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Environmental DNA Reveals the Fine-Grained and Hierarchical
www.nature.com/scientificreports OPEN Environmental DNA reveals the fne‑grained and hierarchical spatial structure of kelp forest fsh communities Thomas Lamy 1,2*, Kathleen J. Pitz 3, Francisco P. Chavez3, Christie E. Yorke1 & Robert J. Miller1 Biodiversity is changing at an accelerating rate at both local and regional scales. Beta diversity, which quantifes species turnover between these two scales, is emerging as a key driver of ecosystem function that can inform spatial conservation. Yet measuring biodiversity remains a major challenge, especially in aquatic ecosystems. Decoding environmental DNA (eDNA) left behind by organisms ofers the possibility of detecting species sans direct observation, a Rosetta Stone for biodiversity. While eDNA has proven useful to illuminate diversity in aquatic ecosystems, its utility for measuring beta diversity over spatial scales small enough to be relevant to conservation purposes is poorly known. Here we tested how eDNA performs relative to underwater visual census (UVC) to evaluate beta diversity of marine communities. We paired UVC with 12S eDNA metabarcoding and used a spatially structured hierarchical sampling design to assess key spatial metrics of fsh communities on temperate rocky reefs in southern California. eDNA provided a more‑detailed picture of the main sources of spatial variation in both taxonomic richness and community turnover, which primarily arose due to strong species fltering within and among rocky reefs. As expected, eDNA detected more taxa at the regional scale (69 vs. 38) which accumulated quickly with space and plateaued at only ~ 11 samples. Conversely, the discovery rate of new taxa was slower with no sign of saturation for UVC. -
2019 Annual Marine Environmental Analysis and Interpretation Report
2019 ANNUAL MARINE ENVIRONMENTAL ANALYSIS AND INTERPRETATION San Onofre Nuclear Generating Station ANNUAL MARINE ENVIRONMENTAL ANALYSIS AND INTERPRETATION San Onofre Nuclear Generating Station July 2020 Page intentionally blank Report Preparation/Data Collection – Oceanography and Marine Biology MBC Aquatic Sciences 3000 Red Hill Avenue Costa Mesa, CA 92626 Page intentionally blank TABLE OF CONTENTS LIST OF FIGURES ........................................................................................................................... iii LIST OF TABLES ...............................................................................................................................v LIST OF APPENDICES ................................................................................................................... vi EXECUTIVE SUMMARY .............................................................................................................. vii CHAPTER 1 STUDY INTRODUCTION AND GENERATING STATION DESCRIPTION 1-1 INTRODUCTION ................................................................................................................... 1-1 PURPOSE OF SAMPLING ......................................................................................... 1-1 REPORT APPROACH AND ORGANIZATION ........................................................ 1-1 DESCRIPTION OF THE STUDY AREA ................................................................... 1-1 HISTORICAL BACKGROUND ........................................................................................... -
A List of Common and Scientific Names of Fishes from the United States And
t a AMERICAN FISHERIES SOCIETY QL 614 .A43 V.2 .A 4-3 AMERICAN FISHERIES SOCIETY Special Publication No. 2 A List of Common and Scientific Names of Fishes -^ ru from the United States m CD and Canada (SECOND EDITION) A/^Ssrf>* '-^\ —---^ Report of the Committee on Names of Fishes, Presented at the Ei^ty-ninth Annual Meeting, Clearwater, Florida, September 16-18, 1959 Reeve M. Bailey, Chairman Ernest A. Lachner, C. C. Lindsey, C. Richard Robins Phil M. Roedel, W. B. Scott, Loren P. Woods Ann Arbor, Michigan • 1960 Copies of this publication may be purchased for $1.00 each (paper cover) or $2.00 (cloth cover). Orders, accompanied by remittance payable to the American Fisheries