Genetic structure of lake whitefish (Coregonus clupeaformis) in Lake Michigan

2009 ◽  
Vol 66 (3) ◽  
pp. 382-393 ◽  
Author(s):  
Justin A. VanDeHey ◽  
Brian L. Sloss ◽  
Paul J. Peeters ◽  
Trent M. Sutton
Keyword(s):  
Lake Michigan ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Genetic Stock ◽  
Data Set ◽  
Genetic Stock Identification ◽  
Genetic Groups ◽  
Mixed Stock

Genetic relationships among lake whitefish ( Coregonus clupeaformis ) spawning aggregates in Lake Michigan were assessed and used to predict a stock or management unit (MU) model for the resource. We hypothesized that distinct spawning aggregates represented potential MUs and that differences at molecular markers underlie population differentiation. Genetic stock identification using 11 microsatellite loci indicated the presence of six genetic MUs. Resolved MUs corresponded to geographically proximate spawning aggregates clustering into genetic groups. Within MUs, analyses suggested that all but one delineated MU was a stable grouping (i.e., no between-population differences), with the exception being the Hog Island – Traverse Bay grouping. Elk Rapids was the most genetically divergent population within Lake Michigan. However, low Fst values suggested that moderate to high levels of gene flow occur or have occurred in the past between MUs. Significant tests of isolation by distance and low pairwise Fst values potentially led to conflicting results between traditional analyses and a Bayesian approach. This data set could provide baseline data from which a comprehensive mixed-stock analysis could be performed, allowing for more efficient and effective management of this economically and socially important resource.

scholarly journals Comparative population genetic structure of two Ixodidae ticks (Ixodes ovatus and Haemaphysalis flava) in Niigata Prefecture, Japan

2019 ◽  
Author(s):  
Maria Angenica Fulo Regilme ◽  
Megumi Sato ◽  
Tsutomu Tamura ◽  
Reiko Arai ◽  
Marcello Otake Sato ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Large Scale ◽  
Southern China ◽  
Isolation By Distance ◽  
Mantel Test ◽  
Rrna Gene ◽  
Data Set ◽  
Genetic Groups ◽  
Niigata Prefecture ◽  
Haemaphysalis Flava

AbstractIxodid tick species such as Ixodes ovatus and Haemaphysalis flava are important vector of tick-borne diseases in Japan. In this study, we used genetic structure at two mitochondrial loci (cox1, 16S rRNA gene) to infer gene flow patterns of I. ovatus and H. flava from Niigata Prefecture, Japan. Samples were collected in 29 (I. ovatus) and 17 (H. flava) sampling locations across Niigata Prefecture (12,584.18 km2). For I. ovatus, pairwise FST and analysis of molecular variance (AMOVA) analyses of cox1 sequences indicated significant among-population differentiation. This was in contrast to H. flava, for which there were few cases of low significant pairwise differentiation. A Mantel test revealed isolation by distance and there was positive spatial autocorrelation of haplotypes in I. ovatus cox1 and 16S sequences, but non-significant results were observed in H. flava in both markers. We found three genetic groups (China 1, China 2 and Japan) in the cox1 I. ovatus tree. Newly sampled I. ovatus grouped together with a published I. ovatus sequence from northern Japan and were distinct from two other I. ovatus groups that were reported from southern China. The three genetic groups in our data set suggest the potential for cryptic species among the groups. While many factors can potentially account for the observed differences in genetic structure between the two species, including population persistence and large-scale patterns of range expansion, the differences in the mobility of hosts of tick immature stages (small mammals in I. ovatus; birds in H. flava) is possibly driving the observed patterns.

scholarly journals Coastal migration patterns of the four largest Barents Sea Atlantic salmon stocks inferred using genetic stock identification methods

2019 ◽  
Vol 76 (6) ◽  
pp. 1379-1389 ◽  
Author(s):  
Martin-A Svenning ◽  
Morten Falkegård ◽  
Eero Niemelä ◽  
Juha-Pekka Vähä ◽  
Vidar Wennevik ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Barents Sea ◽  
Catch Per Unit Effort ◽  
Genetic Stock ◽  
Migration Patterns ◽  
The North ◽  
Genetic Stock Identification ◽  
Temporal And Spatial ◽  
Catch Composition ◽  
Mixed Stock

