Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Lauren M. Overdyk ◽  
Heather E. Braid ◽  
Stephen S. Crawford ◽  
Robert H. Hanner
Keyword(s):  
Dna Barcoding ◽  
Lake Huron ◽  
Coi Gene ◽  
Sampling Effort ◽  
Coregonus Clupeaformis ◽  
Dna Barcodes ◽  
Lake Whitefish ◽  
Life Data ◽  
New Perspective ◽  
St Lawrence River

AbstractDNA barcoding is a useful tool for both species identification and discovery, but the latter requires denser sampling than typically used in barcode studies. Lake Whitefish (Coregonus clupeaformis) is a valuable species, fished traditionally, commercially, and recreationally in Lake Huron. Based on the natural geographic and bathymetric separation of the three major basins in Lake Huron, the potential separation of Lake Whitefish within these basins, and the variation among life history (early and late spawning), we predicted that Lake Huron might harbour cryptic lineages of Lake Whitefish at the basin level. To test this prediction, DNA barcodes of the mitochondrial 5’ cytochrome c oxidase subunit I (COI) gene sequences were recovered from spawning phase Lake Whitefish (n = 5 per site), which were collected from sites (n = 28) around Lake Huron during Fall 2012. These sequences, combined with other publically available DNA barcodes from the Barcode of Life Data System (BOLD), revealed twelve unique haplotypes across North America, with seven unique to Lake Huron. The dominant haplotype was found throughout Lake Huron and east to the St. Lawrence River. No deep divergences were revealed. This comprehensive lake-wide sampling effort offers a new perspective on C. clupeaformis, and can provide insight for environmental assessments and fisheries management.

scholarly journals Parasitic wasps as natural enemies of aphid populations in the Mashhad region of Iran: New data from DNA barcodes and SEM

2011 ◽  
Vol 63 (4) ◽  
pp. 1225-1234 ◽  
Author(s):  
Reyhaneh Darsouei ◽  
Javad Karimi ◽  
Mehdi Modarres-Awal
Keyword(s):  
Dna Barcoding ◽  
Modern Method ◽  
Diaeretiella Rapae ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Parasitic Wasps ◽  
Pome Fruit ◽  
Initial Attempt ◽  
Morphometric Characters ◽  
Preliminary Identification

DNA barcoding is a modern method for the identification of different species, including insects. Among animals, the major emphasis of DNA barcoding is on insects. Due to this global trend we addressed this approach for surveying a group of insects. The parasitic wasps (including primary and hyperparasitoids) of pome fruit orchard aphids were collected from Iran-Mashhad during 2009-2010. Preliminary identification of this group was performed by using morphological and morphometric characters and SEM. The COI gene in the specimens was amplified and sequenced. In this survey, Aphidius matricariae, Binodoxys angelicae, Diaeretiella rapae, Ephedrus persicae, Lysiphlebus fabarum and Praon volucre parasitoids and Alloxysta sp., Asaphes suspensus, Dendrocerus carpenteri, Pachyneuron aphidis, Syrphophagus aphidivorus hyperparasitoids were studied. Based on intra-interspecies distances and phylogenetic analysis using NJ, all species possess diagnostic barcode sequences. The results of this study show that the COI sequence could be useful in identification study of this group of insects. Here we have provided the first GenBank data for the COI gene of the above-mentioned hyperparasitoids as well as an initial attempt toward preparing DNA barcodes for Iranian parasitoid and hyperparasitoid aphids.

scholarly journals Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

2018 ◽  
Author(s):  
Kam-Cheng Yeong ◽  
Haruo Takizawa ◽  
Thor-Seng Liew
Keyword(s):  
Dna Barcoding ◽  
West Coast ◽  
Leaf Beetle ◽  
Coi Gene ◽  
Beetle Species ◽  
Dna Barcodes ◽  
The West ◽  
Leaf Beetles ◽  
Baseline Knowledge ◽  
Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

Genetic structure of lake whitefish, Coregonus clupeaformis, populations in the northern main basin of Lake Huron

2012 ◽  
Vol 63 ◽  
pp. 241-260
Author(s):  
W. Stott ◽  
M.P. Ebener ◽  
L. Mohr ◽  
J. Schaeffer ◽  
E.F. Roseman ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Lake Huron ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Main Basin

DNA barcodes for Cladocera and Copepoda from Mexico and Guatemala, highlights and new discoveries

