Eurypterida and Chasmataspidida (the last two extinct), are all known as body Keywords: fossils from the Ordovician. The fourth group, Arachnida, was found monophyletic in most recent studies. Arachnida Arachnids are known unequivocally from the Silurian (a putative Ordovician mite remains controversial), Fossil record and the balance of evidence favours a common, terrestrial ancestor. Recent work recognises four prin- Phylogeny Evolutionary tree cipal arachnid clades: Stethostomata, Haplocnemata, Acaromorpha and Pantetrapulmonata, of which the pantetrapulmonates (spiders and their relatives) are probably the most robust grouping. Stethostomata includes Scorpiones (Silurian–Recent) and Opiliones (Devonian–Recent), while -
Tetrapod Limb and Sarcopterygian Fin Regeneration Share a Core Genetic
ARTICLE Received 28 Apr 2016 | Accepted 27 Sep 2016 | Published 2 Nov 2016 DOI: 10.1038/ncomms13364 OPEN Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme Acacio F. Nogueira1,*, Carinne M. Costa1,*, Jamily Lorena1, Rodrigo N. Moreira1, Gabriela N. Frota-Lima1, Carolina Furtado2, Mark Robinson3, Chris T. Amemiya3,4, Sylvain Darnet1 & Igor Schneider1 Salamanders are the only living tetrapods capable of fully regenerating limbs. The discovery of salamander lineage-specific genes (LSGs) expressed during limb regeneration suggests that this capacity is a salamander novelty. Conversely, recent paleontological evidence supports a deeper evolutionary origin, before the occurrence of salamanders in the fossil record. Here we show that lungfishes, the sister group of tetrapods, regenerate their fins through morphological steps equivalent to those seen in salamanders. Lungfish de novo transcriptome assembly and differential gene expression analysis reveal notable parallels between lungfish and salamander appendage regeneration, including strong downregulation of muscle proteins and upregulation of oncogenes, developmental genes and lungfish LSGs. MARCKS-like protein (MLP), recently discovered as a regeneration-initiating molecule in salamander, is likewise upregulated during early stages of lungfish fin regeneration. Taken together, our results lend strong support for the hypothesis that tetrapods inherited a bona fide limb regeneration programme concomitant with the fin-to-limb transition. 1 Instituto de Cieˆncias Biolo´gicas, Universidade Federal do Para´, Rua Augusto Correa, 01, Bele´m66075-110,Brazil.2 Unidade Genoˆmica, Programa de Gene´tica, Instituto Nacional do Caˆncer, Rio de Janeiro 20230-240, Brazil. 3 Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, Washington 98101, USA. 4 Department of Biology, University of Washington 106 Kincaid, Seattle, Washington 98195, USA. -
Evolution of the Muscular System in Tetrapod Limbs Tatsuya Hirasawa1* and Shigeru Kuratani1,2
Hirasawa and Kuratani Zoological Letters (2018) 4:27 https://doi.org/10.1186/s40851-018-0110-2 REVIEW Open Access Evolution of the muscular system in tetrapod limbs Tatsuya Hirasawa1* and Shigeru Kuratani1,2 Abstract While skeletal evolution has been extensively studied, the evolution of limb muscles and brachial plexus has received less attention. In this review, we focus on the tempo and mode of evolution of forelimb muscles in the vertebrate history, and on the developmental mechanisms that have affected the evolution of their morphology. Tetrapod limb muscles develop from diffuse migrating cells derived from dermomyotomes, and the limb-innervating nerves lose their segmental patterns to form the brachial plexus distally. Despite such seemingly disorganized developmental processes, limb muscle homology has been highly conserved in tetrapod evolution, with the apparent exception of the mammalian diaphragm. The limb mesenchyme of lateral plate mesoderm likely plays a pivotal role in the subdivision of the myogenic cell population into individual muscles through the formation of interstitial muscle connective tissues. Interactions with tendons and motoneuron axons are involved in the early and late phases of limb muscle morphogenesis, respectively. The mechanism underlying the recurrent generation of limb muscle homology likely resides in these developmental processes, which should be studied from an evolutionary perspective in the future. Keywords: Development, Evolution, Homology, Fossils, Regeneration, Tetrapods Background other morphological characters that may change during The fossil record reveals that the evolutionary rate of growth. Skeletal muscles thus exhibit clear advantages vertebrate morphology has been variable, and morpho- for the integration of paleontology and evolutionary logical deviations and alterations have taken place unevenly developmental biology. -
The Early Paleozoic World: Cambrian Period (544-459 MY)
The Early Paleozoic World: Cambrian Period (544-459 MY) Jarðsaga 1 -Saga Lífs og Lands – Ólafur Ingólfsson The Cambrian Period: Precambrian Super- continent has broken up and life explodes... • Sea level rose throughout the Cambrian – very widespread deposition of marine sediments • Rodina Supercontinent broken up • Skeletal animals appear in the fossil record • Predation becomes a way-of-life • Trilobates appear on the scene, and develop rapidly • A major diversification of large animals • Trilobate mass extinctions towards the end of the period Cambrian key-sites Cambrian sediments occur on all Earths continents Cambrian was named by the 19th-century English geologist Adam Sedgwick, who first studied the great sequence of rocks characteristic of the period near Cambria, Wales. Early Cambrian continental configuration Rodina had broken up by early Cambrian, and Laurentia, Siberia and Baltica were separated from “Proto-Gondwana” Early Cambrian climate Early Cambrian climate was warm, but not too hot, and there is no evidence of any glacial ice at the poles. Transgression of sea onto continental cratons! http://www.scotese.com/ What caused the Cambrian transgression? What can cause globally rising sea-levels? 1. A decrease in ocean basin volume due to: • Formation of new mid-ocean ridges • Increased area of continents (rifting) • Accumulation of sediments on the sea-floor 2. An increase in water volume by melting of glaciers on land What can cause regionally/locally rising sea-levels? 1. Subsidence of land along a passive continental margin 2. Local/regional glacio-isostatic loading The vidence for a global Cambrian transgression 1. Wide-spread marine sediments on all cratons 2.