Exploring Approximate Bayesian Computation for inferring recent demographic history with genomic markers in nonmodel species

• Published in: Molecular ecology resources 2018-05, Vol.18 (3), p.525-540
• Main Authors: Elleouet, Joane S., Aitken, Sally N.
• Format: Article
• Language: English
• Subjects: approximate Bayesian computation; Bayesian analysis; coalescent simulations; Computation; Computer simulation; Datasets; demographic inference; Demographics; Deoxyribonucleic acid; DNA; Frequency spectrum; Gene sequencing; Genomes; Genotyping; Haplotypes; Markers; Mathematical models; Migration; Nucleotide sequence; Parameter estimation; Parameter uncertainty; population genetics; Population number; spatial expansion; Species
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12758

Approximate Bayesian computation (ABC) is widely used to infer demographic history of populations and species using DNA markers. Genomic markers can now be developed for nonmodel species using reduced representation library (RRL) sequencing methods that select a fraction of the genome using targeted sequence capture or restriction enzymes (genotyping‐by‐sequencing, GBS). We explored the influence of marker number and length, knowledge of gametic phase, and tradeoffs between sample size and sequencing depth on the quality of demographic inferences performed with ABC. We focused on two‐population models of recent spatial expansion with varying numbers of unknown parameters. Performing ABC on simulated data sets with known parameter values, we found that the timing of a recent spatial expansion event could be precisely estimated in a three‐parameter model. Taking into account uncertainty in parameters such as initial population size and migration rate collectively decreased the precision of inferences dramatically. Phasing haplotypes did not improve results, regardless of sequence length. Numerous short sequences were as valuable as fewer, longer sequences, and performed best when a large sample size was sequenced at low individual depth, even when sequencing errors were added. ABC results were similar to results obtained with an alternative method based on the site frequency spectrum (SFS) when performed with unphased GBS‐type markers. We conclude that unphased GBS‐type data sets can be sufficient to precisely infer simple demographic models, and discuss possible improvements for the use of ABC with genomic data.