Population Genetic Approaches to Speciation of Wild Tomatoes with Special Reference to Solanum habrochaites and S. arcanum

This thesis entails the results of three research projects. These
have focused on the influence of diversity, demography and
structure in the divergence (i.e. the speciation process) of four
wild tomato species. In the first project, using coalescent
simulations, we studied the impact of three different sampling
schemes on patterns of neutral diversity in structured populations.
Specifically, we evaluated two summary statistics based on the site
frequency spectrum (Tajima’s D and Fu and Li’s D) as a function of
migration rate, demographic history of the entire metapopulation
and the sampling scheme. Using simulations, we demonstrate strong
effects of the sampling scheme on Tajima’s D and Fu and Li’s D
statistics, particularly under specieswide expansions. Under such
scenarios, the effects of spatial sampling may persist up to very
high levels of gene flow (Nm > 25). This suggests that
validating the assumption of panmixia is crucial if robust
demographic inferences are to be made from local or pooled samples.
For the second project, we investigated how selection acts in four
species of wild tomatoes (S. habrochaites, S. arcanum, S.
peruvianum, and S. chilense) using sequence data from eight
housekeeping genes. Our analysis quantified the number of adaptive
and deleterious mutations, and the distribution of fitness effects
of new mutations (its mean and variance) taking into account the
demography of the species. We found no evidence for adaptive
mutations but very strong purifying selection in coding regions of
the four species. More interestingly, the four species exhibit
different strength of purifying selection in non-coding regions
(introns). Taking into account the results from the first project,
we also highlighted the utility of analyzing pooled samples and
local samples from a metapopulation in order to measure selection
and the distribution of fitness effects. Finally, the third project
deals with the estimation of nucleotide diversity and population
structure in S. habrochaites and S. arcanum. We also compared these
results to those of S. peruvianum and S. chilense. We found that S.
arcanum and S. habrochaites present lower diversity levels than S.
peruvianum and S. chilense. Our neutrality tests have not revealed
any particular pattern, leading us to conclude that the loci
sequenced for the present study have not evolved under strong
positive selection, although they show a distinctive pattern of
purifying selection (second project). We also tested the demography
of all four species and found a strong expansion after a bottleneck
in the recent past for S. peruvianum and a similar statistically
significant pattern for S. arcanum, even though the signal seemed
weaker in this case. Additionally, we found moderate levels of
population sub-structure in these species, similar to previous
results found in S. peruvianum and S. chilense. Still, regardless
of the levels of population structure, we found at least two (Rupe
and San Juan from S. arcanum) populations collected in the field
that could actually be considered as a single deme. We also
expanded these population structure analyses to gain insight into
the phylogenetic relations between the four species in order to
contribute to the taxonomical treatment of the Solanum section
Lycopersicon from a population genetics perspective. Thus, we found
a clear differentiation between S. arcanum and S. peruvianum based
on all polymorphic sites.