Arctic grayling neutral genomic microsatellite loci from the Kuparuk, the Sagavanirktok (primarily Oksrukuyik Creek) and the Itkillik (primarily the I-Minus outlet stream) watersheds, 2010-2014

Abstract: 

Since 2009, The FISHSCAPE Project (National Science Foundation grants: 1719267, 1417754, and 0902153), based at Toolik Field Station, has monitored physical, chemical, and biological parameters within three watersheds: The Kuparuk (including Toolik Lake and Toolik outlet stream), The Sagavanirktok (primarily Oksrukuyik Creek, but also including sections of the Atigun River and Tea and Galbraith Lakes), and Itkillik (primarily the I-Minus outlet stream a tributary that that feeds into the Itkilik River).  Goals of the FISHSCAPE project are to understand and predict the adaptability and persistence of a key Arctic species, the Arctic grayling (Thymallus arcticus), to changing climate and hydrology. Research questions include: (1) Does landscape structure determine movement within and among watersheds; (2) do populations adapt to stream characteristics at local and regional scales; and (3) will the relative adaptability of populations determine their persistence under future climate change.

We used genetics to investigate population structure and landscape genetics for Arctic grayling. Adult and young-of-the-year fish were captured at sampling locations and coordinates and/or specific station locations were noted. Fin clip samples (adults) or whole fish (young-of-the-year) were collected and preserved in 95% ethanol until Deoxyribonucleic acid (DNA) was extracted. Polymerase chain reaction (PCR) products from neutral genomic microsatellite loci were scored and used to assess population genetic structure and other population parameters. Adult capture and movement data, including length, weight and Passive Integrated Transponder (PIT) tag information, can be found in a separate data package.

Project Keywords: 

Data set ID: 

20066

EML revision ID: 

2
Published on EDI/LTER Data Portal

Citation: 

Golden, H. 2019. Arctic grayling neutral genomic microsatellite loci from the Kuparuk, the Sagavanirktok (primarily Oksrukuyik Creek) and the Itkillik (primarily the I-Minus outlet stream) watersheds, 2010-2014 Environmental Data Initiative. http://dx.doi.org/10.6073/pasta/bd8c1cc011851190a291862d6b3bfa52
People

Owner/Creator: 

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Additional People: 

Associated Researcher
Associated Researcher
Associated Researcher
Dates

Date Range: 

Thursday, June 24, 2010 to Friday, August 1, 2014

Publication Date: 

2019

Methods: 

Some protocols can be found here:
http://arc-lter.ecosystems.mbl.edu/streams/arctic-lter-streams-protocol

Summary of Site Locations:
See sheet titles: FISHSCAPE sites 2009 - 2017 and FishscapeGeneticSiteLocations

Summary of Methods:

Fish Collection:
All fish (adults, juveniles and young-of-the-year) captured during the field season are measured, weighed, and usually tagged and released. Fish are captured using fyke nets, weirs, or by angling. Fish greater than 30 cm were tagged with Full (FDX) or Half duplex tags (HDX) internal tags.  Arctic grayling between 20 and 30 cm in total length were tagged with external floy tags (indicated by a color and a number). Adult and young-of-the-year (YOY) fish were captured at sampling locations and GPS coordinates and/or specific station locations were noted. Fin clip samples (adults) or whole fish (young-of -the-year) were collected and preserved in 95% ethanol until DNA was extracted. PCR products from neutral genomic microsatellite loci were scored and used to assess population genetic structure and other population parameters. Adult capture and movement data, including length, weight and PIT-tag information, can be found in a separate data package.


Genotyping

DNA was extracted from fin tissue using DNeasy blood and tissue kits (Qiagen, CA). Multiplex PCR reactions were optimized for allelic range for twelve highly variable nuclear microsatellite markers specific to Arctic grayling. Supporting information). PCR products were analyzed on an ABI DNA sequencer, and allele sizes were scored along with positive and negative controls using the program GeneMarker (Softgenetic, Inc.). All genotypes were checked for accuracy. Amplifications that were too weak to resolve peaks or had excess stutter were re-amplified and rerun for better resolution. Any remaining unresolved alleles were treated as missing data.

We screened for null alleles, large allele dropout and scoring errors using the program MICRO-CHECKER v.2.2.3.. Exact tests were used to test for deviations from Hardy-Weinberg equilibrium across all loci and all populations with 1,000,000 Markov Chain Monte Carlo (MCMC) and 100,000 dememorization steps in the program ARLEQUIN v3.5. We also used ARLEQUIN v3.5 to test for deviations from linkage disequilibrium across all pairs of loci using an expectation-maximization algorithm with 10,000 permutations. Probability values were Bonferroni-corrected whenever multiple testing occurred.

Version Changes: 

Version 1 uploaded to data portal
Version 2:  Updated title and abstract to remove acronym

Sites sampled.

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