Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Category of simulation study
Topic
Citations
Infer history
Infer Demography
(Schneider & Excoffier 1999; Pritchard et al. 2000; Campos
et al. 2010; Pinsky et al. 2010; Rodríguez et al. 2011; Alter
et al. 2012; Marino et al. 2013; Zhu et al. 2013)
Infer invasion Route or
(Estoup et al. 2001, 2004; Fabbri et al. 2007; Ficetola et al.
colonization details
2008; Bronnenhuber et al. 2011; Spear et al. 2012; Boubou
et al. 2013; Konečný et al. 2013)
Infer biology
Infer population connectivity
(Epps et al. 2005, 2013; Mardulyn & Milinkovitch 2005;
Banks et al. 2010)
Infer dispersal
(Wang et al. 2007; De-Lucas et al. 2009; Estoup et al.
2010; Currat & Excoffier 2011; Moreau et al. 2011; Puebla
et al. 2012)
Predict outcome to future
environmental changes
Climate change
(Wasserman et al. 2012, 2013; Amos et al. 2012)
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Predict response to
Roads
(Jackson & Fahrig 2011)
Logging
(Degen et al. 2006; Cloutier et al. 2007; Ng et al. 2009)
Harvest
(Bischof et al. 2008; Daleszczyk & Bunevich 2009; Pérez-
management
Figueroa et al. 2012)
Corridors
(Bruford et al. 2010)
Hybridization
(Perrier et al. 2012)
Population viability
(Kenney et al. 1995; Moehlman et al. 1996; Vonholdt et al.
2008; Alves et al. 2011)
Captive management
Evaluate method
(Haig et al. 1990)
Evaluate MSVAR, bottleneck tests (Williamson-Natesan 2005; Hundertmark & Daele 2010;
Chikhi et al. 2010; Girod et al. 2011; Paz-Vinas et al. 2013;
Hoban et al. 2013b)
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Evaluate Neutrality tests
(Ramírez-Soriano et al. 2008)
Evaluate clustering
(Evanno et al. 2005; Guillot 2008; Landguth et al. 2010;
Blair et al. 2012; Lloyd et al. 2013)
Evaluate adaptive loci detection
(De Mita et al. 2013)
tests
Evaluate potential sample
Optimize spatial genetic sampling (Cavers et al. 2005; Landguth et al. 2012; Oyler-McCance
strategies
et al. 2013)
Optimize bottleneck sampling
(Cornuet & Luikart 1996; Chikhi et al. 2010; Paz-Vinas et
al. 2013; Hoban et al. 2013a)
Optimize population genetic
(Ryman & Palm 2006; Ryman et al. 2006; Hoban et al.
sampling
2013a)
Optimize for estimating Ne or Nb
(Antao et al. 2011; Whiteley et al. 2012)
Compare SNPS and
(Narum et al. 2008; Santure et al. 2010; Tokarska et al.
microsatellites
2012)
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Explore process/model
Ancient DNA sampling
(Mona et al. 2010)
Optimize assignment tests
(Manel et al. 2002)
Verify theoretical/ analytical
(Kimura & Weiss 1964; Ohta & Kimura 1974; Nei et al.
calculations
1975; Kimura 1980; Maruyama & Kimura 1980; Maruyama
& Fuerst 1985; Rousset 1996)
Range edge dynamics
(Currat et al. 2008; Excoffier et al. 2009; Peischl et al.
2013)
Climate shifts
(Travis et al. 2007; Mustin et al. 2009; Atkins & Travis
2010; Schiffers et al. 2013)
Effects of overlapping generations (Hoelzel 1999; Martinez-Cruz et al. 2004; Hailer et al.
2006; Hundertmark & Daele 2010)
Adaptation and fragmentation
(Jaquiery et al. 2008; Lopez et al. 2009; Ejsmond &
Radwan 2011; Landguth & Balkenhol 2012)
CITATIONS
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Alter SE, Newsome SD, Palumbi SR (2012) Pre-whaling genetic diversity and population ecology in Eastern Pacific gray
whales: Insights from ancient DNA and stable isotopes. PLoS ONE, 7, 1–12.
