R programming in phylogenetics and evolution

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.