Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal

Hoffman J, Grant SM, Forcada J, Phillips CD (2011)
Molecular Ecology 20(19): 3989-4008.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ;
Erscheinungsjahr
Zeitschriftentitel
Molecular Ecology
Band
20
Zeitschriftennummer
19
Seite
3989-4008
ISSN
PUB-ID

Zitieren

Hoffman J, Grant SM, Forcada J, Phillips CD. Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Molecular Ecology. 2011;20(19):3989-4008.
Hoffman, J., Grant, S. M., Forcada, J., & Phillips, C. D. (2011). Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Molecular Ecology, 20(19), 3989-4008. doi:10.1111/j.1365-294X.2011.05248.x
Hoffman, J., Grant, S. M., Forcada, J., and Phillips, C. D. (2011). Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Molecular Ecology 20, 3989-4008.
Hoffman, J., et al., 2011. Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Molecular Ecology, 20(19), p 3989-4008.
J. Hoffman, et al., “Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal”, Molecular Ecology, vol. 20, 2011, pp. 3989-4008.
Hoffman, J., Grant, S.M., Forcada, J., Phillips, C.D.: Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Molecular Ecology. 20, 3989-4008 (2011).
Hoffman, Joseph, Grant, S. M., Forcada, J., and Phillips, C. D. “Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal”. Molecular Ecology 20.19 (2011): 3989-4008.

