This dissertation addresses the application of the statistical computing language
R in the study of evolution and diversification of plants. The topics included
range from the worldwide historical biogeography of the cucurbit family and the
phylogenetic composition of the Mediterranean Oxalis flora in central Chile to the
interplay between population genetics and climatic niche evolution in four Horde-
um clades in the Americas. In these studies, I drew on existing methods in R and
on java and C programs that could be easily integrated with R. Whenever necessary,
I created additional software available in four new R packages. R's features,
e.g., intersystem-interfaces, extensibility, reproducibility and advanced graphical
capability, proved well suited for evolutionary and phylogenetic research.
My coauthors and I addressed the history of Cucurbitaceae, one of the most economically
important families of plants, using a multi-gene phylogeny for 114 of the
115 genera and 25 per cent of the 960 species. Worldwide sampling was achieved by
using specimens from 30 herbaria. Results reveal an Asian origin of Cucurbitaceae
in the Late Cretaceous, followed by the repeated spread of lineages into the African,
American and Australian continents via transoceanic long-distance dispersal
(LDD). North American cucurbits stem from at least seven range expansions of
Central and South American lineages; Madagascar was colonized 13 times, always
from Africa; Australia was reached 12 times, apparently always from Southeast
Asia. Overall, Cucurbitaceae underwent at least 43 successful LDD events over
the past 60 Myr, which would translate into an average of seven LDDs every 10
Myr. These and similar findings from other angiosperms stress the need for an increased
tapping of museum collections to achieve extensive geographical sampling in plant phylogenetics.
The second study focused on the interplay of population demography with the
evolution of ecological niches during or after speciation in Hordeum. While large
populations maintain a high level of standing genetic diversity, gene
ow and recombination buffers against fast alterations in ecological adaptation. Small populations harbor lower allele diversity but can more easily shift to new niches if
they initially survive under changed conditions. Thus, large populations should
be more conservative regarding niche changes in comparison to small populations.
My coauthors and I used environmental niche modeling together with phylogenetic,
phylogeographic and population genetic analyses to infer the correlation of
population demography with changes in ecological niche dimensions in 12 diploid
Hordeum species from the New World, forming four monophyletic groups. Our
analyses found both shifts and conservatism in certain niche dimensions within
and among clades. Speciation due to vicariance resulted in three species with no
pronounced climate niche differences, while species originating due to long-distance
dispersals or otherwise encountering genetic bottlenecks mostly revealed climate
niche shifts. Niche convergence among clades indicates a niche-filling pattern during
the last 2 Myr in South American Hordeum. We provide evidence that species
that did not encounter population reductions mainly show ecoclimatic niche conservatism,
while major niche shifts have occurred in species that have undergone
population bottlenecks. Our analyses allow the conclusion that population demography
influences adaptation and niche shifts or conservatism in South American
Hordeum species.
Finally, I studied the phylogenetic composition of Oxalis flora of Mediterranean
zone of Chile by asking whether in such a species-rich clade xerophytic adaptations
arose in parallel, at different times, or simultaneously. Answering this type
of question has been a major concern of evolutionary biology over the past few
years, with a growing consensus that lineages tend to be conservative in their vegetative
traits and niche requirements. Combined nuclear and chloroplast DNA
sequences for 112 species of Oxalidales (4900 aligned nucleotides) were used for
a fossil-calibrated phylogeny that includes 43 of the 54 species of Chilean Oxalis,
and species distribution models (SDMs) incorporating precipitation, temperature,
and fog, and the phylogeny were used to reconstruct ancestral habitat preferences,
relying on likelihood and Bayesian techniques. Since uneven collecting can reduce the power of SDMs, we compared 3 strategies to correct for collecting effort. Unexpectedly,
the Oxalis flora of Chile consists of 7 distant lineages that originated
at different times prior to the last Andean uplift pulse; some had features preadapting
them to seasonally arid or xeric conditions. Models that incorporated fog
and a `collecting activity surface' performed best and identified the Mediterranean
zone as a hotspot of Oxalis species as well as lineage diversity because it harbors
a mix of ancient and young groups, including insuficiently arid-adapted species.
There is no evidence of rapid adaptive radiation