Society, should be addressed to E. A. Seaman, Secretary-Treasurer, American Fisheries Society, Box 483, McLean, Virginia. Copyright 1960 American Fisheries Society Printed by Waverly Press, Inc. Baltimore, Maryland lutroduction This second list of the names of fishes of The shore fishes from Greenland, eastern the United States and Canada is not sim- Canada and the United States, and the ply a reprinting with corrections, but con- northern Gulf of Mexico to the mouth of stitutes a major revision and enlargement. the Rio Grande are included, but those The earlier list, published in 1948 as Special from Iceland, Bermuda, the Bahamas, Cuba Publication No. 1 of the American Fisheries and the other West Indian islands, and Society, has been widely used and has Mexico are excluded unless they occur also contributed substantially toward its goal of in the region covered. In the Pacific, the achieving uniformity and avoiding confusion area treated includes that part of the conti- in nomenclature. -
CALIFORNIA FISH and GAME “Journal for Conservation and Management of California’S Species and Ecosystems”
CALIFORNIA FISH AND GAME “Journal for Conservation and Management of California’s Species and Ecosystems” Volume 105 Fall 2019 Number 4 Lorraine Elrod © California Academy of Sciences Published Quarterly by the California Department of Fish and Wildlife STATE OF CALIFORNIA Gavin Newsom, Governor CALIFORNIA NATURAL RESOURCES AGENCY Wade Crowfoot, Secretary for Natural Resources FISH AND GAME COMMISSION Eric Sklar, President Jacque Hostler-Carmesin, Vice President Russell Burns, Member Peter S. Silva, Member Samantha Murray, Member Melissa Miller-Henson, Acting Executive Director DEPARTMENT OF FISH AND WILDLIFE Charlton “Chuck” Bonham, Director CALIFORNIA FISH AND GAME EDITORIAL STAFF Ange Darnell Baker ...........................................................................Editor-in-Chief Lorna Bernard ...........................Office of Communication, Education and Outreach Neil Clipperton, Scott Osborn, Laura Patterson, Joel Trumbo, Dan Skalos, and Karen Converse .................................................... Wildlife Branch Felipe La Luz ...................................................................................... Water Branch Jeff Rodzen, Jeff Weaver, and Ken Kundargi ................................. Fisheries Branch Cherilyn Burton ........................................... Habitat Conservation Planning Branch Kevin Fleming ...............................................Watershed Restoration Grants Branch Jeff Villepique, Steve Parmenter ............................................ Inland Deserts Region Paul Reilly, -
Blennioidei: Clinidae)
BULLETIN OF MARINE SCIENCE, 41(1): 45-58,1987 COLOR PATTERN AND HABITAT DIFFERENCES BETWEEN MALE, FEMALE AND JUVENILE GIANT KELPFISH (BLENNIOIDEI: CLINIDAE) Carol A. Stepien ABSTRACT The giant kelpfish, Heterostjehus ROSTRATUS occurs in three color morphs; red, brown, and green, which vary in shade according to number ofmelanophores. Color morphs were usually collected from plant habitats matching their colors. Frequencies of the color morphs were linked to sexual dimorphism; adult males are brown (infrequently olive green) and adult females exhibit all three morphs. Juveniles are either brown or green and not sexually di- morphic. In addition to color differences between the sexes, adult males and females display different melanin patterns. These patterns are apparently used for intraspecific communication and cryptic coloration. Brown males are distinguishable from brown females by their sexually dimorphic melanin patterns. Melanin patterns, unlike coloration, change (often rapidly) dur- ing courtship and territorial displays. Adult males and females occupy plant habitats that differ in depth, predominant color, and species composition. The brown males closely ap- proximate color of the plants where the nests they guard are found. Females occupy other habitats, including red algae, green surfgrass, and other species of brown algae. Females venture away from matching habitats during the spawning season to reach male territories. The giant kelpfish Heterostichus ROSTRATUS Girard is one of the largest members of the family Clinidae, reaching a total length of 41.2 cm (J. E. Fitch in Feder et aI., 1974). Ranging from British Columbia (Canada) to Cape San Lucas, Baja California (Mexico), it is most commonly encountered from Point Conception to central Baja California (Roedel, 1953). -