Alves DA, Imperatriz-Fonseca VL, Francoy TM et al. (2011) Successful maintenance of a stingless bee population despite
a severe genetic bottleneck. Conservation Genetics, 12, 647–658.
Amos JN, Bennett AF, Nally R Mac et al. (2012) Predicting landscape-genetic consequences of habitat loss,
fragmentation and mobility for multiple species of woodland birds. PloS ONE, 7, e30888.
Antao T, Pérez-Figueroa A, Luikart G (2011) Early detection of population declines: high power of genetic monitoring
using effective population size estimators. Evolutionary Applications, 4, 144–154.
Atkins KE, Travis JMJ (2010) Local adaptation and the evolution of species’ ranges under climate change. Journal of
Theoretical Biology, 266, 449–457.
Banks SC, Ling SD, Johnson CR et al. (2010) Genetic structure of a recent climate change-driven range extension.
Molecular Ecology, 19, 2011–2024.
Bischof R, Mysterud A, Swenson JE (2008) Should hunting mortality mimic the patterns of natural mortality? Biology
Letters, 4, 307–310.
Blair C, Weigel DE, Balazik M et al. (2012) A simulation-based evaluation of methods for inferring linear barriers to gene
flow. Molecular ecology resources, 12, 822–33.
Boubou A, Migeon A, Roderick GK et al. (2013) Test of Colonisation Scenarios Reveals Complex Invasion History of the
Red Tomato Spider Mite Tetranychus evansi. PLoS ONE, 7.
Bronnenhuber JE, Dufour B a, Higgs DM, Heath DD (2011) Dispersal strategies, secondary range expansion and invasion
genetics of the nonindigenous round goby, Neogobius melanostomus, in Great Lakes tributaries. Molecular Ecology,
20, 1845–59.
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Bruford MW, Ancrenaz M, Chikhi L et al. (2010) Projecting genetic diversity and population viability for the fragmented
orang-utan population in the Kinabatangan floodplain, Sabah, Malaysia. Endangered Species Research, 12, 249–
261.
Campos PF, Kristensen T, Orlando L et al. (2010) Ancient DNA sequences point to a large loss of mitochondrial genetic
diversity in the saiga antelope (Saiga tatarica) since the Pleistocene. Molecular Ecology, 19, 4863–4875.
Cavers S, Degen B, Caron H et al. (2005) Optimal sampling strategy for estimation of spatial genetic structure in tree
populations. Heredity, 95, 281–289.
Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont M a (2010) The confounding effects of population structure, genetic
diversity and the sampling scheme on the detection and quantification of population size changes. Genetics, 186,
983–95.
Cloutier D, Kanashiro M, Ciampi AY, Schoen DJ (2007) Impact of selective logging on inbreeding and gene dispersal in
an Amazonian tree population of Carapa guianensis Aubl. Molecular Ecology, 16, 797–809.
Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from
allele frequency data. Genetics, 144, 2001–2014.
Currat M, Excoffier L (2011) Strong reproductive isolation between humans and Neanderthals inferred from observed
patterns of introgression. PNAS, 108, 15129–15134.
Currat M, Ruedi M, Petit RJ, Excoffier L (2008) The hidden side of invasions: massive introgression by local genes.
Evolution, 62, 1908–20.
Daleszczyk K, Bunevich AN (2009) Population viability analysis of European bison populations in Polish and Belarusian
parts of Białowieża Forest with and without gene exchange. Biological Conservation, 142, 3068–3075.
Degen B, Blanc L, Caron H et al. (2006) Impact of selective logging on genetic composition and demographic structure of
four tropical tree species. Biological Conservation, 131, 386–401.
