The Evolution of Eyes: IR Schwab Major Steps
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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Biophotonic Probes for Bio-Detection and Imaging Ting Pan1,Dengyunlu1, Hongbao Xin 1 and Baojun Li 1
Pan et al. Light: Science & Applications (2021) 10:124 Official journal of the CIOMP 2047-7538 https://doi.org/10.1038/s41377-021-00561-2 www.nature.com/lsa REVIEW ARTICLE Open Access Biophotonic probes for bio-detection and imaging Ting Pan1,DengyunLu1, Hongbao Xin 1 and Baojun Li 1 Abstract The rapid development of biophotonics and biomedical sciences makes a high demand on photonic structures to be interfaced with biological systems that are capable of manipulating light at small scales for sensitive detection of biological signals and precise imaging of cellular structures. However, conventional photonic structures based on artificial materials (either inorganic or toxic organic) inevitably show incompatibility and invasiveness when interfacing with biological systems. The design of biophotonic probes from the abundant natural materials, particularly biological entities such as virus, cells and tissues, with the capability of multifunctional light manipulation at target sites greatly increases the biocompatibility and minimizes the invasiveness to biological microenvironment. In this review, advances in biophotonic probes for bio-detection and imaging are reviewed. We emphatically and systematically describe biological entities-based photonic probes that offer appropriate optical properties, biocompatibility, and biodegradability with different optical functions from light generation, to light transportation and light modulation. Three representative biophotonic probes, i.e., biological lasers, cell-based biophotonic waveguides and -
Animal Eyes and the Darwinian Theory of the Evolution of the Human
Animal Eyes We can learn a lot from the wonder of, and the wonder in, animal eyes. Aldo Leopold a pioneer in the conservation movement did. He wrote in Thinking like a Mountain, “We reached the old wolf in time to watch a fierce green fire dying in her eyes. I realized then, and have known ever since, that there was something new to me in those eyes – something known only to her and to the mountain. I was young then, and full of trigger-itch; I thought that because fewer wolves meant more deer, that no wolves would mean hunters’ paradise. But after seeing the green fire die, I sensed that neither the wolf nor the mountain agreed with such a view.” For Aldo Leopold, the green fire in the wolf’s eyes symbolized a new way of seeing our place in the world, and with his new insight, he provided a new ethical perspective for the environmental movement. http://vimeo.com/8669977 Light contains information about the environment, and animals without eyes can make use of the information provided by environmental light without forming an image. Euglena, a single-celled organism that did not fit nicely into Carl Linnaeus’ two kingdom system of classification, quite clearly responds to light. Its plant-like nature responds to light by photosynthesizing and its animal- like nature responds to light by moving to and staying in the light. Light causes an increase in the swimming speed, a response known as 165 photokinesis. Light also causes another response in Euglena, known as an accumulation response (phototaxis). -
Online Dictionary of Invertebrate Zoology Parasitology, Harold W
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Armand R. Maggenti Online Dictionary of Invertebrate Zoology Parasitology, Harold W. Manter Laboratory of September 2005 Online Dictionary of Invertebrate Zoology: S Mary Ann Basinger Maggenti University of California-Davis Armand R. Maggenti University of California, Davis Scott Gardner University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/onlinedictinvertzoology Part of the Zoology Commons Maggenti, Mary Ann Basinger; Maggenti, Armand R.; and Gardner, Scott, "Online Dictionary of Invertebrate Zoology: S" (2005). Armand R. Maggenti Online Dictionary of Invertebrate Zoology. 6. https://digitalcommons.unl.edu/onlinedictinvertzoology/6 This Article is brought to you for free and open access by the Parasitology, Harold W. Manter Laboratory of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Armand R. Maggenti Online Dictionary of Invertebrate Zoology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Online Dictionary of Invertebrate Zoology 800 sagittal triact (PORIF) A three-rayed megasclere spicule hav- S ing one ray very unlike others, generally T-shaped. sagittal triradiates (PORIF) Tetraxon spicules with two equal angles and one dissimilar angle. see triradiate(s). sagittate a. [L. sagitta, arrow] Having the shape of an arrow- sabulous, sabulose a. [L. sabulum, sand] Sandy, gritty. head; sagittiform. sac n. [L. saccus, bag] A bladder, pouch or bag-like structure. sagittocysts n. [L. sagitta, arrow; Gr. kystis, bladder] (PLATY: saccate a. [L. saccus, bag] Sac-shaped; gibbous or inflated at Turbellaria) Pointed vesicles with a protrusible rod or nee- one end. dle. saccharobiose n. -
Lafranca Moth Article.Pdf
