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Phylogeny Classification Additional Readings Clupeomorpha and Ostariophysi
Teleostei - AccessScience from McGraw-Hill Education http://www.accessscience.com/content/teleostei/680400 (http://www.accessscience.com/) Article by: Boschung, Herbert Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama. Gardiner, Brian Linnean Society of London, Burlington House, Piccadilly, London, United Kingdom. Publication year: 2014 DOI: http://dx.doi.org/10.1036/1097-8542.680400 (http://dx.doi.org/10.1036/1097-8542.680400) Content Morphology Euteleostei Bibliography Phylogeny Classification Additional Readings Clupeomorpha and Ostariophysi The most recent group of actinopterygians (rayfin fishes), first appearing in the Upper Triassic (Fig. 1). About 26,840 species are contained within the Teleostei, accounting for more than half of all living vertebrates and over 96% of all living fishes. Teleosts comprise 517 families, of which 69 are extinct, leaving 448 extant families; of these, about 43% have no fossil record. See also: Actinopterygii (/content/actinopterygii/009100); Osteichthyes (/content/osteichthyes/478500) Fig. 1 Cladogram showing the relationships of the extant teleosts with the other extant actinopterygians. (J. S. Nelson, Fishes of the World, 4th ed., Wiley, New York, 2006) 1 of 9 10/7/2015 1:07 PM Teleostei - AccessScience from McGraw-Hill Education http://www.accessscience.com/content/teleostei/680400 Morphology Much of the evidence for teleost monophyly (evolving from a common ancestral form) and relationships comes from the caudal skeleton and concomitant acquisition of a homocercal tail (upper and lower lobes of the caudal fin are symmetrical). This type of tail primitively results from an ontogenetic fusion of centra (bodies of vertebrae) and the possession of paired bracing bones located bilaterally along the dorsal region of the caudal skeleton, derived ontogenetically from the neural arches (uroneurals) of the ural (tail) centra. -
1 Exon Probe Sets and Bioinformatics Pipelines for All Levels of Fish Phylogenomics
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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 Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics 2 3 Lily C. Hughes1,2,3,*, Guillermo Ortí1,3, Hadeel Saad1, Chenhong Li4, William T. White5, Carole 4 C. Baldwin3, Keith A. Crandall1,2, Dahiana Arcila3,6,7, and Ricardo Betancur-R.7 5 6 1 Department of Biological Sciences, George Washington University, Washington, D.C., U.S.A. 7 2 Computational Biology Institute, Milken Institute of Public Health, George Washington 8 University, Washington, D.C., U.S.A. 9 3 Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian 10 Institution, Washington, D.C., U.S.A. 11 4 College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China 12 5 CSIRO Australian National Fish Collection, National Research Collections of Australia, 13 Hobart, TAS, Australia 14 6 Sam Noble Oklahoma Museum of Natural History, Norman, O.K., U.S.A. 15 7 Department of Biology, University of Oklahoma, Norman, O.K., U.S.A. 16 17 *Corresponding author: Lily C. Hughes, [email protected]. 18 Current address: Department of Organismal Biology and Anatomy, University of Chicago, 19 Chicago, IL. 20 21 Keywords: Actinopterygii, Protein coding, Systematics, Phylogenetics, Evolution, Target 22 capture 23 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.18.949735; this version posted February 19, 2020. -
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly Dustin J. Wcisel North Carolina State University J. Thomas Howard North Carolina State University Jeffrey A. Yoder North Carolina State University Alex Dornburg ( [email protected] ) NC Museum of Natural Sciences https://orcid.org/0000-0003-0863-2283 Software Keywords: BUSCO ortholog assembly, Cetacean and teleost sh phylogeny, Missing Data Visualization, Transcriptome, Concatenated Alignment Posted Date: March 12th, 2020 DOI: https://doi.org/10.21203/rs.2.16269/v4 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at BMC Evolutionary Biology on March 30th, 2020. See the published version at https://doi.org/10.1186/s12862-020-01603-w. Page 1/18 Abstract Background Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to eciently identify orthologous sequences currently hinders effective harnessing of this resource. Results We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-dened acceptable missing data levels for a given research question. -
Copyrighted Material