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
De-Lucas AI, GonzaLez-Martinez SC, Vendramin GG, Hidalgo E, Heuertz M (2009) Spatial genetic structure in
continuous and fragmented populations of Pinus pinaster Aiton. Molecular Ecology, 18, 4564–4576.
Ejsmond MJ, Radwan J (2011) MHC diversity in bottlenecked populations: a simulation model. Conservation Genetics,
12, 129–137.
Epps CW, Palsbøll PJ, Wehausen JD et al. (2005) Highways block gene flow and cause a rapid decline in genetic
diversity of desert bighorn sheep. Ecology Letters, 8, 1029–1038.
Epps CW, Wasser SK, Keim JL, Mutayoba BM, Brashares JS (2013) Quantifying past and present connectivity illuminates
a rapidly changing landscape for the African elephant. Molecular ecology, 22, 1574–88.
Estoup A, Baird SJE, Ray N et al. (2010) Combining genetic, historical and geographical data to reconstruct the dynamics
of bioinvasions: application to the cane toad Bufo marinus. Molecular Ecology Resources, 10, 886–901.
Estoup A, Beaumont M, Sennedot F, Moritz C, Cornuet J-M (2004) Genetic analysis of complex demographic scenarios:
spatially expanding populations of the cane toad, Bufo marinus. Evolution, 58, 2021–2036.
Estoup A, Wilson IJ, Sullivan C, Cornuet J-M, Moritz C (2001) Inferring Population History From Microsatellite and
Enzyme Data in Serially Introduced Cane Toads, Bufo marinus. Genetics, 159, 1671–1687.
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a
simulation study. Molecular Ecology, 14, 2611–2620.
Excoffier L, Foll M, Petit R (2009) Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and
Systematics, 40, 481–501.
Fabbri E, Miquel C, Lucchini V et al. (2007) From the Apennines to the Alps: colonization genetics of the naturally
expanding Italian wolf (Canis lupus) population. Molecular Ecology, 16, 1661–1671.
Ficetola GF, Bonin A, Miaud C (2008) Population genetics reveals origin and number of founders in a biological invasion.
Molecular Ecology, 17, 773–782.
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Girod C, Vitalis R, Leblois R, Freville H (2011) Inferring population decline and expansion from microsatellite data: A
simulation-based evaluation of the Msvar method. Genetics, 188, 165–179.
Guillot G (2008) Inference of structure in subdivided populations at low levels of genetic differentiation. The correlated
allele frequencies model revisited. Bioinformatics, 24, 2222–2228.
Haig SM, Ballou JD, Derrickson SR (1990) Management options for preserving genetic diversity: reintroduction of Guam
Rails to the wild. Conservation Biology, 4, 290–300.
Hailer F, Helander B, Folkestad AO et al. (2006) Bottlenecked but long-lived: high genetic diversity retained in white-tailed
eagles upon recovery from population decline. Biology Letters, 2, 316–319.
Hoban SM, Gaggiotti OE, Bertorelle G (2013a) Sample Planning Optimization Tool for conservation and population
Genetics (SPOTG): a software for choosing the appropriate number of markers and samples (RB O’Hara, Ed,).
Methods in Ecology and Evolution, 4, 299–303.
Hoban SM, Mezzavilla M, Gaggiotti OE et al. (2013b) High variance in reproductive success generates a false signature
of a genetic bottleneck in populations of constant size: a simulation study. BMC bioinformatics, 14, 309.
Hoelzel AR (1999) Impact of population bottlenecks on genetic variation and the importance of life-history; a case study of
the northern elephant seal. Biological Journal of the Linnean Society, 68, 23–39.
Hundertmark KJ, Daele LJ Van (2010) Founder effect and bottleneck signatures in an introduced, insular population of
elk. Conservation Genetics, 11, 139–147.
Jackson ND, Fahrig L (2011) Relative effects of road mortality and decreased connectivity on population genetic diversity.
Biological Conservation, 144, 3143–3148.
