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Smith and De Leo Barkley Canyon Bone
Biodiversity, connectivity and ecosystem function in organic-rich whale-bone and wood- fall habitats in Barkley Canyon PIs Craig R. Smith1 and Fabio De Leo2 1University of Hawaii at Manoa, 2ONC Background: Organic-rich habitat islands support specialized communities throughout natural ecosystems and often play fundamental roles in maintaining alpha and beta diversity, thus facilitating adaptive radiation and evolutionary novelty. In the deep sea, whale-bone and wood falls occur widely and may contribute fundamentally to biodiversity and evolutionary novelty; nonetheless, large-scale patterns of biodiversity, connectivity and ecosystem function in these organic-rich metacommunies remain essentially unexplored. We propose to deploy whale bones and wood in Barkley Canyon at ONC POD3 as part of a novel comparative experimental approach, in which bone and wood substrates are being used to evaluate bathymetric, regional and inter-basin variations in biodiversity and connectivity, as well as interactions between biodiversity and ecosystem function, in whale-bone and wood- fall habitats at the deep-sea floor. The experiments in Barkley Canyon will test fundamental hypotheses concerning biodiversity and biogeography of resource-rich habitats in energy- and oxygen-limited deep-sea environments, and explore the utility of whale-bone and wood falls as model experimental systems to address patterns of connectivity and decomposer function in the deep sea. General Study Design: Two packages of humpback (Megaptera novaeangliae) ribs, and two blocks of Douglas Fir (Pseudotsuga menziesii), will be deployed by ROV on the seafloor at 890- m depth in Barkley Canyon, within view of the POD3 Video Camera (Fig. 1). After deployment, video monitoring of the bone/wood packages will occur every three hours for 5 minutes, with a different experimental package monitored during each 3-h interval; thus, each package will be monitored for two 5-minute periods per day. -
Editorial Submitting an Article
Journal of Natural Science Collections 2015: Volume 2 Editorial Welcome to the second Volume of the Journal The articles presented here aim to provide guid- of Natural Science Collections : a Journal for ance for working with natural science collec- you who work with natural science collections tions. If colleagues are wanting to undertake everyday. I hope that the articles in this Volume specific conservation work on areas in their prove to be interesting, and useful for all. collection, and are unsure as where to begin, please do contact one of the NatSCA commit- There are a large variety of topics covered in tee who will be able to advise. this Volume. The first article examines proto- cols for destructive sampling in natural history All the articles from Volume 1 are now available specimens, providing a nice case study and for free to view on the NatSCA website destructive sampling forms for researchers that (www.natsca.org). Please also have a look at can be adapted for your own institution. A pa- the NatSCA blog, which has more informal write per examines the fascinating natural history ups of views, book reviews and conferences displays of old and new, with surprising results. (http://naturalsciencecollections.wordpress.com/). An interesting article can assist with the mu- seum curators decision to lend specimens for I am very excited about the NatSCA 2015 con- research, where the article examines whether ference and AGM. The theme is all about how Micro-CT scanning affects DNA in specimens. we use traditional and social media to talk Conservators share their methods of cleaning a about our collections. -
Mitochondrial Genomes of Two Polydora
www.nature.com/scientificreports OPEN Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved Lingtong Ye1*, Tuo Yao1, Jie Lu1, Jingzhe Jiang1 & Changming Bai2 Contrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identifed an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identifed sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures. Abbreviations NCR Non-coding region PCG Protein-coding gene Metazoan mitochondrial genomes (mitogenomes) usually encode the set of 37 genes, comprising 2 rRNAs, 22 tRNAs, and 13 proteins, encoded on both genomic strands. -
The Potent Respiratory System of Osedax Mucofloris (Siboglinidae, Annelida) - a Prerequisite for the Origin of Bone-Eating Osedax?