35 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding.
Humble E, Dasmahapatra KK, Martinez-Barrio A, Gregório I, Forcada J, Polikeit AC, Goldsworthy SD, Goebel ME, Kalinowski J, Wolf JBW, Hoffman JI., G3 (Bethesda) 8(8), 2018
PMID: 29954843
Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species.
Dussex N, Taylor HR, Stovall WR, Rutherford K, Dodds KG, Clarke SM, Gemmell NJ., Ecol Evol 8(17), 2018
PMID: 30271541
A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal.
Hoffman JI, Bauer E, Paijmans AJ, Humble E, Beckmann LM, Kubetschek C, Christaller F, Kröcker N, Fuchs B, Moreras A, Shihlomule YD, Bester MN, Cleary AC, De Bruyn PJN, Forcada J, Goebel ME, Goldsworthy SD, Guinet C, Hoelzel AR, Lydersen C, Kovacs KM, Lowther A., R Soc Open Sci 5(10), 2018
PMID: 30473858
Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history.
Stoffel MA, Humble E, Paijmans AJ, Acevedo-Whitehouse K, Chilvers BL, Dickerson B, Galimberti F, Gemmell NJ, Goldsworthy SD, Nichols HJ, Krüger O, Negro S, Osborne A, Pastor T, Robertson BC, Sanvito S, Schultz JK, Shafer ABA, Wolf JBW, Hoffman JI., Nat Commun 9(1), 2018
PMID: 30446730
Ecological and genetic impact of the 2011 Tohoku Earthquake Tsunami on intertidal mud snails.
Miura O, Kanaya G, Nakai S, Itoh H, Chiba S, Makino W, Nishimura T, Kojima S, Urabe J., Sci Rep 7(), 2017
PMID: 28281698
Reconsidering connectivity in the sub-Antarctic.
Moon KL, Chown SL, Fraser CI., Biol Rev Camb Philos Soc 92(4), 2017
PMID: 28371192
Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population.
Hoffman JI, Kowalski GJ, Klimova A, Eberhart-Phillips LJ, Staniland IJ, Baylis AM., R Soc Open Sci 3(7), 2016
PMID: 27493782
Low Spatial Genetic Differentiation Associated with Rapid Recolonization in the New Zealand Fur Seal Arctocephalus forsteri.
Dussex N, Robertson BC, Salis AT, Kalinin A, Best H, Gemmell NJ., J Hered 107(7), 2016
PMID: 27563072
Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises.
Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A., Ecol Evol 5(3), 2015
PMID: 25691990
Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity, endemism, and dispersal.
Eberhart-Phillips LJ, Hoffman JI, Brede EG, Zefania S, Kamrad MJ, Székely T, Bruford MW., Ecol Evol 5(5), 2015
PMID: 25798218
Fine-scale matrilineal population structure in the Galapagos fur seal and its implications for conservation management
Lopes F, Hoffman JI, Valiati VH, Bonatto SL, Wolf JBW, Trillmich F, Oliveira LR., Conserv Genet 16(5), 2015
PMID: IND604394511
Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes.
Ciosi M, Masiga DK, Turner CM., PLoS Negl Trop Dis 8(2), 2014
PMID: 24551260
Greece: a Balkan subrefuge for a remnant red deer (cervus elaphus) population.
Karaiskou N, Tsakogiannis A, Gkagkavouzis K, Operator of Parnitha National Park, Papika S, Latsoudis P, Kavakiotis I, Pantis J, Abatzopoulos TJ, Triantaphyllidis C, Triantafyllidis A., J Hered 105(3), 2014
PMID: 24558101
High genetic diversity in a small population: the case of Chilean blue whales.
Torres-Florez JP, Hucke-Gaete R, Rosenbaum H, Figueroa CC., Ecol Evol 4(8), 2014
PMID: 24834336
Demographic history of a recent invasion of house mice on the isolated Island of Gough.
Gray MM, Wegmann D, Haasl RJ, White MA, Gabriel SI, Searle JB, Cuthbert RJ, Ryan PG, Payseur BA., Mol Ecol 23(8), 2014
PMID: 24617968
Detecting past changes of effective population size.
Nikolic N, Chevalet C., Evol Appl 7(6), 2014
PMID: 25067949
Global population structure and demographic history of the grey seal.
Klimova A, Phillips CD, Fietz K, Olsen MT, Harwood J, Amos W, Hoffman JI., Mol Ecol 23(16), 2014
PMID: 25041117
Museum DNA reveals the demographic history of the endangered Seychelles warbler.
Spurgin LG, Wright DJ, van der Velde M, Collar NJ, Komdeur J, Burke T, Richardson DS., Evol Appl 7(9), 2014
PMID: 25553073
Demographic histories and genetic diversities of Fennoscandian marine and landlocked ringed seal subspecies.
Nyman T, Valtonen M, Aspi J, Ruokonen M, Kunnasranta M, Palo JU., Ecol Evol 4(17), 2014
PMID: 25535558
Inferring recent historic abundance from current genetic diversity.
Palsbøll PJ, Zachariah Peery M, Olsen MT, Beissinger SR, Bérubé M., Mol Ecol 22(1), 2013
PMID: 23181682
Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data.
Nadachowska-Brzyska K, Burri R, Olason PI, Kawakami T, Smeds L, Ellegren H., PLoS Genet 9(11), 2013
PMID: 24244198
Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices.
Phillips CD, Hoffman JI, George JC, Suydam RS, Huebinger RM, Patton JC, Bickham JW., Ecol Evol 3(1), 2012
PMID: 23403722
Reliability of genetic bottleneck tests for detecting recent population declines.
Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-Bëer E, Robinson S, Vásquez-Carrillo C, Pauli JN, Palsbøll PJ., Mol Ecol 21(14), 2012
PMID: 22646281
Cape buffalo mitogenomics reveals a Holocene shift in the African human-megafauna dynamics.
Heller R, Brüniche-Olsen A, Siegismund HR., Mol Ecol 21(16), 2012
PMID: 22725969

101 References

Daten bereitgestellt von Europe PubMed Central.

Bank voles in linear habitats show restricted gene flow as revealed by mitochondrial DNA (mtDNA).
Aars J, Ims RA, Liu HP, Mulvey M, Smith MH., Mol. Ecol. 7(10), 1998
PMID: 9787447
Factors affecting levels of genetic diversity in natural populations
Amos, Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 353(), 1998
Monte Carlo evaluation of the likelihood for N(e) from temporally spaced samples.
Anderson EC, Williamson EG, Thompson EA., Genetics 156(4), 2000
PMID: 11102399
Median-joining networks for inferring intraspecific phylogenies.
Bandelt HJ, Forster P, Rohl A., Mol. Biol. Evol. 16(1), 1999
PMID: 10331250
Approximate Bayesian computation in population genetics.
Beaumont MA, Zhang W, Balding DJ., Genetics 162(4), 2002
PMID: 12524368
Application of genetic bottleneck testing to the investigation of Amphibian declines: a case study with Natterjack Toads
Beebee, Conservation Biology 15(), 2001

