21948
AFSC/RACE/EcoFOCI: NPRB_1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically important fish species and selected invertebrates in the northeast Pacif
AFSC/RACE/EcoFOCI: NPRB 1220:Mitochondrial DNA-based identification of eggs, larvae and dietary components of commercially and ecologically im
Data Set
Published / External
22352
Recruitment Processes Program
Project
Completed
Accurate identification of various life history stages and prey items of marine fishes and invertebrates is central for understanding distribution,abundance, trophic ecology, and biodiversity of these species. Taxonomic approaches have been successfully applied to ichthyoplankton identification and diet analysis efforts for many years. Identification to the species level requires varying degrees of taxonomic expertise. and diagnostic characters for eggs or larvae in some species have not been elucidated.
In the current dataset we assembled a mitochondrial DNA (mtDNA) database for which
used standard laboratory protocols (restriction fragment length polymorphism
and Sanger DNA sequencing) to accurately identify any life history stages of selected fish and
shrimp species, with special emphasis on those species that have been difficult or impossible
to identify by conventional taxonomic means. Fish and shrimp specimens were collected between 2010 - 2013.
We developed a restriction fragment length polymorphism (RFLP)protocol, based upon mitochondrial DNA sequences
to distinguish between Pacific halibut and Greenland halibut, but were unable to develop one to discriminate
between Bering flounder and flathead sole. We used direct Sanger sequencing of mitochondrial DNA for species
identification of 32 species of sculpin and four species of caridean shrimp. PCR products from fish and shrimp
samples were sequenced using an ABI 3730 automated sequencer (Applied Biosystems, Inc). DNA sequences from museum
voucher specimens were compared with entries in the public databases for those species. Sequences from voucher
specimens have greater taxonomic authority for use in species identification than those without vouchers,
adding greater confidence to species identifications based upon our data.
To develop cost effective molecular protocols for accurate identification of flatfish eggs, larvae and digested prey remains of sculpins and caridean marine shrimps.
Loaded by FGDC Metadata Uploader, batch 5028, 07-18-2014 14:16
The following FGDC sections are not currently supported in InPort, but were preserved and will be included in the FGDC export:
- Taxonomy (FGDC:taxonomy)
- Entity Attribute Information (FGDC:eainfo)
Theme
ISO 19115 Topic Category
biota
Theme
PARR Exclusion
Non-Federal Funding
Theme
DNA barcoding
Theme
ND1
Theme
control region
Theme
cytochrome b
Theme
cytochrome oxidase
Theme
gut contents
Theme
mitochondrial DNA
Theme
species identification
Spatial
Alaska
Spatial
Bering Sea
Spatial
Chuckchi Sea
Spatial
Oregon State
Spatial
Puget Sound
Spatial
Washington State
Alaska Fisheries Science Center
Seattle
WA
USA
Data Set
Database
None Planned
Table (digital)
N/A
N/A
N/A
Data Steward
2015
Person
Canino, Michael F
mike.canino@noaa.gov
206 526 4108
email
Distributor
2014-07-18
Person
Canino, Michael F
mike.canino@noaa.gov
206 526 4108
Metadata Contact
2014-07-18
Person
MC, Metadata Coordinators
AFSC.metadata@noaa.gov
Originator
2014-07-18
Person
Canino, Michael F
mike.canino@noaa.gov
206 526 4108
Originator
2014-07-18
Organization
Alaska Fisheries Science Center
AFSC
afsc.webmaster@noaa.gov
7600 Sand Point Way N.E., Building 4
Seattle
WA
98115
USA
(206) 526-4000
(206) 526-4004
https://www.fisheries.noaa.gov/about/alaska-fisheries-science-center
AKFSC Home Page
Online Resource
0700-1700 Pacific Time
Point of Contact
2014-07-18
Person
Canino, Michael F
mike.canino@noaa.gov
206 526 4108
Ground Condition
-178.46
-120.1
71.5
42.42
Chukchi Sea, Bering Sea, Gulf of Alaska, northeastern Pacific Ocean, Washington State, Puget Sound, Oregon State
Range
2000
2013
Unclassified
Contact Distributor
Contact Distributor
There are no legal restrictions on access to the data. They reside in public
domain and can be freely distributed.
