Phylogenetic genomics of the founding population of Newfoundland: insights from complete mtDNA sequences

Pope, Angela Michelle (2007) Phylogenetic genomics of the founding population of Newfoundland: insights from complete mtDNA sequences. Masters thesis, Memorial University of Newfoundland.

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Abstract

The importance of the island of Newfoundland as a place to study genetics stems from the history of its early settlement. Beginning in the early part of the 17th century, the island was settled by fewer than 25 000 founders. The genetic structure of the modern-day descendants of these settlers is expected to be influenced both by the initial founder effects and subsequent inbreeding and genetic drift. Therefore, it is of interest to explore the population genetic structure of Newfoundlanders for evidence of these phenomena. -- Complete (16 570 bp) mitochondrial DNA sequences were obtained for 27 individual Newfoundlanders by conventional dideoxy sequencing as well as a novel microarray technology (GeneChip: Affymetrix). A total of 220 SNPs were found; every individual had a unique sequence. Two individuals were sequenced by both methods. In both cases, microarray sequencing was shown to be highly efficient and accurate: 99.99% and 99.97% of bases were called by the algorithm, and 100.0% of SNPs were detected, with no false positives. -- In combination with published data from 42 other European, Eurasian, and First Nations individuals, phylogenetic analysis showed that 25 Newfoundland individuals could be associated with one of five major haplogroups (H, J, K, T, and U) previously identified in Europeans from mtDNA Control Region (CR) profiles. Phylogenetic analysis of complete genomes more clearly defines the relationships among these haplogroups than do CR profiles alone, and shows that haplogroups U (with respect to K) and H (with respect to subtypes H3 and H16) are not monophyletic. One individual was assignable to haplogroup A, which has not previously been seen in Europeans but which is common in northeastern First Nations peoples. Another individual had a signature most similar to haplogroup I, a rare Scandinavian type: the phylogenetic relationships of this lineage to H, (U+K), and (J+ T) are unresolved. -- In contrast with expectations from the genetics of small populations and the historical settlement patterns, "genome-type" diversity in the Newfoundland samples is high and closely parallels patterns in western Europeans, with no loss of haplotypes or significant shifts in their relative frequencies.

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