Assessment of Coastal Water Resources and Watershed Conditions at Channel Islands National Park, California
National Park Service U.S. Department of the Interior Technical Report NPS/NRWRD/NRTR-2006/354 Water Resources Division Natural Resource Program Center Natural Resource Program Centerent of the Interior ASSESSMENT OF COASTAL WATER RESOURCES AND WATERSHED CONDITIONS AT CHANNEL ISLANDS NATIONAL PARK, CALIFORNIA Dr. Diana L. Engle The National Park Service Water Resources Division is responsible for providing water resources management policy and guidelines, planning, technical assistance, training, and operational support to units of the National Park System. Program areas include water rights, water resources planning, marine resource management, regulatory guidance and review, hydrology, water quality, watershed management, watershed studies, and aquatic ecology. Technical Reports The National Park Service disseminates the results of biological, physical, and social research through the Natural Resources Technical Report Series. Natural resources inventories and monitoring activities, scientific literature reviews, bibliographies, and proceedings of technical workshops and conferences are also disseminated through this series. Mention of trade names or commercial products does not constitute endorsement or recommendation for use by the National Park Service. Copies of this report are available from the following: National Park Service (970) 225-3500 Water Resources Division 1201 Oak Ridge Drive, Suite 250 Fort Collins, CO 80525 National Park Service (303) 969-2130 Technical Information Center Denver Service Center P.O. Box 25287 Denver, CO 80225-0287 Cover photos: Top Left: Santa Cruz, Kristen Keteles Top Right: Brown Pelican, NPS photo Bottom Left: Red Abalone, NPS photo Bottom Left: Santa Rosa, Kristen Keteles Bottom Middle: Anacapa, Kristen Keteles Assessment of Coastal Water Resources and Watershed Conditions at Channel Islands National Park, California Dr. -
Bony Fish Classification
Reading Handout: Bony Fish Scientific Classification The information below shows the scientific classification of bony fishes that still exist today. KINGDOM Animalia PHYLUM Chordata SUBPHYLUM Vertebrata CLASS Actinopterygii (old name = Osteichthyes) Class Actinopterygii includes all the bony fishes that are ray-finned (vs. lobed-finned, Class Sarcopterygii). Bony fishes are ectothermic (cold-blooded) and are vertebrates (have a spine/backbone). Most bony fishes have scales, breathe with gills, have fins (lacking in some), and have a two-chambered heart. Most bony fishes lay eggs. Actinopterygians are the dominant class of vertebrates, comprising nearly 99% of the over 30,000 species of fishes. They are found in both freshwater and marine environments and from the deep sea to the highest mountain streams. Extant species can range in size from a minnow, at 8 mm (0.3 in), to the massive ocean sunfish, at 2,300 kg (5,070 lb), and the long-bodied oarfish, at 11 m (36 ft). INFRACLASS Teleostei Teleostei is one of three infraclasses in Class Actinopterygii, the ray-finned fishes. This diverse group, which arose in the Triassic period, includes 26,840 extant species in about 40 orders and 448 families; most living fishes are members of this group. ORDER (approximately 40) FAMILY (approximately 448) GENUS and SPECIES (approximately 26,840) Page 1 of 3 Some fishy facts: Did you know… the garibaldi is the California State Marine Fish and is protected by law? It is one of only a few species of damselfishes found in California and can be found from Monterey Bay to southern Baja California. -
61661147.Pdf