Zootaxa ◽  
2008 ◽  
Vol 1839 (1) ◽  
pp. 1 ◽  
Author(s):  
MANUEL ELÍAS-GUTIÉRREZ ◽  
FERNANDO MARTÍNEZ JERÓNIMO ◽  
NATALIA V. IVANOVA ◽  
MARTHA VALDEZ-MORENO ◽  
PAUL D. N. HEBERT
Keyword(s):  
Dna Barcoding ◽  
Classification Systems ◽  
Coi Gene ◽  
Aquatic Environments ◽  
Dna Barcodes ◽  
Chydorus Sphaericus ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Current Classification ◽  
Excellent Tool

DNA barcoding, based on sequence diversity in the mitochondrial COI gene, has proven an excellent tool for identifying species in many animal groups. Here, we report the first barcode studies for freshwater zooplankton from Mexico and Guatemala and discuss the taxonomic and biological implications of this work. Our studies examined 61 species of Cladocera and 21 of Copepoda, about 40% of the known fauna in this region. Sequence divergences among conspecific individuals of cladocerans and copepods averaged 0.82% and 0.79%, respectively, while sequence divergences among congeneric taxa were on average 15-20 times as high. Barcodes were successful in discriminating all species in our study, but sequences for Mexican Daphnia exilis overlapped with those of D. spinulata from Argentina. Our barcode data revealed evidence of many species overlooked by current classification systems —for example, based on COI genotypes the Diapahanosoma birgei group appears to include 5 species, while Ceriodaphnia cf. rigaudi, Moina cf. micrura, Mastigodiaptomus albuquerquensis and Mastigodiaptomus reidae all include 2–3 taxa. The barcode results support recent taxonomic revisions, such as recognition of the genus Leberis, and the presence of several species in the D. birgei and Chydorus sphaericus complexes. The present results indicate that DNA barcoding will provide powerful new insights into both the incidence of cryptic species and a better understanding of zooplankton distributions, aiding evaluation of the factors influencing competitive outcomes, and the colonization of aquatic environments.

Lake Whitefish (Coregonus clupeaformis) Stocks of the Ontario Waters of Lake Huron

1981 ◽  
Vol 38 (12) ◽  
pp. 1772-1789 ◽  
Author(s):  
J. M. Casselman ◽  
J. J. Collins ◽  
E. J. Grossman ◽  
P. E. Ihssen ◽  
G. R. Spangler
Keyword(s):  
Growth Rate ◽  
Genetic Distances ◽  
Lake Huron ◽  
Starch Gel Electrophoresis ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Meristic Characters ◽  
Hardy Weinberg Equilibrium ◽  
Starch Gel ◽  
South Shore

Historical and contemporary data on lake whitefish (Coregonus clupeaformis) from the Ontario waters of Lake Huron were examined for evidence of stocks with the objective of defining population boundaries. We delineated the spatial distribution of five stocks from tag–recapture data and the general location of six additional stocks on the basis of population parameters such as growth rate, age structure, and abundance trends.Samples of fish collected (summer and fall) from 5 of the 11 potential stocks were evaluated on the basis of 11 morphometric and 7 meristic characters. We also examined osseometric features such as shape of scales and otoliths, and electrophoretic characteristics at 32 loci associated with 12 enzyme systems.The summer and fall samples for each group were generally not significantly different. For the phenotypes examined electrophoretically, each stock was in Hardy–Weinberg equilibrium; 12 of the 32 loci considered were polymorphic and 4 of the 10 possible genetic distances differed significantly from zero.The Inner Basin stock was distinctly different from all other stocks. The Blind River stock was also found to be different by osseometrics, but not by morphometrics or electrophoresis. Osseometrics separated the stocks by basin of origin. Two stocks, Outer Basin and Burnt Island, appeared to be the most similar and could be separated from each other only on the basis of growth rate and tagging data. These two stocks are adjacent to each other in the main basin of Lake Huron, along the south shore of Manitoulin Island.Whitefish stocks of Lake Huron represent groups of fish that differ phenotypically and genotypically in varying degrees, are spatially separated, and behave as cohesive units. We conclude that they should be regarded as functional units for management purposes.Key words: lake whitefish, Coregonus clupeaformis, Lake Huron, stocks, tag–recapture data, population structure, morphometrics, meristics, osseometrics, scale and otolith shape, starch gel electrophoresis, biochemical genetic variation

Assessment of the United States Lake Whitefish (Coregonus clupeaformis) Fisheries of Lake Superior, Lake Michigan, and Lake Huron

1976 ◽  
Vol 33 (4) ◽  
pp. 747-759 ◽  
Author(s):  
A. L. Jensen
Keyword(s):  
Lake Michigan ◽  
Lake Superior ◽  
The United States ◽  
Sea Lamprey ◽  
Maximum Sustainable Yield ◽  
Lake Huron ◽  
Production Model ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Surplus Production Model

