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Title: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species

Abstract

Not provided.

Authors:
ORCiD logo [1];  [2];  [2];  [3];  [1]
  1. Department of Biology, University of Kentucky, Lexington KY 40506 USA
  2. Savannah River Ecology Laboratory, University of Georgia, P O Drawer E Aiken SC 29802 USA
  3. Department of Biology, Florida State University, Tallahassee FL 32306 USA
Publication Date:
Research Org.:
Univ. of Georgia, Athens, GA (United States)
Sponsoring Org.:
USDOE Office of Environmental Management (EM)
OSTI Identifier:
1536760
DOE Contract Number:  
FC09-07SR22506
Resource Type:
Journal Article
Journal Name:
Molecular Ecology
Additional Journal Information:
Journal Volume: 26; Journal Issue: 4; Journal ID: ISSN 0962-1083
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology

Citation Formats

Nunziata, Schyler O., Lance, Stacey L., Scott, David E., Lemmon, Emily Moriarty, and Weisrock, David W. Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species. United States: N. p., 2017. Web. doi:10.1111/mec.13988.
Nunziata, Schyler O., Lance, Stacey L., Scott, David E., Lemmon, Emily Moriarty, & Weisrock, David W. Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species. United States. doi:10.1111/mec.13988.
Nunziata, Schyler O., Lance, Stacey L., Scott, David E., Lemmon, Emily Moriarty, and Weisrock, David W. Sat . "Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species". United States. doi:10.1111/mec.13988.
@article{osti_1536760,
title = {Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species},
author = {Nunziata, Schyler O. and Lance, Stacey L. and Scott, David E. and Lemmon, Emily Moriarty and Weisrock, David W.},
abstractNote = {Not provided.},
doi = {10.1111/mec.13988},
journal = {Molecular Ecology},
issn = {0962-1083},
number = 4,
volume = 26,
place = {United States},
year = {2017},
month = {1}
}

Works referenced in this record:

Identifying adaptive genetic divergence among populations from genome scans
journal, April 2004


Unlocking the vault: next-generation museum population genomics
journal, October 2013

  • Bi, Ke; Linderoth, Tyler; Vanderpool, Dan
  • Molecular Ecology, Vol. 22, Issue 24
  • DOI: 10.1111/mec.12516

Climate Change and the Past, Present, and Future of Biotic Interactions
journal, August 2013


The utility of single nucleotide polymorphisms in inferences of population history
journal, May 2003


Stacks: an analysis tool set for population genomics
journal, May 2013

  • Catchen, Julian; Hohenlohe, Paul A.; Bassham, Susan
  • Molecular Ecology, Vol. 22, Issue 11
  • DOI: 10.1111/mec.12354

The variant call format and VCFtools
journal, June 2011


Amphibian Population Declines at Savannah River site are Linked to Climate, not Chytridiomycosis
journal, December 2005

  • Daszak, P.; Scott, D. E.; Kilpatrick, A. M.
  • Ecology, Vol. 86, Issue 12
  • DOI: 10.1890/05-0598

NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size ( N e ) from genetic data
journal, August 2013


Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
journal, February 2005


Robust Demographic Inference from Genomic and SNP Data
journal, October 2013


How large must populations be to retain evolutionary potential?
journal, February 1998


Fidelity and dispersal in the pond-breeding amphibian, Ambystoma opacum: Implications for spatio-temporal population dynamics and conservation
journal, October 2007


Genome size and microsatellites: the effect of nuclear size on amplification potential
journal, February 2002


Effects of a Population Bottleneck on Whooping Crane Mitochondrial DNA Variation
journal, October 1999


Demographic history and rare allele sharing among human populations
journal, July 2011

  • Gravel, S.; Henn, B. M.; Gutenkunst, R. N.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 29
  • DOI: 10.1073/pnas.1019276108

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
journal, October 2009


Estimation of effective population size from data on linkage disequilibrium
journal, December 1981


Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences
journal, July 2014


Accounting for Bias from Sequencing Error in Population Genetic Estimates
journal, November 2007

  • Johnson, P. L. F.; Slatkin, M.
  • Molecular Biology and Evolution, Vol. 25, Issue 1
  • DOI: 10.1093/molbev/msm239

Effects of recent population bottlenecks on reconstructing the demographic history of prairie-chickens
journal, June 2007


Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing
journal, November 2015

  • Keinath, Melissa C.; Timoshevskiy, Vladimir A.; Timoshevskaya, Nataliya Y.
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep16413

