Comprehensive integration of paleontological and molecular data remains a
sought-after goal of evolutionary research. This thesis presents a dataset unlike any
previously studied to document changes over time in the evolutionary history of the
New Zealand marine mollusc genus Alcithoe.
In order to study evolutionary relationships in the Alcithoe, DNA sequence of
approximately 8Kb of mitochondrial DNA was generated using universal and newly
developed PCR primers. The gene composition of the resulting sequences has been
thoroughly analysed, using a novel splits-based approach, to gain a clear
understanding of the underlying phylogenetic signals in the data. Refinement of the
phylogeny was achieved by considering subsets of both the taxa and genes. Taking
these analyses into account the combined a robust phylogeny for the Alcithoe is
presented for use in subsequent analyses.
The Alcithoe genus includes species that are exemplars of the problem of correctly
identifying species by morphological traits, in both the living and extinct taxa.
Taxonomic assignments were explored in a population level analysis of the highly
morphologically variable species A. wilsonae. Analyses revealed that the various
recognised forms of A. wilsonae are genetically indistinguishable and that the
previously recognised species A. knoxi is a synonym of A. wilsonae. This result has
significant implications for the interpretation of the paleontological data, as A.
knoxi specimens are known from the Tongaporutuan stage (10.92 – 6.5 Ma) of the
New Zealand geological timescale. Therefore, this finding also has implications on
the assignment of calibration data in molecular clock analysis.
To ensure accurate estimation of divergence times and rates of molecular evolution,
extensive explorations of parameter space in molecular-clock analyses were carried
out. These analyses identified the most appropriate models and calibration settings
for Alcithoe the dataset. The fossil data used to calibrate this analysis is amongst
the most robust applied to molecular clock analyses to date. Statistical sampling
uncertainty derived from the paleontological data was included in the calculation of
prior distributions. Divergence dates inferred for the extant Alcithoe are largely
consistent with the fossil record. However, the root of the tree was consistently
inferred to be younger then expected. Rates of evolution in the species of Alcithoe
included in this analysis are broadly consistent. However, some small rate
differences are observed in some branches, for example, Alcithoe fusus appears to
have a faster rate then the rest of the genus. This rate increase is the likely cause of
topological inconsistencies observed for four closely related taxa, including A.
fusus, and indicates that slight rate differences can cause phylogenetic instability
when small genetic distances are involved.
Direct comparison of diversification rates between the molecular and
paleontological data for the Alcithoe illustrated that modern Alcithoe species have
origins that are around 13 millions years younger then the oldest known Alcithoe
fossils. The suggestion that A. fusus is descended from a series of fossil Leporemax
species is directly contradicted by the molecular tree. In light of the molecular
evidence this result highlights the problem of morphological convergence in the
interpretation of fossil Alcithoe species. Comparison of the molecular and
paleontological datasets was difficult for absolute speciation and extinction rates, as
errors inherent to each dataset led to disparate estimates. For example, the fossil
record clearly fails to record most recent speciation events observed in the
molecular phylogeny, but the molecular data cannot sufficiently account for the
amount of extinction evident in the fossil record. It is clear that the assumption of a
constant and equal probability of speciation and extinction for all lineages is
violated in the Alcithoe. However, the general long-term trends estimated for both
datasets are concordant, and demonstrate an increase in both speciation and
extinction rates over the Cenozoic era.
The research described in this thesis represents significant progress toward the goal
of more thorough integration of molecular and paleontological in the study of
evolution. I have shown that reconciliation of molecular and paleontological data is
not only possible, but can substantially improve the resulting interpretation of
evolution. This study is the broadest analysis of the evolution in a single genus
using combined molecular and paleontological data that the author is currently
aware of. It illustrates the advantage of having quality paleontological data to
compare to emerging molecular data, and how the molecular data can further
inform the paleontological data. Furthermore, it adds support to the shift in
perspective from an adversarial to a complementary approach to the consideration
of molecular and paleontological data. This thesis is a comprehensive first step in
the synthesis of molecular and paleontological data in the study of evolution of the
New Zealand mollusc fauna, and alludes to many promising avenues for future