Resource Inventory of Marine and Estuarine Fishes of the West Coast and Alaska: A Checklist of North Pacific and Arctic Ocean Species from Baja California to the Alaska–Yukon Border OCS Study MMS 2005-030 and USGS/NBII 2005-001 Project Cooperation This research addressed an information need identified Milton S. Love by the USGS Western Fisheries Research Center and the Marine Science Institute University of California, Santa Barbara to the Department University of California of the Interior’s Minerals Management Service, Pacific Santa Barbara, CA 93106 OCS Region, Camarillo, California. The resource inventory [email protected] information was further supported by the USGS’s National www.id.ucsb.edu/lovelab Biological Information Infrastructure as part of its ongoing aquatic GAP project in Puget Sound, Washington. Catherine W. Mecklenburg T. Anthony Mecklenburg Report Availability Pt. Stephens Research Available for viewing and in PDF at: P. O. Box 210307 http://wfrc.usgs.gov Auke Bay, AK 99821 http://far.nbii.gov [email protected] http://www.id.ucsb.edu/lovelab Lyman K. Thorsteinson Printed copies available from: Western Fisheries Research Center Milton Love U. S. Geological Survey Marine Science Institute 6505 NE 65th St. University of California, Santa Barbara Seattle, WA 98115 Santa Barbara, CA 93106 [email protected] (805) 893-2935 June 2005 Lyman Thorsteinson Western Fisheries Research Center Much of the research was performed under a coopera- U. S. Geological Survey tive agreement between the USGS’s Western Fisheries -
Seasonal Fish and Invertebrate Communities in Three Northern
SEASONAL FISH AND INVERTEBRATE COMMUNITIES IN THREE NORTHERN CALIFORNIA ESTUARIES By Katherine Osborn A Thesis Presented to The Faculty of Humboldt State University In Partial Fulfillment of the Requirements for the Degree Master of Science in Natural Resources: Fisheries Committee Membership Dr. Timothy Mulligan, Committee Chair Dr. Andre Buchheister, Committee Member Dr. Darren Ward, Committee Member Dr. Frank Shaughnessy, Committee Member Dr. Alison O’Dowd, Graduate Coordinator December 2017 ABSTRACT SEASONAL FISH AND INVERTEBRATE COMMUNITIES IN THREE NORTHERN CALIFORNIA ESTUARIES Katherine Osborn The majority of Northern California estuaries are small, flooded, river valleys that are largely unstudied due to their small sizes and remote locations. Yet these estuaries serve as important nursery areas for many marine fish species including rockfish, flatfish, smelt, and herring, and they are vital to anadromous species such as Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (O. mykiss). I sampled the summer and winter fish and invertebrate communities of the Big, Mad, and Ten Mile river estuaries. Fish were sampled via beach seine or fyke net and invertebrates were sampled via benthic cores, June 2014-June 2016. This research is part of a larger suite of studies establishing baseline conditions in Northern California Marine Protected Areas (MPAs). Big and Ten Mile river estuaries in Mendocino County were designated as MPAs in 2012. The Mad River Estuary in Humboldt County was selected as a non-MPA site to investigate its potential as a reference estuary. In the Mad River Estuary, additional sampling was conducted and a diet study was carried out on the feeding habits of two benthic fishes: Pacific Staghorn Sculpin (Leptocottus armatus) and English Sole (Parophrys vetulus). -
California Kelp Forest Restoration
CALIFORNIA SCIENCE CONTENT STANDARDS, with language arts, mathematics and history-social science standards. The introduction to the California Science Content Standards defines the essential skills and knowledge in science that students are expected to acquire at each grade level in the State of California. The con- tent within each grade level or span is organized into strands. Science content strands for Grades K-5 are Earth Sciences, Life Sciences, Physical Sciences and Investigation and Experimentation. Science content strands are organized with a concentration for Grades 6-8 in Earth Science, grade 7 in Life Sciences, and Physical Sciences in grade 8. SCIENCE SKILLS: Observing: using all five senses: seeing, hearing, touching, smelling & tasting Classifying: identifying like and unlike objects, grouping into sets Measuring: using numbers to describe size, weight, quantity, volume or time Organizing: analyzing and interpreting data Inferring: drawing conclusions from data Predicting: forming hypotheses based on past observations and results Experimenting: identifying and controlling variables in testing hypotheses Deducing: deriving a conclusion from something known or assumed Communicating: verbal, written, or other methods of informing others about results C a l i f o r n i a K e l p and conclusions Forests Restoration Project First Edition 2006 © D a w n N . E r i c s o n Activities and Projects P u b l i s h e r providing science skills are indicated with this “seal” of approval. Manta Publications www.mantapublications.com The study of kelp and the kelp forest offers a unique opportunity to understand vital science concepts while having fun learning about our own unique California environment. -
