title: Sampling strategies for frequency spectrum-based population genomic inference.
abstract: BACKGROUND
  The allele frequency spectrum (AFS) consists of counts of the number of single nucleotide polymorphism (SNP) loci with derived variants present at each given frequency in a sample. Multiple approaches have recently been developed for parameter estimation and calculation of model likelihoods based on the joint AFS from two or more populations. We conducted a simulation study of one of these approaches, implemented in the Python module δaδi, to compare parameter estimation and model selection accuracy given different sample sizes under one- and two-population models.
  
  
  RESULTS
  Our simulations included a variety of demographic models and two parameterizations that differed in the timing of events (divergence or size change). Using a number of SNPs reasonably obtained through next-generation sequencing approaches (10,000 - 50,000), accurate parameter estimates and model selection were possible for models with more ancient demographic events, even given relatively small numbers of sampled individuals. However, for recent events, larger numbers of individuals were required to achieve accuracy and precision in parameter estimates similar to that seen for models with older divergence or population size changes. We quantify i) the uncertainty in model selection, using tools from information theory, and ii) the accuracy and precision of parameter estimates, using the root mean squared error, as a function of the timing of demographic events, sample sizes used in the analysis, and complexity of the simulated models.
  
  
  CONCLUSIONS
  Here, we illustrate the utility of the genome-wide AFS for estimating demographic history and provide recommendations to guide sampling in population genomics studies that seek to draw inference from the AFS. Our results indicate that larger samples of individuals (and thus larger AFS) provide greater power for model selection and parameter estimation for more recent demographic events.
authors.affiliation: Department of Biology, City College of New York, New York, NY, 10031, USA. RobinsonJ@dnr.sc.gov.|Current Address: South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, SC, 29412, USA. RobinsonJ@dnr.sc.gov.
authors.forename: John D
authors.initials: JD
authors.lastname: Robinson
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA. acoffman@email.arizona.edu.
authors.forename: Alec J
authors.initials: AJ
authors.lastname: Coffman
authors.affiliation: Department of Biology, City College of New York, New York, NY, 10031, USA. mhickerson@ccny.cuny.edu.|Subprogram in Ecology, Evolution and Behavior, the Graduate Center of the City University of New York, New York, NY, 10016, USA. mhickerson@ccny.cuny.edu.|Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA. mhickerson@ccny.cuny.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Hickerson
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA. rgutenk@email.arizona.edu.
authors.forename: Ryan N
authors.initials: RN
authors.lastname: Gutenkunst
mesh_terms: D000818:Animals; D005787:Gene Frequency; D005828:Genetics, Population; D023281:Genomics / Q000592:standards*; D006801:Humans; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011156:Population Density; D012015:Reference Standards