Carton, Robert
(2017)
Next generation sequencing technology
and phylogenomics enhance the
resolution of deep node phylogenies:
A study of the Protostomia.
PhD thesis, National University of Ireland Maynooth.
Abstract
This magnum opus concerns the generation of genomic level data, through next
generation sequencing technologies, and the application of these new molecular
libraries to various aspects of protostome evolution.
In Chapter 1 I introduce the most important contribution to the field of
evolution: Darwin’s Theory of natural selection, the keystone to our current
understanding and methodologies. Following this I discuss the first applications of
such knowledge to morphological and molecular data, the theory behind the
bioinformatics techniques used to analyse such information, and how recent
advancements in sequencing technologies have opened the door to large-scale studies
of evolution. After these principles are established a summary of the clade of animals
that are the focus of this thesis: the Protostomia is provided.
Chapter 2 is a study of a remarkably adaptable group of ecdysozoans called
the tardigrades or “water bears”. Their rapidly evolving nature has made the
phylogenetic affinity of the Tardigrada ambiguous with three alternative hypotheses
contesting their placement. A phylogenomic approach was implemented in order to
clarify their position in conjunction with signal dissection experiments to minimize
systematic error. The origin of the Tardigrada was also investigated using a series of
molecular clocks. Important findings from this chapter include evidence that the
tardigrade-nematode grouping is a systematic artifact known as long branch
attraction, their true affinity lying with the onychophorans, and that the tardigrade
lineage diverged some 480 million years ago in the Lower Ordovician period, slightly
older than previously thought (Rota-Stabelli et al. 2013).
Chapter 3 comprises a detailed study of one of the first animal predators to
originate: the Chaetognatha. Molecules and morphology have clashed on its bilaterian
affinity and molecular studies remain in wide disagreement as to their exact position
with the Protostomia. The newly sequenced Parasagitta sp. genome was incorporated
in to a pre-existing ecdysozoan dataset and phylogenomic reconstruction methods and
divergence time estimation experiments were implemented to uncover the eventful
520 million year evolutionary history of these ancient carnivores.
Results from these experiments show that the chaetognaths are unequivocally
protostomes with a deuterostome-like development and that their true placement
within this group is as basal lophotrochozoans. Moreover a large discrepancy
discovered between the age of the fossil and extant chaetognaths points to an
extinction event within the lineage that had previously not been reported. This
signifies a remarkable example of an animal that has undergone a complete role
reversal in the food chain during its 500 million year reign: from ancient predators to
contemporary prey.
Chapter 4 describes my involvement in a collaborative work on a
palaeobiological exploration of arthropod terrestrialization. New molecular libraries
from the Crustacea and Myriapoda were used to investigate the independent
colonization events of the arthropod subphyla. Our results from this study support
Erwin et al. (2011) and dos Reis et al. (2015) findings of a Cryogenian origination for
the Metazoa and a Lower Cambrian radiation of animal lineages. The arachnids were
the last of the terrestrial arthropods to colonize land in the Upper Ordovician (450
MYA), with the hexapods colonizing land in the Lower Ordovician (483 MYA)
broadly in agreement with the fossil record. However the Myriapods colonized land
twice, initially in the Cambrian (543 MYA) and then in the Lower Ordovician (473
MYA). The implications of which suggest that terrestrial ecosystems capable of
supporting life existed as far back as the Cambrian time period over 500 MYA.
Finally Chapter 5 details the application of phylostratigraphy to a large-scale
study of novel protein families spanning the Metazoa with a focus on the Protostomia
and Ecdysozoa. Twenty-eight taxa from next generation sequencing experiments
contributed to this work and were the subject of homology searches using BLAST and
protein family clustering using MCL, which were then distributed across a forty-eight
node cladogram ranging from the roots of the Animal Kingdom to the tips of the
arthropod subphyla. The rate of protein family acquisition has increased in ancient
high-level taxonomic nodes compared to that of the younger nodes and lineages in the
tree, suggesting that protein families functioning within extant animals have existed
for a considerable amount of time before these animals diverged. The tweaking of
these families, more so than the gradual increase in family numbers, has influenced
the evolution and diversification of the animal lineages existing today.
| Item Type: |
Thesis
(PhD)
|
| Keywords: |
Next generation sequencing technology;
phylogenomics; deep node phylogenies;
Protostomia; |
| Academic Unit: |
Faculty of Science and Engineering > Biology |
| Item ID: |
8848 |
| Depositing User: |
IR eTheses
|
| Date Deposited: |
27 Sep 2017 08:21 |
| URI: |
|
| Use Licence: |
This item is available under a Creative Commons Attribution Non Commercial Share Alike Licence (CC BY-NC-SA). Details of this licence are available
here |
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