Data from: Genetic diversity of the endemic Canary Island pine tree, Pinus canariensis (Ph.D. thesis)

The Canary Island pine, Pinus canariensis, is an endemic tree that forms
one of the main forest ecosystems within the archipelago, and whose
distribution has been reduced in the last five centuries by clear cutting
for the extraction of timber and tar. It was in the XXth century that
exploitation declined and reforestation programs were brought forward for
the restoration of an ecosystem that harbours a number of endangered
endemic species of plants and animals. In addition to reforestation
efforts, an understanding of population genetic processes is also
necessary for the successful conservation management of the Canarian pine
forest, particularly in light of gathering evidence for local adaptation.
In this thesis historical and contemporary gene flow within P. canariensis
was studied with nuclear and chloroplast microsatellite markers. High
immigration rates (0.68–0.75) were estimated as expected for an
outcrossing wind-pollinated tree. Nevertheless, significant population
differentiation (FST=0.019, RST=0.044) was detectable for sites separated
by only a few kilometres. Within the context of reforestation programs the
high levels of gene flow detected would appear to have a positive effect,
by facilitating the immigration of local alleles from natural stands into
potentially genetically depauperate first generation gene pools of
reforested stands. Historical population growth was revealed with
chloroplast microsatellites for most populations of P. canariensis.
Population expansions for the pine parasite weevil Brachyderes rugatus
were also detected, broadly coinciding with the population expansions
within the Canary Island pine forests. Given the estimated times of
expansion, these population demographic increases would seem likely
related to the process of colonisation of newly emerged islands or local
patches after volcanic disturbance. Detection and dating of these
expansions from chloroplast microsatellites was, to some degree,
negatively affected by homoplasy (i.e. parallel and back mutations).
Coalescent simulations of the evolution of chloroplast microsatellites
were applied to study the effects of homoplasy in the statistical analysis
of population structuring. Measures of genetic diversity based on number
of haplotypes and measures based on genetic distances were differently
affected. Genetic distances were underestimated but were proportional to
the actual value. These effects help to explain the lower performance of
statistical analyses for the detection and dating of population
expansions. Further research on the effects of homoplasy in the analysis
of population differentiation using chloroplast microsatellites is
essential.