AUTHOR UNKNOWN, 0
Pup production and distribution of breeding Antarctic fur seals (Arctocephalus gazella) at South Georgia
Boyd, Antarctic Science 5(), 1993
Tooth growth in male Antarctic fur seals (Arctocephalus gazella) from South Georgia - an indicator of long-term growth history
Boyd, Journal of Zoology (London) 229(), 1993
Microsatellites from the Atlantic walrus Odobenus rosmarus rosmarus.
Buchanan FC, Maiers LD, Thue TD, De March BG, Stewart RE., Mol. Ecol. 7(8), 1998
PMID: 9711867

Caswell, 2001
The distribution of coalescence times and distances between microsatellite alleles with changing effective population size
Chevalet, Theoretical Population Biology 77(), 2011
TCS: a computer program to estimate gene genealogies.
Clement M, Posada D, Crandall KA., Mol. Ecol. 9(10), 2000
PMID: 11050560
Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation.
Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, Balding DJ, Guillemaud T, Estoup A., Bioinformatics 24(23), 2008
PMID: 18842597
Pleistocene population expansions of Antarctic seals.
Curtis C, Stewart BS, Karl SA., Mol. Ecol. 18(10), 2009
PMID: 19344354
Dinucleotide microsatellite markers from the Antarctic seals and their use in other pinnipeds
Davis, Molecular Ecology Notes 2(), 2002
Mutational processes of simple sequence repeat loci in human populations
Di, Proceedings of the National Academy of Sciences, USA 91(), 1994
Density-dependent pup mortality in the Antarctic fur seal Arctocephalus gazella at South Georgia
Doidge, Journal of Zoology (London) 202(), 1984
BEAST: Bayesian evolutionary analysis by sampling trees.
Drummond AJ, Rambaut A., BMC Evol. Biol. 7(), 2007
PMID: 17996036
Bayesian coalescent inference of past population dynamics from molecular sequences.
Drummond AJ, Rambaut A, Shapiro B, Pybus OG., Mol. Biol. Evol. 22(5), 2005
PMID: 15703244
Microsatellites: simple sequences with complex evolution.
Ellegren H., Nat. Rev. Genet. 5(6), 2004
PMID: 15153996
Why hunter-gatherer populations do not show signs of Pleistocene demographic expansions
Excoffier, Proceedings of the National Academy of Sciences, USA 96(), 1999
Bayesian analysis of an admixture model with mutations and arbitrarily linked markers.
Excoffier L, Estoup A, Cornuet JM., Genetics 169(3), 2005
PMID: 15654099
Statistical evaluation of alternative models of human evolution
Fagundes, Proceedings of the National Acadamy of Sciences, USA 104(), 2007

Fanning, 1833

AUTHOR UNKNOWN, 0
Do population size bottlenecks reduce evolutionary potential?
Frankham, Animal Conservation 2(), 1999
Detection of reduction in population size using data from microsatellite loci.
Garza JC, Williamson EG., Mol. Ecol. 10(2), 2001
PMID: 11298947
Interspecific microsatellite markers for the study of pinniped populations.
Gemmell NJ, Allen PJ, Goodman SJ, Reed JZ., Mol. Ecol. 6(7), 1997
PMID: 9226947
Variation in the mitochondrial control region in the Juan Fernandez fur seal (Arctocephalus philippii).
Goldsworthy S, Francis J, Boness D, Fleischer R., J. Hered. 91(5), 2000
PMID: 10994703
FSTAT (version 1.2): a computer program to calculate F-statistics
Goudet, Journal of Heredity 86(), 1995
Evaluation of methodology for detection of genetic bottlenecks: inferences from temporally replicated lake trout populations
Guinand, Comptus Rendus Biologies 326(), 2003
BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT
Hall, Nucleic Acids Symposium Series 41(), 1999

