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Aitken, S. N.

Publications and source records attributed to Aitken, S. N..

2 recordsLinked to original sources
bioRxiv2018

The interplay between demography and neutral evolution at the expansion front of a widespread conifer, Picea sitchensis

Tree species in the northern hemisphere have advanced and retreated with interglacial and glacial periods, and are currently subject to rapid anthropogenic climate change. These observations prompt questions about the mechanisms allowing tree populations to respond quickly to selection pressures when establishing into new areas. Focusing on the northern expanding range edge of Picea sitchensis, a widespread conifer of western North America, we ask how genetic structure and diversity develop during colonization, and assess the role of demographic history in shaping the evolutionary trajectory of a colonizing population. By combining nearly 500 years of tree-ring and genetic data at the expansion front on the Kodiak Archipelago, we show that allelic richness - but not expected heterozygosity - increased rapidly during early stages of establishment in the 1600s, while genetic differentiation from populations further from the front decreased. This trend ended in the 1700s, after an increase in population growth rate. These findings highlight the major role of long-distance pollen dispersal in the recovery of genetic diversity during initial stages of colonization, and suggest that demographic dynamics including an initial lag in population growth are likely limiting factors in the adaptation of tree populations tracking their niche in a changing climate.

evolutionary biology↗
bioRxiv2018

Exploring Approximate Bayesian Computation for inferring recent demographic history with genomicmarkers in non-model species

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 non-model 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 2-population models of recent spatial expansion with varying numbers of unknown parameters. Performing ABC on simulated datasets with known parameter values, we found that the timing of a recent spatial expansion event could be precisely estimated in a 3-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 datasets can be sufficient to precisely infer simple demographic models, and discuss possible improvements for the use of ABC with genomic data.

evolutionary biology↗