The Neotropics is the most species-rich area in the world and the mechanisms that
generated and maintain its biodiversity are still debated. This thesis contributes to the
debate by investigating the evolutionary and biogeographic history of the genus Ceiba.
Ceiba comprises 18 mostly neotropical species endemic to two major biomes, seasonally
dry tropical forests (SDTFs) and rain forests, and therefore represents an ideal case
to shed light on patterns of neotropical plant evolution and diversification. Species of
Ceiba, with their swollen, spiny trunks and large, beautiful flowers are one of the most
characteristic elements of neotropical SDTF, one of the most threatened biomes in the
tropics. Despite this, Ceiba has an historically complex taxonomy with some issues
of species delimitation unresolved, especially within a species complex (Ceiba insignis
agg.).
Initial phylogenetic analyses of DNA sequence data from the nuclear ribosomal
internal transcribed spacers (ITS) for 24 accessions representing 14 species of Ceiba
recovered the genus as monophyletic and showed geographical and ecological structure
in three main clades: (i) a humid forest lineage of three accessions of C. pentandra
sister to the remaining species; (ii) a highly supported clade composed of C. schottii
and C. aesculifolia from Central American and Mexican SDTF plus two accessions of
C. samauma from inter Andean valleys from Peru; and (iii) a highly supported South
American SDTF clade including 10 species showing little sequence variation. Within
this South American clade, no species represented by multiple accessions were resolved
as monophyletic.
To investigate unresolved species relationships further, next-generation hybrid capture
was used to sequence 377 loci for 103 accessions representing all 18 Ceiba species.
This data set was assembled using different approaches (de novo and reference mapping)
and with different software and settings to assess their impact in downstream
phylogenetic analysis. The 377 loci were concatenated and analysed under the maximum
likelihood framework treated as a single partition. The well resolved and sampled
NGS phylogenies showed a similar pattern of geographical and ecological structure
as inferred using ITS. The genus Neobuchia was recovered within the SDTF Central
American and Mexican clade, and should therefore be incorporated within Ceiba. In
the South American SDTF clade, there were multiple examples where a monophyletic
group recognised as a taxonomic species was nested within another, paraphyletic taxonomic
species, which suggests recent, ancestor-descendent species relationships. Within
this clade, individual gene trees showed high conflict. Coalescent-based species delimitation
analysis and morphological data revealed no clear species boundaries between
C. pubiflora and C. glaziovii, and these species should be synonymised.
A subset of 111 loci was used to generate a dated phylogeny based on penalised likelihood
analysis using the fossil flower of Eriotheca prima from the middle to late Eocene
as a primary calibration. The stem node age of Ceiba was estimated as 45 Ma. The
rain forest species C. pentandra and C. samauma, and the campos rupestres species C.
jasminodora, were resolved with long stem lineages and shallow crown groups. Whilst
some SDTF species were very old (e.g., C. trischistandra) and monophyletic, many
South American SDTF species were resolved with short stem lineages and relatively
deep crown groups, possibly suggesting low rates of extinction in the large Caatinga
SDTF region. In addition, several South American SDTF species were not resolved
as monophyletic. Such results of younger, non-monophyletic SDTF species and older,
monophyletic rain forest species contrast with recent predictions that rain forest species
may, on average, have more recent origins than SDTF species and will more often be
non-monophyletic.
Ceiba has different and distinctive phylogenetic patterns that contradict recent theoretical
predictions. It demonstrates that studies of other clades sampled densely with
multiple accessions of each species using a multi-locus approach are needed if we are to
understand the nature of species and their boundaries, and the diversification process
in neotropical trees