Headland, 1989
Conservation Genetics: Techniques and Fundamentals.
Hedrick PW, Miller PS., Ecol Appl 2(1), 1992
PMID: 27759190
Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees
Heyer, American Journal of Human Genetics 69(), 2001
Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset.
Higdon JW, Bininda-Emonds OR, Beck RM, Ferguson SH., BMC Evol. Biol. 7(), 2007
PMID: 17996107
Alpha-male paternity in elephant seals
Hoelzel, Behavioral Ecology and Sociobiology 46(), 1999
Ten novel dinucleotide microsatellite loci cloned from the Galápagos sea lion (Zalophus californianus wollebaeki) are polymorphic in other pinniped species
Hoffman, Moleular Ecology Notes 7(), 2007
Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation.
Hoffman JI, Dasmahapatra KK, Amos W, Phillips CD, Gelatt TS, Bickham JW., Mol. Ecol. 18(14), 2009
PMID: 19500256
Immigration and the ephemerality of a natural population bottleneck: evidence from molecular markers
Keller, Proceedings of the Royal Society of London Series B-Biological Sciences 268(), 2001
Stepwise mutation model and distribution of allelic frequencies in a finite population.
Kimura M, Ohta T., Proc. Natl. Acad. Sci. U.S.A. 75(6), 1978
PMID: 275857
Risk of population extinction from fixation of new deleterious mutations
Lande, Evolution 48(), 1994

AUTHOR UNKNOWN, 0
Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data
Luikart, Conservation Biology 12(), 1998
Distortion of allele frequency distributions provides a test for recent population bottlenecks.
Luikart G, Allendorf FW, Cornuet JM, Sherwin WB., J. Hered. 89(3), 1998
PMID: 9656466
Temporal changes in allele frequencies provide estimates of population bottleneck size
Luikart, Conservation Biology 13(), 1999
Mutation accumulation and the extinction of small populations
Lynch, American Naturalist 146(), 1995

Mill, 1905
Demographic consequences of inbreeding in remnant populations
Mills, American Naturalist 144(), 1994
Growth of a fur seal population
Payne, Philosophical Transactions of the Royal Society of London, B 279(), 1977
Assessing substitution patterns, rates and homoplasy at HVRI of Steller sea lions, Eumetopias jubatus.
Phillips CD, Trujillo RG, Gelatt TS, Smolen MJ, Matson CW, Honeycutt RL, Patton JC, Bickham JW., Mol. Ecol. 18(16), 2009
PMID: 19627492
BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data
Piry, Journal of Heredity 90(), 1999
jModelTest: phylogenetic model averaging.
Posada D., Mol. Biol. Evol. 25(7), 2008
PMID: 18397919
Inference of population structure using multilocus genotype data.
Pritchard JK, Stephens M, Donnelly P., Genetics 155(2), 2000
PMID: 10835412

R, 2005
Genepop (Version 1.2) - population genetics software for exact tests of ecumenicism
Raymond, Journal of Heredity 86(), 1995
Temporal changes in allele frequencies and a population’s history of severe bottlenecks
Richards, Conservation Biology 10(), 1996
Population growth makes waves in the distribution of pairwise genetic differences.
Rogers AR, Harpending H., Mol. Biol. Evol. 9(3), 1992
PMID: 1316531
Evidence of a genetic bottleneck in an El Nino affected population of South American fur seals, Arctocephalus australis
Rosa, Journal of the Marine Biological Association of the United Kingdom 89(), 2009

Schneider, 2000
Molecular evidence for historical and recent population size reductions of tiger salamanders (Ambystoma tigrinum) in Yellowstone National Park
Spear, Conservation Genetics 7(), 2006
A near-extinction event in lynx: do microsatellite data tell the tale?
Spong, Conservation Ecology 6(), 2002
High mitogenomic evolutionary rates and time dependency.
Subramanian S, Denver DR, Millar CD, Heupink T, Aschrafi A, Emslie SD, Baroni C, Lambert DM., Trends Genet. 25(11), 2009
PMID: 19836098
Mutation of human short tandem repeats.
Weber JL, Wong C., Hum. Mol. Genet. 2(8), 1993
PMID: 8401493

Weddell, 1825
Comparison of methods for detecting bottlenecks from microsatellite loci
Williamson-Natesan EG., Conserv. Genet. 6(4), 2005
PMID: IND43971996
Mitochondrial DNA and two perspectives on evolutionary genetics
Wilson, Biological Journal of the Linnean Sociey 26(), 1985
Postsealing genetic variation and population structure of two species of fur seal (Arctocephalus gazella and A. tropicalis).
Wynen LP, Goldsworthy SD, Guinet C, Bester MN, Boyd IL, Gjertz I, Hofmeyr GJ, White RW, Slade R., Mol. Ecol. 9(3), 2000
PMID: 10736028

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21895820
PubMed | Europe PMC

Suchen in

Google Scholar