What you may not know about... MScientific classificationoths Kingdom: Animalia Phylum: Arthropoda Class: Insecta Photography and article written by Milena LaFranca order: Lepidoptera [email protected] At roughly 160,000, there are nearly day or nighttime. Butterflies are only above: scales on moth wing, shot at 2x above: SEM image of individual wing scale, 1500x ten times the number of species of known to be diurnal insects and moths of moths have thin butterfly-like of microscopic ridges and bumps moths compared to butterflies, which are mostly nocturnal insects. So if the antennae but they lack the club ends. that reflect light in various angles are in the same order. While most sun is out, it is most likely a butterfly and Moths utilize a wing-coupling that create iridescent coloring. moth species are nocturnal, there are if the moon is out, it is definitely a moth. mechanism that includes two I t i s c o m m o n f o r m o t h w i n g s t o h a v e some that are crepuscular and others A subtler clue in butterfly/moth structures, the retinaculum and patterns that are not in the human that are diurnal. Crepuscular meaning detection is to compare the placement the frenulum. The frenulum is a visible light spectrum. Moths have that they are active during twilight of their wings at rest. Unless warming spine at the base of the hind wing. the ability to see in ultra-violet wave hours. Diurnal themselves, The retinaculum is a loop on the lengths. -
The Case of Deirocheline Turtles
bioRxiv preprint doi: https://doi.org/10.1101/556670; this version posted February 21, 2019. 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 Body coloration and mechanisms of colour production in Archelosauria: 2 The case of deirocheline turtles 3 Jindřich Brejcha1,2*†, José Vicente Bataller3, Zuzana Bosáková4, Jan Geryk5, 4 Martina Havlíková4, Karel Kleisner1, Petr Maršík6, Enrique Font7 5 1 Department of Philosophy and History of Science, Faculty of Science, Charles University, Viničná 7, Prague 6 2, 128 00, Czech Republic 7 2 Department of Zoology, Natural History Museum, National Museum, Václavské nám. 68, Prague 1, 110 00, 8 Czech Republic 9 3 Centro de Conservación de Especies Dulceacuícolas de la Comunidad Valenciana. VAERSA-Generalitat 10 Valenciana, El Palmar, València, 46012, Spain. 11 4 Department of Analytical Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 2, 128 43, 12 Czech Republic 13 5 Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University 14 Hospital Motol, V Úvalu 84, 150 06 Prague, Czech Republic 15 6 Department of Food Science, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life 16 Sciences, Kamýcká 129, Prague 6, 165 00, Czech Republic 17 7 Ethology Lab, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, C/ 18 Catedrátic José Beltrán Martinez 2, Paterna, València, 46980, Spain 19 Keywords: Chelonia, Trachemys scripta, Pseudemys concinna, nanostructure, pigments, chromatophores 20 21 Abstract 22 Animal body coloration is a complex trait resulting from the interplay of multiple colour-producing mechanisms. -
Pupillary Response to Light in Three Species of Cubozoa (Box Jellyfish)
Plankton Benthos Res 15(2): 73–77, 2020 Plankton & Benthos Research © The Plankton Society of Japan Pupillary response to light in three species of Cubozoa (box jellyfish) JAMIE E. SEYMOUR* & EMILY P. O’HARA Australian Institute for Tropical Health and Medicine, James Cook University, 11 McGregor Road, Smithfield, Qld 4878, Australia Received 12 August 2019; Accepted 20 December 2019 Responsible Editor: Ryota Nakajima doi: 10.3800/pbr.15.73 Abstract: Pupillary response under varying conditions of bright light and darkness was compared in three species of Cubozoa with differing ecologies. Maximal and minimal pupil area in relation to total eye area was measured and the rate of change recorded. In Carukia barnesi, the rate of pupil constriction was faster and final constriction greater than in Chironex fleckeri, which itself showed faster and greater constriction than in Chiropsella bronzie. We suggest this allows for differing degrees of visual acuity between the species. We propose that these differences are correlated with variations in the environment which each of these species inhabit, with Ca. barnesi found fishing for larval fish in and around waters of structurally complex coral reefs, Ch. fleckeri regularly found acquiring fish in similarly complex mangrove habitats, while Ch. bronzie spends the majority of its time in the comparably less complex but more turbid environments of shallow sandy beaches where their food source of small shrimps is highly aggregated and less mobile. Key words: box jellyfish, cubozoan, pupillary mobility, vision invertebrates (Douglas et al. 2005, O’Connor et al. 2009), Introduction none exist directly comparing pupillary movement be- The primary function of pupil constriction and dilation tween species in relation to their habitat and lifestyle. -
N REPTILIA: SQUAMATA: SAURIA: PHRYNOSOMATIDAE PHRYNOSOMA Phrynosoma Modestum Girard
630.1 n REPTILIA: SQUAMATA: SAURIA: PHRYNOSOMATIDAE PHRYNOSOMAMODESTUM Catalogue of American Amphibians and Reptiles. Whiting, M.J. and J.R. Dixon. 