Abstract Combining detailed temporal and spatial catch data, including catch per unit effort, with a high-resolution microsatellite genetic baseline facilitated the development of stock-specific coastal migration models for the four largest Atlantic salmon (Salmo salar) populations, Målselv, Alta, Tana and Kola rivers, contributing to the Barents Sea mixed-stock fishery. Målselv salmon displayed a restricted coastal movement with 85% of the fish captured within 20 km of their natal river. Kola salmon also demonstrated limited coastal movements in Norwegian waters, with most (> 90%) caught in eastern Finnmark. Multi-sea-winter (MSW) Alta salmon were caught west of Alta fjord across a broader stretch of coast while one-sea-winter (1SW) fish migrated more extensively along the coast prior to river entry. Tana salmon, however, were detected over a broad expanse (600 km) of the North-Norwegian coast. For all populations MSW salmon dominating catches earlier in the season (May–June) while 1SW fish were more common from July to August. This study provides an example of how traditional catch and effort information may be combined with genetic methods to obtain insights into spatial and temporal changes in Atlantic salmon catch composition and their associated migration patterns in a mixed-stock coastal fishery.

Genetic structure of the four wild tomato species in the Solanum peruvianum s.l. species complex

Genome ◽  
2014 ◽  
Vol 57 (3) ◽  
pp. 169-180 ◽  
Author(s):  
Joanne A. Labate ◽  
Larry D. Robertson ◽  
Susan R. Strickler ◽  
Lukas A. Mueller
Keyword(s):  
Species Complex ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Geographical Information ◽  
Germplasm Management ◽  
Data Set ◽  
Wild Tomato ◽  
Wild Tomato Species ◽  
Tomato Species ◽  
A Genome

The most diverse wild tomato species Solanum peruvianum sensu lato (s.l.) has been reclassified into four separate species: Solanum peruvianum sensu stricto (s.s.), Solanum corneliomuelleri, Solanum huaylasense, and Solanum arcanum. However, reproductive barriers among the species are incomplete and this can lead to discrepancies regarding genetic identity of germplasm. We used genotyping by sequencing (GBS) of S. peruvianum s.l., Solanum neorickii, and Solanum chmielewskii to develop tens of thousands of mapped single nucleotide polymorphisms (SNPs) to analyze genetic relationships within and among species. The data set was condensed to 14 043 SNPs with no missing data across 46 sampled plants. Origins of accessions were mapped using geographical information systems (GIS). Isolation by distance, pairwise genetic distances, and number of clusters were estimated using population genetics approaches. Isolation by distance was strongly supported, especially between interspecific pairs. Eriopersicon (S. peruvianum s.s., S. corneliomuelleri, S. huaylasense) and Arcanum (S. arcanum, S. neorickii, S. chmielewskii) species groups were genetically distinct, except for S. huaylasense which showed 50% membership proportions in each group. Solanum peruvianum and S. corneliomuelleri were not significantly differentiated from each other. Many thousands of SNP markers were identified that could potentially be used to distinguish pairs of species, including S. peruvianum versus S. corneliomuelleri, if they are verified on larger numbers of samples. Diagnostic markers will be valuable for delimiting morphologically similar and interfertile species in germplasm management. Approximately 12% of the SNPs rejected a genome-wide test of selective neutrality based on differentiation among species of S. peruvianum s.l. These are candidates for more comprehensive studies of microevolutionary processes within this species complex.

scholarly journals Managing mixed-stock fisheries: genotyping multi-SNP haplotypes increases power for genetic stock identification

2017 ◽  
Vol 74 (4) ◽  
pp. 429-434 ◽  
Author(s):  
Garrett J. McKinney ◽  
James E. Seeb ◽  
Lisa W. Seeb
Keyword(s):  
Oncorhynchus Tshawytscha ◽  
Mixture Analysis ◽  
Genetic Stock ◽  
Multiple Snps ◽  
Relative Contribution ◽  
Genetic Stock Identification ◽  
Percentage Points ◽  
Haplotype Data ◽  
Increase In Accuracy ◽  
Mixed Stock