Index INDEX Note: page numbers in italics refer to fi gures, those in bold refer to tables and boxes. abducens nerve 55 activity cycles 499–522 inhibition 485 absorption effi ciency 72 annual patterns 515, 516, 517–22 interactions 485–6 abyssal zone 393 circadian rhythms 505 prey 445 Acanthaster planci (Crown-of-Thorns Starfi sh) diel patterns 499, 500, 501–2, 503–4, reduction 484 579 504–7 aggressive mimicry 428, 432–3 Acanthocybium (Wahoo) 15 light-induced 499, 500, 501–2, 503–4, aggressive resemblance 425–6 Acanthodii 178, 179 505 aglomerular 52 Acanthomorpha 284–8, 289 lunar patterns 507–9 agnathans Acanthopterygii 291–325 seasonal 509–15 gills 59, 60 Atherinomorpha 293–6 semilunar patterns 507–9 osmoregulation 101, 102 characteristics 291–2 supra-annual patterns 515, 516, 517–22 phylogeny 202 distribution 349, 350 tidal patterns 506–7 ventilation 59, 60 jaws 291 see also migration see also hagfi shes; lampreys Mugilomorpha 292–3, 294 adaptive response 106 agnathous fi shes see jawless fi shes pelagic 405 adaptive zones 534 agonistic interactions 83–4, 485–8 Percomorpha 296–325 adenohypophysis 91, 92 chemically mediated 484 pharyngeal jaws 291 adenosine triphosphate (ATP) 57 sound production 461–2 phylogeny 292, 293, 294 adipose fi n 35 visual 479 spines 449, 450 adrenocorticotropic hormone (ACTH) 92 agricultural chemicals 605 Acanthothoraciformes 177 adrianichthyids 295 air breathing 60, 61–2, 62–4 acanthurids 318–19 adult fi shes 153, 154, 155–7 ammonia production 64, 100–1 Acanthuroidei 12, 318–19 death 156–7 amphibious 60 Acanthurus bahianus -
Evidence of Hidden Diversity and Taxonomic Conflicts in Five Stream Fishes from the Eastern Zimbabwe Highlands Freshwater Ecoregion
A peer-reviewed open-access journal ZooKeys 768: 69–95Evidence (2018) of hidden diversity and taxonomic conflicts in five stream fishes... 69 doi: 10.3897/zookeys.768.21944 RESEARCH ARTICLE http://zookeys.pensoft.net Launched to accelerate biodiversity research Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion Albert Chakona1,2, Wilbert T. Kadye2, Taurai Bere3, Daniel N. Mazungula1,2, Emmanuel Vreven4,5 1 South African Institute for Aquatic Biodiversity, Private Bag 1015, Grahamstown, South Africa, 6140 2 Department of Ichthyology and Fisheries Science, Rhodes University, P.O. Box 94, Grahamstown, South Africa, 6140 3 School of Wildlife, Ecology and Conservation, Chinhoyi University of Technology, P. Bag 7724, Chinhoyi, Zimbabwe 4 Royal Museum for Central Africa, Section of Vertebrates, Ichthyology, Leuvensesteenweg 13, 3080, Tervuren, Belgium 5 KU Leuven, Department of Biology, Laboratory of Biodiversity and Evolutio- nary Genomics, Deberiotstraat 32, 3000 Leuven, Belgium Corresponding author: Albert Chakona ([email protected]) Academic editor: N. Bogutskaya | Received 30 October 2018 | Accepted 25 April 2018 | Published 19 June 2018 http://zoobank.org/9621930C-8C43-40D0-8554-684035E99FAA Citation: Chakona A, Kadye WT, Bere T, Mazungula DN, Vreven E (2018) Evidence of hidden diversity and taxonomic conflicts in five stream fishes from the Eastern Zimbabwe Highlands freshwater ecoregion. ZooKeys 768: 69–95. https://doi.org/10.3897/zookeys.768.21944 Abstract -
Wild About Learning
WILD ABOUT LEARNING An Interdisciplinary Unit Fostering Discovery Learning Written on a 4th grade reading level, Wild Discoveries: Wacky New Animals, is perfect for every kid who loves wacky animals! With engaging full-color photos throughout, the book draws readers right into the animal action! Wild Discoveries features newly discovered species from around the world--such as the Shocking Pink Dragon and the Green Bomber. These wacky species are organized by region with fun facts about each one's amazing abilities and traits. The book concludes with a special section featuring new species discovered by kids! Heather L. Montgomery writes about science and nature for kids. Her subject matter ranges from snake tongues to snail poop. Heather is an award-winning teacher who uses yuck appeal to engage young minds. During a typical school visit, petrified parts and tree guts inspire reluctant writers and encourage scientific thinking. Heather has a B.S. in Biology and a M.S. in Environmental Education. When she is not writing, you can find her painting her face with mud at the McDowell Environmental Center where she is the Education Coordinator. Heather resides on the Tennessee/Alabama border. Learn more about her ten books at www.HeatherLMontgomery.com. Dear Teachers, Photo by Sonya Sones As I wrote Wild Discoveries: Wacky New Animals, I was astounded by how much I learned. As expected, I learned amazing facts about animals and the process of scientifically describing new species, but my knowledge also grew in subjects such as geography, math and language arts. I have developed this unit to share that learning growth with children. -