Jaquiery J, Guillaume F, Perrin N (2008) Predicting the deleterious effects of mutation load in fragmented populations.
Conservation Biology, 23, 207–218.
Kenney JS, Smith JLD, Starfield AM, McDougal CW (1995) Long-term effects of tiger poaching on population viability.
Conservation Biology, 9, 1127–1133.
Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Kimura M (1980) Average time until fixation of a mutant allele in a finite population under continued mutation pressure:
Studies by analytical, numerical, and pseudo-sampling methods. PNAS, 77, 522–526.
Kimura M, Weiss GH (1964) The stepping stone model of population structure and the decrease of genetic correlation
with distance. Genetics, 49, 561–576.
Konečný A, Estoup A, Duplantier J-M et al. (2013) Invasion genetics of the introduced black rat (Rattus rattus) in Senegal,
West Africa. Molecular Ecology, 22, 286–300.
Landguth EL, Balkenhol N (2012) Relative sensitivity of neutral versus adaptive genetic data for assessing population
differentiation. Conservation Genetics, 13, 1421–1426.
Landguth EL, Cushman SS, Schwartz MK et al. (2010) Quantifying the lag time to detect barriers in landscape genetics.
Molecular Ecology, 19, 4179–4191.
Landguth EL, Fedy BC, Oyler-McCance SJ et al. (2012) Effects of sample size, number of markers, and allelic richness
on the detection of spatial genetic pattern. Molecular Ecology Resources, 12, 276–284.
Lloyd MW, Campbell L, Neel MC (2013) The power to detect recent fragmentation events using genetic differentiation
methods. PloS one, 8, e63981.
Lopez S, Rousset F, Shaw FH, Shaw RG, Ronce O (2009) Joint Effects of Inbreeding and Local Adaptation on the
Evolution of Genetic Load after Fragmentation. Conservation Biology, 23, 1618–1627.
Manel S, Berthier P, Luikart G (2002) Detecting wildlife poaching: identifying the origin of multilocus genotypes.
Conservation Biology, 16, 650–659.
Mardulyn P, Milinkovitch MC (2005) Inferring contemporary levels of gene flow and demographic history in a local
population of the leaf beetle Gonioctena olivacea from mitochondrial DNA sequence variation. Molecular Ecology, 14,
1641–1653.
Marino IAM, Benazzo A, Agostini C et al. (2013) Evidence for past and present hybridization in three Antarctic icefish
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Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Martinez-Cruz B, Godoy JA, Negro JJ (2004) Population genetics after fragmentation: the case of the endangered
Spanish imperial eagle (Aquila adalberti). Molecular Ecology, 13, 2243–55.
Maruyama T, Fuerst PA (1985) Population bottlenecks and nonequilibrium models in population genetics. II. Number of
alleles in a small population that was formed by a recent bottleneck. Evolution, 111, 675–689.
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subpopulations are frequent. PNAS, 77, 6710–6714.
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and their effectiveness for outbreeding and selfing populations. Molecular ecology, 22, 1383–99.
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Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
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Genetics, 76, 615–624.
Oyler-McCance SJ, Fedy BC, Landguth EL (2013) Sample design effects in landscape genetics. Conservation Genetics,
14, 275–285.
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Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Rousset F (1996) Equilibrium Values of Measures of Population Subdivision for Stepwise Mutation Processes. Genetics,
142, 1357–1362.
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Supplemental Table 1: Nearly 100 additional citations of simulation-based studies, divided into the seven categories of use and the
particular task or interest of the investigators.
Wang S, Lewis CM, Jakobsson M et al. (2007) Genetic variation and population structure in native Americans. PLoS
Genetics, 3, 2045–2067.
Wasserman TN, Cushman SA, Littell JS, Shirk AJ, Landguth EL (2013) Population connectivity and genetic diversity of
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population connectivity of American marten (Martes americana) in the northern Rocky Mountains. Landscape
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