Annotated Checklist of Fishes from Monterey Bay National Marine Sanctuary with Notes on Extralimital Species
ISSN 1313-2970 (online) ISSN 1313-2989 (print) A peer-reviewed open-access journal ZooKeys 887 2019 Launched to accelerate biodiversity research Monterey Bay National Marine Sanctuary (MBNMS), a federal marine protected area located off central California, is host to a diverse fish fauna occupying a variety of habitats. The rich history of ichthyological research and surveys off central California provide a wealth of information to ANNOTATED CHECKLIST OF construct the first inventory of fishes occurring within MBNMS. FISHES FROM MONTEREY BAY Critical analyses of material from ichthyological collections at natural NATIONAL MARINE SANCTUARY history museums, the literature, and visual records were critical in creating WITH NOTES ON an annotated checklist of fishes occurring within MBNMS. The checklist EXTRALIMITAL SPECIES presented herein provides sources of basis, occurrence of fishes during cold- or warm-water events, records of historically occurring fishes, special BY places of occurrence (i.e., Davidson Seamount, Elkhorn Slough), introduced ERICA J. BURTON, RObeRT N. LEA species, and reference to original species descriptions from within MBNMS. Geographical errors in the literature based on misidentifications in the field are noted. This inventory provides evidence of occurrence for 507 fishes within MBNMS and an additional 18 species considered to be extralimital. This annotated checklist of fishes can be used by those interested in zoogeography, marine protected areas, ichthyology, regional natural history, and sanctuary management. ZooKeys 887 2019 http://zookeys.pensoft.net Special Issue ! http://zookeys.pensoft.net AUTHOR GUIDELINES Accepted Papers: Same as above, but are not limited to: Authors are kindly requested to sub- but ‘’In press’’ appears instead the • Zoobank (www.zoobank.org), mit their manuscript only through page numbers. -
Supplementary Information to “Environmental DNA Reveals the Fine-Grained and Hierarchical Spatial Structure of Kelp Forest Fish Communities”
Supplementary Information to “Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities”. Thomas Lamy, Kathleen J. Pitz, Francisco P. Chavez, Christie E. Yorke and Robert J. Miller. Table SM1. List of the 38 taxa detected using Underwater Visual Census (UVC). For each taxon we indicate its relative biomass (%) and total number of individuals (N) observed across all surveyed transects (N = 27). When a taxon was also detected using eDNA metabarcoding, the corresponding taxonomic level (eDNA) and the number of reads across all samples (Reads) are provided. For instance, nine taxa of rockfishes (Sebastes spp.) were lumped at the genus level to match detection of the genus Sebastes using eDNA metabarcoding. eDNA metabarcoding detected 3,220 sequence reads of Sebastes spp. across all samples. “No reference” indicates the absence of reference sequences in GenBank. 1No reference at the species level; 2eDNA sequence found but only 4 reads; 3303 reads but merged at the genus level; 4no reference at the species and genus level; 5eDNA sequence found but only 3 reads. Order Family Taxa % N eDNA Reads Perciformes Clinidae Gibbonsia spp. (Crevice Kelpfish) 0.054 8 Species 3179 Perciformes Embiotocidae Brachyistius frenatus (Kelp Surfperch) 0.034 13 Species 2581 Perciformes Embiotocidae Embiotoca jacksoni (Black Surfperch) 8.010 71 Species 23895 Perciformes Embiotocidae Rhacochilus vacca (Pile Surfperch) 0.883 9 Species 3076 Perciformes Kyphosidae Medialuna californiensis (Halfmoon) 7.164 15 Species