The logistic surplus production model is applied to lake whitefish (Coregonus clupeaformis) yield and effort data from Lake Superior, Lake Michigan, and Lake Huron. The fitted models indicate that the whitefish populations in most areas of the lakes have been overexploited, and that in these areas yield was below the maximum sustainable yield before sea lamprey (Petromyzon marinus) predation took its toll. In some areas of Lake Superior the whitefish populations are not overexploited. The sea lamprey is the apparent cause of the drastic decrease in the whitefish population that occurred in northern Lake Michigan during the 1950’s.

scholarly journals Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding

2018 ◽  
Author(s):  
Kam-Cheng Yeong ◽  
Haruo Takizawa ◽  
Thor-Seng Liew
Keyword(s):  
Dna Barcoding ◽  
West Coast ◽  
Leaf Beetle ◽  
Coi Gene ◽  
Beetle Species ◽  
Dna Barcodes ◽  
The West ◽  
Leaf Beetles ◽  
Baseline Knowledge ◽  
Island Habitats

Sabah, northern Borneo is one of the world’s most well-recognized biodiversity hotspots famous for the incredible diversity of its flora and fauna. Plenty of studies of leaf beetle fauna from this region have been conducted over the past 30 years. Yet, our knowledge of the leaf beetle fauna from island habitats remains scarce despite Sabah having the highest number of islands in Malaysia (ca. 500 islands). In this study, we collected leaf beetle fauna from 13 islands off the west coast of Sabah between January 2016 and March 2017. All specimens were identified to species level. Species names were assigned when the specimens fitted the description of species in the literature and morpho-species were assigned when the species names could not be determined. In addition, DNA barcodes – mitochondarial COI gene – of the species were sequenced. A total of 68 species from 31 genera and 5 subfamilies were collected with 12 species name being determined. From the data it was established that Pulau Gaya has the highest species richness (42 species), followed by Pulau Tiga (22 species) and Pulau Sapangar (18 species). Furthermore, a total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from 60 leaf beetle species. The mean intraspecific and interspecific distances were determined as 0.77 % and 16.11 %, respectively. In addition, DNA barcoding also reveals phenotypic variation in leaf beetle species, particularly in the case of the subfamily Galerucinae. This study provides baseline knowledge and information about the DNA barcodes of leaf beetle species on Sabah’s island habitats for use in future studies.

scholarly journals DNA barcoding for identification of some fish species (Carangidae) in Vietnam coastal area

2020 ◽  
Vol 19 (4) ◽  
pp. 527-536
Author(s):  
Pham The Thu ◽  
Nguyen Manh Linh ◽  
Nguyen Van Quan ◽  
Pham Van Chien ◽  
Dao Huong Ly ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Nucleotide Diversity ◽  
Haplotype Diversity ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Yellow Card ◽  
Mtdna Coi ◽  
Seriola Quinqueradiata ◽  
Mitochondrial Cytochrome Oxidase ◽  
The Eu

Carangidae family has got about 148 species belonging to 32 genera. In Vietnam, Carangidae is of high commercial value and playing an important role in the ecosystem. In the context Vietnam has received yellow card for seafood since Nov. 2017 by the EU, in which one of the main reasons was related to the restriction of traceability. In this study, DNA barcoding technique of mitochondrial cytochrome oxidase I (COI) gene was used to classify 56 specimens of Carangidae from three coastal areas (Northern, Central and Southern) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 21 species belonging to 16 genera were determined by the COI barcode while 18 species (16 genera) were determined when using morphological method. Seriola quinqueradiata and Trachinotus anak were newly recorded in Vietnam. From 56 sequences with 660 bp of mtDNA (COI), total 27 haplotypes were detected; haplotype diversity (h) and nucleotide diversity (π) were 0.903 ± 0.00060 and 0.14%, respectively. The DNA barcodes of COI gene of 21 species in Carangidae which were developed in this study could be used as a basis for comparison and traceability of their products. In addition, the results showed the high potentiality in using COI barcode to identify Carangidae fish in Vietnam.

Spatial and temporal genetic diversity of lake whitefish (Coregonus clupeaformis (Mitchill)) from Lake Huron and Lake Erie

2013 ◽  
Vol 64 ◽  
pp. 205-222 ◽  
Author(s):  
Wendylee Stott ◽  
Mark P. Ebener ◽  
Lloyd Mohr ◽  
Travis Hartman ◽  
Jim Johnson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Lake Erie ◽  
Lake Huron ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Temporal Genetic Diversity
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