1996. Phrynosoma modestum. Phrynosoma modestum Girard Roundtail Homed Lizard Phrynosoma modesturn Girard, in Baird and Girard, 1852:69 (see Banta, 1971). Type-locality, "from the valley of the Rio Grande west of San Antonio .....and from between San Antonio and El Paso del Norte." Syntypes, National Mu- seum of Natural History (USNM) 164 (7 specimens), sub- Figure. Adult Phrynosoma modestum from Doha Ana County, adult male, adult male, and 5 adult females, USNM 165660, New Mexico. Photograph by Suzanne L. Collins, courtesy of an adult male, and Museum of Natural History, University The Center for North American Amphibians and Reptiles. of Illinois at Urbana-Champaign (UIMNH) 40746, an adult male, collected by J.H. lark in May or June 1851 (Axtell, 1988) (not examined by authors). See Remarks. Phrynosomaplatyrhynus: Hemck,Terry, and Hemck, 1899: 136. Doliosaurus modestus: Girard, 1858:409. Phrynosoma modestrum: Morafka, Adest, Reyes, Aguirre L., A(nota). modesta: Cope, 1896:834. and Lieberman, 1992:2 14. Lapsus. Content. No subspecies have been described. and Degenhardt et al. (1996). Habitat photographs appeared in Sherbrooke (1981) and Switak (1979). Definition. Phrynosoma modestum is the smallest horned liz- ard, with a maximum SVL of 66 mm in males and 71 mm in Distribution. Phrynosoma modestum occurs in southern and females (Fitch, 1981). It is the sister taxon to l? platyrhinos, western Texas, southern New Mexico, southeastern Arizona and and is part of the "northern radiation" (sensu Montanucci, 1987). north-central Mexico. -
Genetic Change and Rates of Cladogenesis
GENETIC CHANGE AND RATES OF CLADOGENESIS JOHN C. AVISE* AND FRANCISCO J. AYALA Depariment of Genetics, University of Californiu, Davis, California 95616 Manuscript received May 12, 1975 Revised copy received July 28, 1975 ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predic- tions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic dis- tance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. -
Lineages, Splits and Divergence Challenge Whether the Terms Anagenesis and Cladogenesis Are Necessary
Biological Journal of the Linnean Society, 2015, , – . With 2 figures. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary FELIX VAUX*, STEVEN A. TREWICK and MARY MORGAN-RICHARDS Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand Received 3 June 2015; revised 22 July 2015; accepted for publication 22 July 2015 Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage-splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage-splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage-splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. -
Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography of Rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus)
City University of New York (CUNY) CUNY Academic Works Publications and Research New York City College of Technology 2016 Diversity-dependent cladogenesis throughout western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) Christopher Blair CUNY New York City College of Technology Santiago Sánchez-Ramírez University of Toronto How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/ny_pubs/344 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] 1Blair, C., Sánchez-Ramírez, S., 2016. Diversity-dependent cladogenesis throughout 2 western Mexico: Evolutionary biogeography of rattlesnakes (Viperidae: Crotalinae: 3 Crotalus and Sistrurus ). Molecular Phylogenetics and Evolution 97, 145–154. 4 https://doi.org/10.1016/j.ympev.2015.12.020. © 2016. This manuscript version is made 5 available under the CC-BY-NC-ND 4.0 license. 6 7 8 Diversity-dependent cladogenesis throughout western Mexico: evolutionary 9 biogeography of rattlesnakes (Viperidae: Crotalinae: Crotalus and Sistrurus) 10 11 12 CHRISTOPHER BLAIR1*, SANTIAGO SÁNCHEZ-RAMÍREZ2,3,4 13 14 15 1Department of Biological Sciences, New York City College of Technology, Biology PhD 16 Program, Graduate Center, The City University of New York, 300 Jay Street, Brooklyn, 17 NY 11201, USA. 18 2Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks 19 Street, Toronto, ON, M5S 3B2, Canada. 20 3Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, 21 ON, M5S 2C6, Canada. 22 4Present address: Environmental Genomics Group, Max Planck Institute for 23 Evolutionary Biology, August-Thienemann-Str. -
Introduction; Environment & Review of Eyes in Different Species
The Biological Vision System: Introduction; Environment & Review of Eyes in Different Species James T. Fulton https://neuronresearch.net/vision/ Abstract: Keywords: Biological, Human, Vision, phylogeny, vitamin A, Electrolytic Theory of the Neuron, liquid crystal, Activa, anatomy, histology, cytology PROCESSES IN BIOLOGICAL VISION: including, ELECTROCHEMISTRY OF THE NEURON Introduction 1- 1 1 Introduction, Phylogeny & Generic Forms 1 “Vision is the process of discovering from images what is present in the world, and where it is” (Marr, 1985) ***When encountering a citation to a Section number in the following material, the first numeric is a chapter number. All cited chapters can be found at https://neuronresearch.net/vision/document.htm *** 1.1 Introduction While the material in this work is designed for the graduate student undertaking independent study of the vision sensory modality of the biological system, with a certain amount of mathematical sophistication on the part of the reader, the major emphasis is on specific models down to specific circuits used within the neuron. The Chapters are written to stand-alone as much as possible following the block diagram in Section 1.5. However, this requires frequent cross-references to other Chapters as the analyses proceed. The results can be followed by anyone with a college degree in Science. However, to replicate the (photon) Excitation/De-excitation Equation, a background in differential equations and integration-by-parts is required. Some background in semiconductor physics is necessary to understand how the active element within a neuron operates and the unique character of liquid-crystalline water (the backbone of the neural system). The level of sophistication in the animal vision system is quite remarkable.