Nuclear and mitochondrial DNA evolution in Adélie penguins : studies of modern and ancient populations : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy (PhD) in Genetics, Allan Wilson Centre for Molecular Ecology and Evolution, Institute for Natural Sciences, Massey University, Auckland, New Zealand
Loading...
Date
2012
DOI
Open Access Location
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Massey University
Rights
The Author
Abstract
The Adélie penguin of Antarctica (Pygoscelis adeliae) breeds on the Antarctic
continent and on offshore islands. Its evolutionary history has been, and its current
biology remains, dependent on a range of climate variables. Over geological time,
glacial warming and cooling periods have resulted in Adélie penguin populations
decreasing and expanding. Therefore, understanding Adélie penguin population
dynamics at a genetic level can provide insights into how the species responds to
changing climates, one reason why Adélie penguins are an important natural model
species. In addition, sub-fossil bone deposits of this species below modern and
abandoned colonies provide an excellent source of ancient DNA that can bring a
temporal dimension to population studies of the species. In combination, these
attributes enable us to address some fundamental questions regarding evolutionary
change.
Making use of known mitochondrial DNA mutation rates and current
population sizes, a positive and significant correlation between population size and
modern mitochondrial control region diversity was detected. This finding supports
the use of mitochondrial DNA for population inferences. Effective population sizes
of breeding colonies are shown to have increased since the late Pleistocene. To
extend current tools available for understanding Adélie penguins, six nuclear intron
loci were recovered from a wide range of introns that can be applied to population
genetics and phylogenetic studies of penguins. Five introns were used to investigate
the persistence of the mitochondrial Antarctic (A) and Ross Sea (RS) lineages. No
evidence for the existence of these lineages was found in the nuclear loci sequenced.
A signature of historical population expansion, preceding the mitochondrial one, was
detected. The utility of four introns in resolving penguin phylogenetic signals was
also determined. Non-coding nuclear sequence of one intron were obtained from
ancient sub-fossil remains of Adélie penguins using multiplex PCR enrichment,
followed by second-generation sequencing of a barcoded library. A shift in haplotype
frequencies was detected between ancient and modern intron sequences in Adélie
penguins, despite a small sample size. In the future, advancing the current
methodologies and extending sampling to additional introns as well as older samples,
is likely to provide a new level of understanding of this remarkable species.
Description
Keywords
Adelie penguins, Pygoscelis adeliae, Adelie penguin genetics, Mitochondrial DNA, Phylogeny, Huia, Penguin populations