MAF Underwatermission Synopsis Final
Conceived by Max Serio Developed by Max Serio, John Hopkins, Martin Kase, Tina Dalton Directed by Max Serio, Tina Dalton Narrated by Rachel King, Juliet Jordan, Marcello Fabrizi Underwater Mission: Cleaner Friends First episode of the series. Our heroes: Sara,Maxi and Emma the sea turtle will explore who are their Cleaner Friends. Their adventure will be supported with the valuable information of "Sea Pad" their "friend-board computer". Cleaner Friends : Cleaner shrimp,moray eel,Blue Streak Cleaner Wrasse,Moorish Idols,Humphead Wrasse,Spadefish, sea star,Mushroom Coral,Bristletooths. Underwater Mission: Predators In this episode Sara and Max will experience an interesting trip with Emma the sea tur- tle. “Sea Pad” is going to show them the most interesting underwater predators and their habbits. Predators : Mooray eel (Ribbon eel, White eyed moray eel), Sand conger eel, Barracudas, Stonefish, Anglerfish, Lionfish, Mantis Shrimp, White tip reef shark, Tiger Shark Underwater Mission: Crazy Colours Maxi and Sara are going to visit the most colourful environment they have ever seen. Emma the sea turtle will take them to an underwater trip where they find the beautiful wolrd of crazy-coloured fish. Crazy-coloured fish : Gold Belly Damsel Fish, Emperor Angelfish, Yellow Ribbon Sweetlip, Peach Fairies, Anemones, Corals, Clown Trigger fish, Butterfly fish, Leopard coral trout, Scribbled Filefish, Lionfish, Cuttlefish, Nudibranch, Parrotfish Underwater Mission: Startling Shapes There are many shapes that the sea creatures and objects have. Emma, Sara and Maxi are going to discover as much of them as they can. Those they can’t spot on the first glance will be uncovered by the trusted clever “Sea pad”. -
Fish, Various Invertebrates
Zambezi Basin Wetlands Volume II : Chapters 7 - 11 - Contents i Back to links page CONTENTS VOLUME II Technical Reviews Page CHAPTER 7 : FRESHWATER FISHES .............................. 393 7.1 Introduction .................................................................... 393 7.2 The origin and zoogeography of Zambezian fishes ....... 393 7.3 Ichthyological regions of the Zambezi .......................... 404 7.4 Threats to biodiversity ................................................... 416 7.5 Wetlands of special interest .......................................... 432 7.6 Conservation and future directions ............................... 440 7.7 References ..................................................................... 443 TABLE 7.2: The fishes of the Zambezi River system .............. 449 APPENDIX 7.1 : Zambezi Delta Survey .................................. 461 CHAPTER 8 : FRESHWATER MOLLUSCS ................... 487 8.1 Introduction ................................................................. 487 8.2 Literature review ......................................................... 488 8.3 The Zambezi River basin ............................................ 489 8.4 The Molluscan fauna .................................................. 491 8.5 Biogeography ............................................................... 508 8.6 Biomphalaria, Bulinis and Schistosomiasis ................ 515 8.7 Conservation ................................................................ 516 8.8 Further investigations ................................................. -
Diverse Deep-Sea Anglerfishes Share a Genetically Reduced Luminous
RESEARCH ARTICLE Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment Lydia J Baker1*, Lindsay L Freed2, Cole G Easson2,3, Jose V Lopez2, Dante´ Fenolio4, Tracey T Sutton2, Spencer V Nyholm5, Tory A Hendry1* 1Department of Microbiology, Cornell University, New York, United States; 2Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States; 3Department of Biology, Middle Tennessee State University, Murfreesboro, United States; 4Center for Conservation and Research, San Antonio Zoo, San Antonio, United States; 5Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States Abstract Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and *For correspondence: that these bacteria have undergone extreme genome reduction although they are not vertically [email protected] (LJB); transmitted. -
The Origins and Evolution of Sleep Alex C