The Potent Respiratory System of Osedax mucofloris (Siboglinidae, Annelida) - A Prerequisite for the Origin of Bone-Eating Osedax? Randi S. Huusgaard1, Bent Vismann1, Michael Ku¨ hl1,2, Martin Macnaugton1, Veronica Colmander1, Greg W. Rouse3, Adrian G. Glover4, Thomas Dahlgren5, Katrine Worsaae1* 1 Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark, 2 Plant Functional Biology and Climate Change Cluster, Department of Environmental Science, University of Technology Sydney, Sydney, Australia, 3 Scripps Institution of Oceanography, University of California San Diego, San Diego, California, United States of America, 4 Zoology Department, The Natural History Museum, London, United Kingdom, 5 Uni Environment/Uni Research, Bergen, Norway Abstract Members of the conspicuous bone-eating genus, Osedax, are widely distributed on whale falls in the Pacific and Atlantic Oceans. These gutless annelids contain endosymbiotic heterotrophic bacteria in a branching root system embedded in the bones of vertebrates, whereas a trunk and anterior palps extend into the surrounding water. The unique life style within a bone environment is challenged by the high bacterial activity on, and within, the bone matrix possibly causing O2 depletion, and build-up of potentially toxic sulphide. We measured the O2 distribution around embedded Osedax and showed that the bone microenvironment is anoxic. Morphological studies showed that ventilation mechanisms in Osedax are restricted to the anterior palps, which are optimized for high O2 uptake by possessing a large surface area, large surface to volume ratio, and short diffusion distances. The blood vascular system comprises large vessels in the trunk, which facilitate an ample supply of oxygenated blood from the anterior crown to a highly vascularised root structure. -
Animal Phylum Poster Porifera
Phylum PORIFERA CNIDARIA PLATYHELMINTHES ANNELIDA MOLLUSCA ECHINODERMATA ARTHROPODA CHORDATA Hexactinellida -- glass (siliceous) Anthozoa -- corals and sea Turbellaria -- free-living or symbiotic Polychaetes -- segmented Gastopods -- snails and slugs Asteroidea -- starfish Trilobitomorpha -- tribolites (extinct) Urochordata -- tunicates Groups sponges anemones flatworms (Dugusia) bristleworms Bivalves -- clams, scallops, mussels Echinoidea -- sea urchins, sand Chelicerata Cephalochordata -- lancelets (organisms studied in detail in Demospongia -- spongin or Hydrazoa -- hydras, some corals Trematoda -- flukes (parasitic) Oligochaetes -- earthworms (Lumbricus) Cephalopods -- squid, octopus, dollars Arachnida -- spiders, scorpions Mixini -- hagfish siliceous sponges Xiphosura -- horseshoe crabs Bio1AL are underlined) Cubozoa -- box jellyfish, sea wasps Cestoda -- tapeworms (parasitic) Hirudinea -- leeches nautilus Holothuroidea -- sea cucumbers Petromyzontida -- lamprey Mandibulata Calcarea -- calcareous sponges Scyphozoa -- jellyfish, sea nettles Monogenea -- parasitic flatworms Polyplacophora -- chitons Ophiuroidea -- brittle stars Chondrichtyes -- sharks, skates Crustacea -- crustaceans (shrimp, crayfish Scleropongiae -- coralline or Crinoidea -- sea lily, feather stars Actinipterygia -- ray-finned fish tropical reef sponges Hexapoda -- insects (cockroach, fruit fly) Sarcopterygia -- lobed-finned fish Myriapoda Amphibia (frog, newt) Chilopoda -- centipedes Diplopoda -- millipedes Reptilia (snake, turtle) Aves (chicken, hummingbird) Mammalia -
BIOSC 041 Overview of Animal Diversity: Animal Body Plans
BIOSC 041 Overview of Animal Diversity: Animal Body Plans Reference: Chapter 32 Outline v Definition and major characteristics of animals v Dividing animals into groups based on: § Body symmetry § Tissues § Type of body cavity § Protostome vs deuterostome development v Animal Phylogeny What is an Animal? v Scientists have identified 1.3 million living species of animals v The definition of an animal § Multicellular § Heterotrophic eukaryotes § Possess tissues that develop from embryonic layers v Common characteristics describe the group 1. Common mode of nutrition 2. Cell structure and specialization 3. Reproduction and development 1. Characteristics of Animals: Nutrition v Animals are heterotrophs (“other-eater”) § Obtain nutrition either from other living organisms or from nonliving organic material § Primary consumers (herbivores), secondary consumers (eat herbivores), tertiary consumers (eat carnivores), and/or detritovores (eat detritus- decaying plants/ animals, feces) 2. Characteristics of Animals: Cell Structure and Specialization 1. Animals are multicellular eukaryotes (Note: single-celled eukaryotes with animal-like behavior are grouped as Protists, such as amoeba) 2. Animal cells lack cell walls 3. Bodies are held together by structural proteins like collagen 4. Bodies are organized into tissues, organs, and organ systems § Tissues are groups of cells that have a common structure, and/or function § Nervous tissue and muscle tissue are unique to animals Amoeba: a protist, not a true animal 3. Characteristics of Animals: Reproduction and Development v Most animals reproduce sexually, with the diploid stage dominating the life cycle v Development occurs in specific stages 1. Fertilization to form zygote 2. Zygote undergoes rapid cell division called cleavage 3. Cleavage leads to formation of a multicellular, hollow blastula (ex: whitefish blastula slides from lab, with cells undergoing rapid mitosis) 4. -
