Contemporary and historical effective population sizes of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus

2018 ◽  
Vol 20 (2) ◽  
pp. 167-184 ◽  
Author(s):  
John Waldman ◽  
S. Elizabeth Alter ◽  
Douglas Peterson ◽  
Lorraine Maceda ◽  
Nirmal Roy ◽  
...  
Keyword(s):  
Atlantic Sturgeon ◽  
Effective Population ◽  
Population Sizes ◽  
Acipenser Oxyrinchus

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

2014 ◽  
Author(s):  
Jonathan Puritz ◽  
Christopher M. Hollenbeck ◽  
John R. Gold
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Variant Calling ◽  
Population Level ◽  
Model Organisms ◽  
Effective Population ◽  
Reduction Techniques ◽  
Indel Polymorphisms ◽  
Indel Calling ◽  
Population Sizes

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genetic polymorphism but for which no genomic resources exist. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is most likely due to the fact that dDocent quality trims instead of filtering and incorporates both forward and reverse reads in assembly, mapping, and SNP calling, thus enabling use of reads with Indel polymorphisms. The pipeline and a comprehensive user guide can be found at (http://dDocent.wordpress.com).

scholarly journals Atlantic sturgeon movements in relation to a cutterhead dredge in the James River, Virginia

2021 ◽  
Author(s):  
Matthew Balazik ◽  
Safra Altman ◽  
Kevin Reine ◽  
Alan Katzenmeyer
Keyword(s):  
Water Quality ◽  
Field Study ◽  
Technical Note ◽  
Atlantic Sturgeon ◽  
James River ◽  
Acipenser Oxyrinchus ◽  
Reduced Water

This technical note describes a field study investigating the movements of federally endangered Atlantic sturgeon, Acipenser oxyrinchus oxyrinchus (ATS), during the summer and fall of 2017 near a cutterhead dredge working in the James River, Virginia, to provide data addressing the concern about the potential impacts of dredging activities (for example, excavation, transit, disposal, sounds, reduced water quality) on the ATS.

Atlantic sturgeon Acipenser oxyrinchus surfacing behaviour

2018 ◽  
Vol 92 (4) ◽  
pp. 929-943
Author(s):  
L. M. Logan-Chesney ◽  
M. J. Dadswell ◽  
R. H. Karsten ◽  
I. Wirgin ◽  
M. J. W. Stokesbury
Keyword(s):  
Atlantic Sturgeon ◽  
Acipenser Oxyrinchus

Anadromous Sturgeons: Habitats, Threats, and Management

2007 ◽  
Keyword(s):  
South Carolina ◽  
Brackish Water ◽  
Data Sets ◽  
Water Interface ◽  
Atlantic Sturgeon ◽  
Gill Net ◽  
Large Numbers ◽  
Class Strength ◽  
Study Designs ◽  
Acipenser Oxyrinchus

<em>Abstract</em>.—The anadromous Atlantic sturgeon <em>Acipenser oxyrinchus</em> once supported an important commercial fishery throughout its range (northern Florida, USA, to Labrador, Canada). All surviving populations are apparently depleted, presumably due to overfishing, pollution, and dam construction. A complete moratorium on the fishery has been established in U.S. waters. Unfortunately, population status is unknown for nearly all systems. Several 1994–2001 data sets from South Carolina rivers were examined for their potential in development of recruitment (year-class abundance) indices. Because Atlantic sturgeon often begin leaving their natal systems at age 2, after which they occupy other systems and then presumably return to natal areas at sexual maturity several years later, a valid river-specific abundance index must be based on either age0–1 or adult fish. Working with three former commercial Atlantic sturgeon fishermen to collect adults in two rivers during the spring and fall of 1998 resulted in collection of only 39 fish in 13 nominal age-classes. In another river, 2 years of monthly sampling with multipanel, anchored gill nets and otter trawls at eight stations throughout the estuary produced only 31 juvenile Atlantic sturgeon. Neither of these study designs provided adequate sample sizes. However, sampling in a clean-bottom section at the freshwater–brackish water interface of the Edisto River with a modified drift gill net produced large numbers of small Atlantic sturgeon. More than 3,000 juveniles have been collected and tagged since 1994. The 1,331 nominal age-1 Atlantic sturgeon that were captured displayed a distinct bimodal length frequency distribution, supporting the hypothesis that there are both spring and fall spawning events. A period of record drought impeded sampling efforts during a portion of this study. However, when flows and bottom configurations allow nets to be fished at the freshwater–brackish water interface, the gears and methods employed in the Edisto River can produce an age-1 Atlantic sturgeon catch per unit effort that is high enough to be used in estimating relative year-class strength.

Anadromous Sturgeons: Habitats, Threats, and Management

2007 ◽  
Keyword(s):  
Large Scale ◽  
Atlantic Coast ◽  
The United States ◽  
Management Plan ◽  
Commercial Fishing ◽  
Atlantic Sturgeon ◽  
Coastal Fisheries ◽  
Number Of Factors ◽  
Acipenser Oxyrinchus ◽  
The U.S

<em>Abstract.</em>—Large-scale commercial fisheries for Atlantic sturgeon <em>Acipenser oxyrinchus</em> in the late 1880s eventually led to substantial reductions in the population size. The coastwide Atlantic sturgeon population of the United States has not recovered to the levels seen prior to the 1900s. A number of factors have contributed to the slow recovery or continued decline of Atlantic sturgeon populations, including continued commercial fishing and the targeting of females for caviar, bycatch in other fisheries, and changes in habitat due to dam construction and water quality degradation. The Atlantic States Marine Fisheries Commission (ASMFC) developed the first coastwide management plan for Atlantic sturgeon in 1990. In response to the shortcomings of that plan, the ASMFC applied new standards and the authority granted to it by the U.S. Congress to adopt a coastwide moratorium on all harvesting in 1998. A federal status review conducted in 1998 concluded that the continued existence of Atlantic sturgeon was not threatened given the situation at the time. Since then, monitoring programs have indicated varying levels of relative abundance in several water bodies along the Atlantic coast. The U.S. government is responsible for undertaking a status review to document any changes since the last review and determining whether those findings warrant a threatened or endangered listing for the species. The government’s findings may have far-reaching effects on many other Atlantic coastal fisheries.

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