© 2018. Published by The Company of Biologists Ltd | Journal of Experimental Biology (2018) 221, jeb159533. doi:10.1242/jeb.159533 REVIEW The origins and evolution of sleep Alex C. Keene1,2,* and Erik R. Duboue1,3,* ABSTRACT times vary widely, ranging from less than 5 h to 10 h or more (Webb Sleep is nearly ubiquitous throughout the animal kingdom, yet little is and Agnew, 1970; Kronholm et al., 2006). Despite a widespread known about how ecological factors or perturbations to the appreciation for the diversity in sleep duration between and within environment shape the duration and timing of sleep. In diverse species, surprisingly little is known about the relationship between ’ animal taxa, poor sleep negatively impacts development, cognitive sleep and an animal s ecological and evolutionary history. abilities and longevity. In addition to mammals, sleep has been Large differences in sleep duration and timing among humans characterized in genetic model organisms, ranging from the suggests that existing genetic variation among individuals potently nematode worm to zebrafish, and, more recently, in emergent affects sleep (Hartmann, 1973; Kronholm et al., 2006; He et al., models with simplified nervous systems such as Aplysia and 2009). While many laboratory studies investigating the molecular jellyfish. In addition, evolutionary models ranging from fruit flies to mechanisms of sleep regulation have relied on highly inbred model cavefish have leveraged natural genetic variation to investigate the systems including mice, zebrafish and fruit flies, the study of sleep relationship between ecology and sleep. Here, we describe the in outbred populations has revealed that geographical location, contributions of classical and emergent genetic model systems to evolutionary history and naturally occurring genetic variation investigate mechanisms underlying sleep regulation. -
Lab 9 - an Introduction to Marine Fishes
Name ___________________________________ Lab 9 - An introduction to marine fishes NOTE: these taxonomic groups have many more species than those shown today; each specimen is but a representative of its particular family or order. PLEASE HANDLE SPECIMENS CAREFULLY!!!! Superclass Agnatha (jawless fishes; ~80 spp.) Class Myxini Order Myxiniformes Family Myxinidae; Hagfish (Myxine glutinosa) Class Cephalaspidomorphi Order Petromyzontiformes Family Petromyzontidae; Sea lamprey (Petromyzon marinus) 1) What are some key differences between Myxinids and Petromyzontids? Superclass Gnathostomata (jawed fishes) Class Chondrichthyes (cartilaginous fishes) Subclass Elasmobranchii (shark-like fishes; 800 spp) Order Squatiniformes; Angel shark (Squatina dumerili) Order Squaliformes; Spiny dogfish (Squalus acanthias) Order Rajiformes; Clearnose skate (Raja eglanteria), Guitarfish (Rhinobatos sp.) Subclass Holocephali (chimaeras; 30 spp) Order Chimaeriformes; Spotted chimaera (Hydrolagus colliei) 2) What are two features that clearly distinguish the order Rajiformes (skates) from sharks? 3) Where in the water column would you expect to find a chimaera? Why? Class Teleostomi (bony fishes) Superorder Clupeomorpha Order Clupeiformes Family Clupeidae; Atlantic herring (Clupea harengus), Menhaden (Brevoortia tyrannus) Family Engraulidae; Anchovy (Anchoa nasuta) 4) What characteristics most clearly separate these two families? 5) These fishes tend to travel in schools. What purpose might the silvery stripe down their sides serve? (Hint: think about this from -
Lepidocephalichthys Sp. (Pisces: Cobitidae)
International Journal of Fisheries and Aquatic Studies 2017; 5(2): 699-711 E-ISSN: 2347-5129 P-ISSN: 2394-0506 Lepidocephalichthys Sp. (Pisces: Cobitidae) - A (ICV-Poland) Impact Value: 5.62 (GIF) Impact Factor: 0.549 taxonomic appraisal, with special reference to IJFAS 2017; 5(2): 699-711 © 2017 IJFAS Lepidocephalichthys annandalei from Doon Valley, www.fisheriesjournal.com Received: 20-01-2017 Dehradun, Uttarakhand Accepted: 21-02-2017 Deepali Rana Deepali Rana and S K Gupta Department of Zoology, Uttaranchal College of Abstract Biomedical Sciences and The present communication deals with the taxonomic analysis and sexual dimorphic characters of Hospital, Sewla Khurd, Lepidocephalichthys guntea and Lepidocephalichthys annandalei. Teratological manifestation in L. Dehradun, Uttarakhand, India guntea, synonymies with reference to L. annandalei, anomalies regarding the number of barbels, mental lobes vs. barbels and variability with reference to origin of dorsal fin are the highlights discussed. Status S K Gupta of Lepidocephalus caudofurcatus (Tilak and Husain, 1977 a) is discussed in the light of the details Department of Zoology, D.B.S. studied for the present material identified as L. annandalei. The latter is established as a valid species and (PG), College, Dehradun, found synonymous to the former. While discussing the distributional aspects, L. annandalei appeared of Uttarakhand, India zoogeographical significance and a new addition to the fish fauna of Suswa River in Eastern Doon. Keywords: Lepidocephalichthys sp., systematics,