User must read and fully comprehend the metadata prior to use. Applications or
inferences derived from the data should be carefully considered for accuracy.
Acknowledgementof NOAA/NMFS/AFSC, as the source from which these data were obtained in
any publications and/or other representations of these, data is suggested.
none
none
http://ncei.noaa.gov
FAS files can bge worked in any simple text editor such as notepad, MS Word 2012
Molecular size standards and restriction maps
Base calls with PHRED scores less than 19 were omitted from analysis. Novel
mutations were verified by sequencing DNA segments in both directions.
See Abstract.
No
Unknown
No
No
unknown
To Be Determined
unknown
unknown
unknown
gov.noaa.nmfs.inport:21948
Nancy Roberson
2014-07-18T14:16:50
SysAdmin InPortAdmin
2024-01-15T12:08:04
2016-05-18
Alaska Fisheries Science Center
AFSC
7600 Sand Point Way N.E., Building 4
Seattle
WA
98115
USA
http://www.afsc.noaa.gov
0700-1700 Pacific Time
1001
Public
No
2016-05-18
1 Year
2017-05-18
None
multiple species
U.S. Department of Agriculture - Agricultural Research Service (ARS)
U.S. Department of Agriculture - Natural Resources Conservation Service (NRCS) Department of the Interior - U.S. Geological Survey Department of Commerce - National Oceanic and Atmospheric Administration (NOAA) Environmental Protection Agency (EPA) Smithsonian Institution - National Museum of Natural History (NMNH)
2013
Integrated Taxonomic Information System (ITIS)
database
http://www.itis.gov
using the scintific name of ther species search the database
Kingdom
Animalia
Animal
animaux
animals
Subkingdom
Bilateria
Infrakingdom
Protostomia
Superphylum
Ecdysozoa
Phylum
Arthropoda
Artropode
arthropodes
arthropods
Subphylum
Crustacea
crustaces
crustaceo
crustaceans
Class
Malacostraca
Subclass
Eumalacostraca
Superorder
Eucarida
camarao
caranguejo
ermitao
lagosta
siri
Order
Decapoda
crabs
crayfishes
lobsters
prawns
shrimp
crabes
crevettes
ecrevisses
homards
Suborder
Pleocyemata
Infraorder
Caridea
Superfamily
Alpheoidea
Family
Hippolytidae
Genus
Spirontocaris
Species
Spirontocaris phippsii
punctate blade shrimp
Species
Spirontocaris murdochi
Murdoch blade shrimp
Species
Spirontocaris arcuata
Rathbun blade shrimp
Species
Spirontocaris spinus
parrot shrimp
Superfamily
Crangonoidea
Family
Crangonidae
Genus
Crangon
Species
Crangon septemspinosa
sand shrimp
sevenspine bay shrimp
Species
Crangon dalli
ridged crangon
Species
Crangon franciscorum
California bay shrimp
California shrimp
Subspecies
Crangon franciscorum
angustimana
Genus
Neocrangon
Species
Neocrangon communis
gray shrimp
grey shrimp
twospine crangon
Infrakingdom
Deuterostomia
Phylum
Chordata
cordes
cordado
chordates
Subphylum
Vertebrata
vertebrado
vertebres
vertebrates
Infraphylum
Gnathostomata
Superclass
Osteichthyes
bony fishes
poissons osseux
osteiceto
peixe osseo
Class
Actinopterygii
ray-finned fishes
spiny rayed fishes
poisson epineux
poissons a nageoires rayonnees
Subclass
Neopterygii
neopterygians
Infraclass
Teleostei
Superorder
Acanthopterygii
Order
Scorpaeniformes
chabots
rascasses
mail-cheeked fishes
scorpion fishes
sculpins
Suborder
Cottoidei
sculpins
chabots
Superfamily
Cottoidea
Family
Cottidae
sculpins
bullheads
scaleless sculpins
chabots de mer
scorpions de mer
chabots
charrascos espinosos
Genus
Icelus
Species
Icelus canaliculatus