Analysis of the Complete Mitochondrial DNA Sequence of the Brachiopod Terebratulina Retusa Places Brachiopoda Within the Protostomes
See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/12415870 Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes Article in Proceedings of the Royal Society B: Biological Sciences · November 1999 DOI: 10.1098/rspb.1999.0885 · Source: PubMed CITATIONS READS 83 50 2 authors, including: Martin Schlegel University of Leipzig 151 PUBLICATIONS 2,931 CITATIONS SEE PROFILE Some of the authors of this publication are also working on these related projects: Rare for a reason? Scale-dependence of factors influencing rarity and diversity of xylobiont beetles View project Bat diversity and vertical niche activity in the fluvial flood forest Leipzig View project All content following this page was uploaded by Martin Schlegel on 22 May 2014. The user has requested enhancement of the downloaded file. Analysis of the complete mitochondrial DNA sequence of the brachiopod Terebratulina retusa places Brachiopoda within the protostomes Alexandra Stechmann* and Martin Schlegel UniversitÌt Leipzig, Institut fÏr Zoologie/Spezielle Zoologie,Talstr. 33, 04103 Leipzig, Germany Brachiopod phylogeny is still a controversial subject. Analyses using nuclear 18SrRNA and mitochondrial 12SrDNA sequences place them within the protostomes but some recent interpretations of morphological data support a relationship with deuterostomes. In order to investigate brachiopod a¤nities within the metazoa further,we compared the gene arrangement on the brachiopod mitochondrial genome with several metazoan taxa. The complete (15 451bp) mitochondrial DNA (mtDNA) sequence of the articulate brachiopod Terebratulina retusa was determined from two overlapping long polymerase chain reaction products. All the genes are encoded on the same strand and gene order comparisons showed that only one major rearrangement is required to interconvert the T.retusa and Katharina tunicata (Mollusca: Polyplaco- phora) mitochondrial genomes. -
Information to Users
INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter ^ce, while others may t>e from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy subm itted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will t>e noted. Also, if unauthorized copyright material had to t>e removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, t>eginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Photographs included in ttie original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black arxt white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. Bell & Howell Information and Learning 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA 800-521-0600 UMI* Phylogeny of Vestimentiferan Tube Worms by Anja Schulze Diplom, University of Bielefeld, 1995 A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY in the Department of Biology We accept this dissertation as conforming to the required standard Dr. -
Phylogenomics of Tubeworms (Siboglinidae, Annelida) and Comparative Performance of Different Reconstruction Methods
Zoologica Scripta Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods YUANNING LI,KEVIN M. KOCOT,NATHAN V. WHELAN,SCOTT R. SANTOS,DAMIEN S. WAITS, DANIEL J. THORNHILL &KENNETH M. HALANYCH Submitted: 28 January 2016 Li, Y., Kocot, K.M., Whelan, N.V., Santos, S.R., Waits, D.S., Thornhill, D.J. & Halanych, Accepted: 18 June 2016 K.M. (2016). Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative perfor- doi:10.1111/zsc.12201 mance of different reconstruction methods. —Zoologica Scripta, 00: 000–000. Deep-sea tubeworms (Annelida, Siboglinidae) represent dominant species in deep-sea chemosynthetic communities (e.g. hydrothermal vents and cold methane seeps) and occur in muddy sediments and organic falls. Siboglinids lack a functional digestive tract as adults, and they rely on endosymbiotic bacteria for energy, making them of evolutionary and physi- ological interest. Despite their importance, inferred evolutionary history of this group has been inconsistent among studies based on different molecular markers. In particular, place- ment of bone-eating Osedax worms has been unclear in part because of their distinctive biol- ogy, including harbouring heterotrophic bacteria as endosymbionts, displaying extreme sexual dimorphism and exhibiting a distinct body plan. Here, we reconstructed siboglinid evolutionary history using 12 newly sequenced transcriptomes. We parsed data into three data sets that accommodated varying levels of missing data, and we evaluate effects of miss- ing data on phylogenomic inference. Additionally, several multispecies-coalescent approaches and Bayesian concordance analysis (BCA) were employed to allow for a compar- ison of results to a supermatrix approach. Every analysis conducted herein strongly sup- ported Osedax being most closely related to the Vestimentifera and Sclerolinum clade, rather than Frenulata, as previously reported. -