Can one hear the shape of a population history?
journal, March 2015


Genetic Variation among Ambystoma Breeding Populations on the Savannah River Site
journal, June 2006


ANGSD: Analysis of Next Generation Sequencing Data
journal, November 2014

  • Korneliussen, Thorfinn Sand; Albrechtsen, Anders; Nielsen, Rasmus
  • BMC Bioinformatics, Vol. 15, Issue 1
  • DOI: 10.1186/s12859-014-0356-4

Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas ( Ochotona collaris )
journal, July 2015

  • Lanier, Hayley C.; Massatti, Rob; He, Qixin
  • Molecular Ecology, Vol. 24, Issue 14
  • DOI: 10.1111/mec.13270

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?
journal, September 2012


Fast and accurate short read alignment with Burrows-Wheeler transform
journal, May 2009


A genomic history of Aboriginal Australia
journal, September 2016

  • Malaspinas, Anna-Sapfo; Westaway, Michael C.; Muller, Craig
  • Nature, Vol. 538, Issue 7624
  • DOI: 10.1038/nature18299

Metapopulation Dynamics and Amphibian Conservation
journal, February 2001


Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population
journal, December 2013

  • McCoy, Rajiv C.; Garud, Nandita R.; Kelley, Joanna L.
  • Molecular Ecology, Vol. 23, Issue 1
  • DOI: 10.1111/mec.12591

Assessing statistical power of SNPs for population structure and conservation studies
journal, January 2009


Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift
journal, October 2014

  • Moura, Andre E.; Kenny, John G.; Chaudhuri, Roy
  • Molecular Ecology, Vol. 23, Issue 21
  • DOI: 10.1111/mec.12929

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
journal, July 2012


Temporal genetic and demographic monitoring of pond-breeding amphibians in three contrasting population systems
journal, June 2015

  • Nunziata, Schyler O.; Scott, David E.; Lance, Stacey L.
  • Conservation Genetics, Vol. 16, Issue 6
  • DOI: 10.1007/s10592-015-0743-z

Declining Amphibian Populations: The Problem of Separating Human Impacts from Natural Fluctuations
journal, August 1991


Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
journal, May 2012


Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach
journal, February 2012


Detecting past population bottlenecks using temporal genetic data
journal, September 2005


Sampling strategies for frequency spectrum-based population genomic inference
journal, December 2014

  • Robinson, John D.; Coffman, Alec J.; Hickerson, Michael J.
  • BMC Evolutionary Biology, Vol. 14, Issue 1
  • DOI: 10.1186/s12862-014-0254-4

Comparative population genomics in animals uncovers the determinants of genetic diversity
journal, August 2014

  • Romiguier, J.; Gayral, P.; Ballenghien, M.
  • Nature, Vol. 515, Issue 7526
  • DOI: 10.1038/nature13685

Genetic monitoring as a promising tool for conservation and management
journal, January 2007


The Effect of Larval Density on Adult Demographic Traits in Ambystoma Opacum
journal, July 1994


Genomics and the challenging translation into conservation practice
journal, February 2015

  • Shafer, Aaron B. A.; Wolf, Jochen B. W.; Alves, Paulo C.
  • Trends in Ecology & Evolution, Vol. 30, Issue 2
  • DOI: 10.1016/j.tree.2014.11.009

How many SNPs are enough?
journal, April 2010


Conservation Genomics of Threatened Animal Species
journal, January 2013


Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod
journal, March 2013

  • Therkildsen, Nina O.; Hemmer-Hansen, Jakob; Als, Thomas D.
  • Molecular Ecology, Vol. 22, Issue 9
  • DOI: 10.1111/mec.12260

Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs
journal, July 2016

  • Thomé, Maria Tereza C.; Carstens, Bryan C.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 29
  • DOI: 10.1073/pnas.1601064113

Climate change correlates with rapid delays and advancements in reproductive timing in an amphibian community
journal, December 2010

  • Todd, Brian D.; Scott, David E.; Pechmann, Joseph H. K.
  • Proceedings of the Royal Society B: Biological Sciences, Vol. 278, Issue 1715
  • DOI: 10.1098/rspb.2010.1768

Influence of Drought on Salamander Occupancy of Isolated Wetlands on the Southeastern Coastal Plain of the United States
journal, March 2013


An empirical genetic assessment of the severity of the northern elephant seal population bottleneck
journal, October 2000