blacknose sculpin
Species
Icelus euryops
wide-eye sculpin
Species
Icelus spatula
spatulate sculpin
icele spatulee
Species
Icelus spiniger
thorny sculpin
Species
Icelus uncinalis
uncinate sculpin
Genus
Artediellus
hookear sculpins
Species
Artediellus pacificus
hookhorned sculpin
hookhorn sculpin
Genus
Enophrys
stone sculpins
Species
Enophrys bison
buffalo sculpin
Species
Enophrys diceraus
antlered sculpin
Genus
Gymnocanthus
Species
Gymnocanthus galeatus
armorhead sculpin
Species
Gymnocanthus pistilliger
thread sculpin
threaded sculpin
Genus
Hemilepidotus
Species
Hemilepidotus hemilepidotus
red Irish lord
Species
Hemilepidotus jordani
yellow Irish lord
Species
Hemilepidotus zapus
longfin Irish lord
Genus
Melletes
Species
Melletes papilio
Genus
Icelinus
Species
Icelinus borealis
northern sculpin
Species
Icelinus filamentosus
threadfin sculpin
Genus
Myoxocephalus
daddy sculpins
great sculpins
shorthorn sculpins
fourhorn sculpins
Species
Myoxocephalus
polyacanthocephalus
great sculpin
Species
Myoxocephalus verrucosus
warty sculpin
Genus
Thyriscus
Species
Thyriscus anoplus
sponge sculpin
Genus
Triglops
Species
Triglops forficatus
scissortail sculpin
Species
Triglops macellus
roughspine sculpin
Species
Triglops scepticus
spectacled sculpin
Species
Triglops pingelii
ribbed sculpin
Genus
Rastrinus
Species
Rastrinus scutiger
roughskin sculpin
Family
Psychrolutidae
flathead sculpins
cabezas gordas
chabots veloutes
fathead sculpins
Genus
Dasycottus
Species
Dasycottus setiger
spinyhead sculpin
Genus
Malacocottus
Species
Malacocottus kincaidi
blackfin sculpin
Species
Malacocottus zonurus
darkfin sculpin
Genus
Psychrolutes
spineless sculpins
Species
Psychrolutes paradoxus
tadpole sculpin
Genus
Eurymen
Species
Eurymen gyrinus
smoothcheek sculpin
Family
Rhamphocottidae
grunt sculpins
chabots grogneurs
charrascos grunones
Genus
Rhamphocottus
Species
Rhamphocottus richardsonii
grunt sculpin
Family
Hemitripteridae
charrascos cuervo
hemitripteres
searavens
Genus
Hemitripterus
sea ravens
Species
Hemitripterus bolini
bigmouth sculpin
Order
Pleuronectiformes
flatfishes
flounders
soles
limandes
plies
poissons plats
Suborder
Pleuronectoidei
Family
Pleuronectidae
halibuts
dabs
righteyed flounders
platijas
plies
righteye flounders
Subfamily
Hippoglossinae
Genus
Reinhardtius
Species
Reinhardtius hippoglossoides
Greenland halibut
platija negra
Greenland turbot
Newfoundland turbot
turbot
greeenland halibut
fletan du Groenland
Genus
Hippoglossus
halibuts
Species
Hippoglossus stenolepis
Pacific halibut
alabato del Pacifico
Subfamily
Hippoglossoidinae
Genus
Hippoglossoides
Species
Hippoglossoides elassodon
flathead sole
Species
Hippoglossoides robustus
Bering flounder
Subfamily
Pleuronectinae
Tribe
Pleuronectini
Genus
Limanda
mud dabs
Species
Limanda aspera
yellowfin sole
Species
Limanda proboscidea
longhead dab
Species
Limanda sakhalinensis
Sakhalin sole
The dataset "Sculpin sequences NPRB Project 1220.fas" contains 252 mitochondrial cytochrome oxidase subunit I (COI) sequences from 32
sculpin species". The dataset "Shrimp sequences NPRB project 1220.fas" 21 COI sequences from four shrimp species. The dataset "Flatfish
sequences NPRB project 1220.fas" contains 128 COI sequences from four flatfish species.
Hall,T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT.
Nucleic Acids Symposium Series 41:95-98.