Tropical Marine Invertebrates CAS BI 569 Phylum ANNELIDA by J
Tropical Marine Invertebrates CAS BI 569 Phylum ANNELIDA by J. R. Finnerty Phylum ANNELIDA Porifera Ctenophora Cnidaria Deuterostomia Ecdysozoa Lophotrochozoa Chordata Arthropoda Annelida Hemichordata Onychophora Mollusca Echinodermata Nematoda Platyhelminthes Acoelomorpha Silicispongiae Calcispongia PROTOSTOMIA “BILATERIA” (=TRIPLOBLASTICA) Bilateral symmetry (?) Mesoderm (triploblasty) Phylum ANNELIDA Porifera Ctenophora Cnidaria Deuterostomia Ecdysozoa Lophotrochozoa Chordata Arthropoda Annelida Hemichordata Onychophora Mollusca Echinodermata Nematoda Platyhelminthes Acoelomorpha Silicispongiae Calcispongia PROTOSTOMIA “COELOMATA” True coelom Coelomata gut cavity endoderm mesoderm coelom ectoderm [note: dorso-ventral inversion] Phylum ANNELIDA Porifera Ctenophora Cnidaria Deuterostomia Ecdysozoa Lophotrochozoa Chordata Arthropoda Annelida Hemichordata Onychophora Mollusca Echinodermata Nematoda Platyhelminthes Acoelomorpha Silicispongiae Calcispongia PROTOSTOMIA PROTOSTOMIA “first mouth” blastopore contributes to mouth ventral nerve cord The Blastopore ! Forms during gastrulation ectoderm blastocoel blastocoel endoderm gut blastoderm BLASTULA blastopore The Gut “internal, epithelium-lined cavity for the digestion and absorption of food sponges lack a gut simplest gut = blind sac (Cnidaria) blastopore gives rise to dual- function mouth/anus through-guts evolve later Protostome = blastopore contributes to the mouth Deuterostome = blastopore becomes the anus; mouth is a second opening Protostomy blastopore mouth anus Deuterostomy blastopore -
Evolutionary Crossroads in Developmental Biology: Cyclostomes (Lamprey and Hagfish) Sebastian M
PRIMER SERIES PRIMER 2091 Development 139, 2091-2099 (2012) doi:10.1242/dev.074716 © 2012. Published by The Company of Biologists Ltd Evolutionary crossroads in developmental biology: cyclostomes (lamprey and hagfish) Sebastian M. Shimeld1,* and Phillip C. J. Donoghue2 Summary and is appealing because it implies a gradual assembly of vertebrate Lampreys and hagfish, which together are known as the characters, and supports the hagfish and lampreys as experimental cyclostomes or ‘agnathans’, are the only surviving lineages of models for distinct craniate and vertebrate evolutionary grades (i.e. jawless fish. They diverged early in vertebrate evolution, perceived ‘stages’ in evolution). However, only comparative before the origin of the hinged jaws that are characteristic of morphology provides support for this phylogenetic hypothesis. The gnathostome (jawed) vertebrates and before the evolution of competing hypothesis, which unites lampreys and hagfish as sister paired appendages. However, they do share numerous taxa in the clade Cyclostomata, thus equally related to characteristics with jawed vertebrates. Studies of cyclostome gnathostomes, has enjoyed unequivocal support from phylogenetic development can thus help us to understand when, and how, analyses of protein-coding sequence data (e.g. Delarbre et al., 2002; key aspects of the vertebrate body evolved. Here, we Furlong and Holland, 2002; Kuraku et al., 1999). Support for summarise the development of cyclostomes, highlighting the cyclostome theory is now overwhelming, with the recognition of key species studied and experimental methods available. We novel families of non-coding microRNAs that are shared then discuss how studies of cyclostomes have provided exclusively by hagfish and lampreys (Heimberg et al., 2010). -
Phylum Porifera
790 Chapter 28 | Invertebrates updated as new information is collected about the organisms of each phylum. 28.1 | Phylum Porifera By the end of this section, you will be able to do the following: • Describe the organizational features of the simplest multicellular organisms • Explain the various body forms and bodily functions of sponges As we have seen, the vast majority of invertebrate animals do not possess a defined bony vertebral endoskeleton, or a bony cranium. However, one of the most ancestral groups of deuterostome invertebrates, the Echinodermata, do produce tiny skeletal “bones” called ossicles that make up a true endoskeleton, or internal skeleton, covered by an epidermis. We will start our investigation with the simplest of all the invertebrates—animals sometimes classified within the clade Parazoa (“beside the animals”). This clade currently includes only the phylum Placozoa (containing a single species, Trichoplax adhaerens), and the phylum Porifera, containing the more familiar sponges (Figure 28.2). The split between the Parazoa and the Eumetazoa (all animal clades above Parazoa) likely took place over a billion years ago. We should reiterate here that the Porifera do not possess “true” tissues that are embryologically homologous to those of all other derived animal groups such as the insects and mammals. This is because they do not create a true gastrula during embryogenesis, and as a result do not produce a true endoderm or ectoderm. But even though they are not considered to have true tissues, they do have specialized cells that perform specific functions like tissues (for example, the external “pinacoderm” of a sponge acts like our epidermis).