A common challenge for fisheries management is resolving the relative contribution of closely related populations where accuracy of genetic assignment may be limited. An overlooked method for increasing assignment accuracy is the use of multi-SNP (single nucleotide polymorphism) haplotypes rather than single-SNP genotypes. Haplotypes increase power for detecting population structure, and loci derived from next-generation sequencing methods often contain multiple SNPs. We evaluated the utility of multi-SNP haplotyping for mixture analysis in western Alaska Chinook salmon (Oncorhynchus tshawytscha). Multi-SNP haplotype data increased the accuracy of mixture analysis for closely related populations by up to seven percentage points relative to single-SNP genotype data for a set of 500 loci; 90% accuracy was achievable with as few as 150 loci with multi-SNP haplotypes but required at least 300 loci with single-SNP genotypes. Individual assignment to reporting groups showed an even greater increase in accuracy of up to 17 percentage points when multi-SNP haplotypes were used. Haplotyping multiple SNPs shows promise to improve the accuracy of assigning unknown fish to population of origin whenever haplotype data are available.

Distinguishing between resident and migrating Atlantic salmon (Salmo salar) stocks by genetic stock composition analysis

1995 ◽  
Vol 52 (4) ◽  
pp. 665-674 ◽  
Author(s):  
Marja-Liisa Koljonen
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Composition Analysis ◽  
The Baltic Sea ◽  
Genetic Stock ◽  
Atlantic Salmon Salmo Salar ◽  
Genetic Stock Identification ◽  
The Baltic ◽  
Catch Composition ◽  
Mixed Stock

The possibility of using the genetic stock identification (GSI) method to distinguish between individual Atlantic salmon (Salmo salar) stocks and stock groups in Finnish catches was studied. In the Baltic Sea, the Atlantic salmon is a target of a mixed-stock fishery, and information about stock composition would be valuable for the management of the species. The salmon catches on the Finnish west coast consist of two seasonally variable components: a group of northern stocks migrating through the area to the Baltic main basin and the resident Neva salmon. The migratory component includes two endangered wild stocks (Tornionjoki and Simojoki). The allele frequency differences at four polymorphic loci among the stocks allowed reliable catch composition estimates to be made of the migratory and resident components; one stock (Oulujoki) from the northern group could also be identified with reasonable accuracy. Northern migrating stocks accounted for over half the catches at the time of this study. The estimate of natural (nonhatchery) stocks was very low (3% in total).

Spatial and temporal variation of maturation schedules of lake whitefish (Coregonus clupeaformis) in the Great Lakes

2008 ◽  
Vol 65 (10) ◽  
pp. 2157-2169 ◽  
Author(s):  
Hui-Yu Wang ◽  
Tomas O. Höök ◽  
Mark P. Ebener ◽  
Lloyd C. Mohr ◽  
Philip J. Schneeberger
Keyword(s):  
Great Lakes ◽  
Lake Michigan ◽  
Spatial And Temporal Variation ◽  
Ecosystem Structure ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Adaptive Responses ◽  
Fish Stocks ◽  
Ecosystem Changes ◽  
Plastic Responses

Fish maturation schedules vary greatly among systems and over time, reflecting both plastic and adaptive responses to ecosystem structure, physical habitats, and mortality (natural and fishing). We examined maturation schedules of commercially exploited lake whitefish ( Coregonus clupeaformis ) in the Laurentian Great Lakes (Lakes Michigan, Huron, and Superior) by estimating ages and lengths at 50% maturity, age-specific maturity ogives (age-specific probability of being mature), and probabilistic maturation reaction norms (PMRNs; a metric that accounts for effects of growth and mortality). Collectively, these estimates indicated variation in maturation schedules between sexes (i.e., males tend to mature at younger ages and shorter lengths than females) and among systems (midpoint estimates of PMRNs were smallest for Lake Michigan fish, intermediate for fish in the main basin of Lake Huron, and largest for fish in Lake Huron’s Georgian Bay and Lake Superior). Temporally, recent increases in age at 50% maturity in Lakes Huron and Michigan may primarily reflect plastic responses to decreased growth rates associated with ecosystem changes (e.g., declines of the native amphipod, Diporeia spp.). As plastic and adaptive changes in maturation schedules of fish stocks may occur simultaneously and require different management considerations, we recommend the concomitant analysis of multiple maturation indices.

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.

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