Molecules, morphology and monophyly : resolving pleuronectiform phylogeny and investigating why it has been so difficult to do.
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Date
2014-09-23
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Abstract
Although adult flatfishes (order Pleuronectiformes) start out in life as bilaterally
symmetrical larvae, they undergo a remarkable metamorphosis, where one eye of the
symmetrical larva migrates to the opposite side of the cranium, resulting in highly
asymmetrical juvenile and adult forms. Because all flatfishes exhibit this bizarre
morphology and variation, both the degree of asymmetry and handedness (direction of
eye migration) exists within the order, this group provides multiple tests of hypotheses
regarding the evolution of bilateral asymmetry and underlying mechanisms.
Unfortunately, undertaking such studies has been elusive because of three major issues
confounding pleuronectiform phylogenetics: 1) relationships of the major groups within
the order remain mostly unresolved, 2) the sister group of flatfishes is unknown, and 3)
monophyly of the assemblage is weakly supported.
To resolve these issues in pleuronectiform phylogenetics, my dissertation research
has focused on: 1) evaluating the effects non-neutral markers on phylogeny estimation,
principally rhodopsin1 (rho), 2) rigorously testing both flatfish monophyly and sistergroup
hypotheses and 3) resolving relationships within the order, re-examining characters
of adult morphology and comparing them to often overlooked larval characters in light of
new phylogenetic hypotheses.
In the first study, Chapter II, I use previously published sequence data from 78
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acanthomorph (including flatfishes) taxa for rho, rnf213, irbp and mll, perform tests for
neutrality, and compare neutral versus non-neutral markers for congruence using tree
distance metrics and topology testing. I find that while the signal provided by rho may
be discordant with the others, neutrality alone does not predict congruence and therefore
should not be used as a justification to omit data.
In the second study, Chapter III, I optimize new molecular markers and sequence
them along with rho and rnf213 for 58 flatfishes and 90 putative outgroups to test
monophyly, intraordinal relationships and sister-group hypotheses. Those sequences
along with data from a previous study are analyzed to determine possible causes for gene
tree incongruence or phylogenetic error. I discover that the new markers are variable,
providing large amounts of data, while being conserved so that alignment is
unambiguous. When combined with the others and analyzed simultaneously, these
markers provide overwhelming support for a monophyletic Pleuronectiformes.
Additionally, I demonstrate that abundant missing data is likely the cause of low
resolution, validate the importance of investigating substitution saturation as a cause of
error and discuss asymmetrical taxonomic distribution as a cause of low resolution at the
base of Carangimorpha.
Finally, in the third study (Chapter IV) I infer an ultrametric tree, recode a
previously published matrix of characters of adult morphology, combine those with new
larval characters and test whether life history is correlated with phylogenic signal.
Further, I investigate the accuracy of ML ancestral character state estimation (ACE) to
determine if these morphological characters provide additional support for hypotheses of
relationships among major pleuronectiform groups. My results suggest that larval
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characters should not be treated as a source of independent data, but do provide
resolution and additional support for novel relationships within Pleuronectiformes,
although they may be in violation of the condition of low rates on ML ACE. Lastly, I
show that because larval characters are mostly pleisiomorphic for the order, and that
larval morphology is similar to that of putative sister groups, these characters are a
potential source of evidence needed to resolve the placement of this lineage within
Acanthomorpha.
Description
xii, 157 leaves : illustrations (some color)
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Thesis
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Keywords
Pleuronectiformes--Phylogeny., Flatfishes--Phylogeny.