Mitogenomic and microsatellite variation in descendants of the founder population of Newfoundland: high genetic diversity in an historically isolated population

Evidence for the persistence of ancient Beothuk and Maritime Archaic mitochondrial DNA genome lineages among modern Native American peoples

The Beothuk were a Native American people who formerly occupied the island of Newfoundland, and who are generally accepted to have become culturally extinct in 1829. The Beothuk succeeded the Maritime Archaic people on the island after a hiatus of ca. 1.4 ka, and were themselves succeeded by the extant Mi'kmaq within historic times. Genetic continuity between ancient and modern Native Americans remains of interest. Complete aDNA mitogenomes from ancient Beothuk and Maritime Archaic were compared with the most closely related modern mitogenomes as obtained by BLAST search of GenBank. Beothuk mitogenomes in five clades are in one case identical to and otherwise differ by minima of three to eight SNPs from the most closely related modern mitogenomes. Maritime Archaic mitogenomes in 12 clades are in one case identical to and otherwise differ by minima of one to nine SNPs from the most similar modern mitogenomes. The single available modern Mi'kmaq mitogenome differs from the most similar Beothuk and Maritime Archaic mitogenomes by 12 and 22 SNPs, respectively. Phylogenetic analysis and sequence similarities imply lineage extinction of most ancient clades, as well as continuity of two Beothuk and at least one Maritime Archaic lineages in modern Native Americans and their descendants.

Phylogeographic mitogenomics of Atlantic cod Gadus morhua: Variation in and among trans-Atlantic, trans-Laurentian, Northern cod, and landlocked fjord populations

The historical phylogeography, biogeography, and ecology of Atlantic cod (Gadus morhua) have been impacted by cyclic Pleistocene glaciations, where drops in sea temperatures led to sequestering of water in ice sheets, emergence of continental shelves, and changes to ocean currents. High-resolution, whole-genome mitogenomic phylogeography can help to elucidate this history. We identified eight major haplogroups among 153 fish from 14 populations by Bayesian, parsimony, and distance methods, including one that extends the species coalescent back to ca. 330 kya. Fish from the Barents and Baltic Seas tend to occur in basal haplogroups versus more recent distribution of fish in the Northwest Atlantic. There was significant differentiation in the majority of trans-Atlantic comparisons (ΦST = .029-.180), but little or none in pairwise comparisons within the Northwest Atlantic of individual populations (ΦST = .000-.060) or defined management stocks (ΦST = .000-.023). Monte Carlo randomization tests of population phylogeography showed significantly nonrandom trans-Atlantic phylogeography versus absence of such structure within various partitions of trans-Laurentian, Northern cod (NAFO 2J3KL) and other management stocks, and Flemish Cap populations. A landlocked meromictic fjord on Baffin Island comprised multiple identical or near-identical mitogenomes in two major polyphyletic clades, and was significantly differentiated from all other populations (ΦST = .153-.340). The phylogeography supports a hypothesis of an eastern origin of genetic diversity ca. 200-250 kya, rapid expansion of a western superhaplogroup comprising four haplogroups ca. 150 kya, and recent postglacial founder populations.

On the persistence and detectability of ancient Beothuk mitochondrial DNA genomes in living First Nations peoples

Claims have long been made as to the survival to the present day of descendants of the Newfoundland Beothuk, a group generally accepted to have become extinct with the death of the last known member, Shanawdithit, in 1829. Interest has recently been revived by the availability of commercial genetic testing, which some claim can assign living individuals to specific Native American groups. We compare complete mitogenome sequences (16569 bp) from aDNA of eight distinct Beothuk lineages, including Shanawdithit's uncle Nonosabasut and his wife Demasduit, with three Newfoundland Mi'kmaq lineages and 21 other living Native Americans drawn from GenBank. A Newfoundland Mi'kmaq lineage in Haplogroup A is more similar to three Native Americans (1-3 SNPs) than to the most closely related Beothuk (24 SNPs). Nonosabasut in Haplogroup X is identical to a non-Beothuk Native American. Demasduit in Haplogroup C differs from three other Native Americans by 1-4 substitutions. Within a 2168 bp region of the HVS sequences available from living Mi'kmaq of the Miawpukek First Nation in Newfoundland, lineages in Haplogroups C, X, and A differ by 1, 4, and 8 substitutions, from the most similar Beothuk, and are more similar to other Native Americans. MtDNA genome sequences in living persons identical or similar to those of Beothuk do not necessarily indicate Beothuk ancestry. Mi'kmaq lineages cannot at this time be associated with any Beothuk lineages more closely than those of other Native Americans.

Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada

Situated at the furthest northeastern edge of Canada, the island of Newfoundland (approximately 110,000 km²) and Labrador (approximately 295,000 km²) today constitute a province characterized by abundant natural resources but low population density. Both landmasses were covered by the Laurentide ice sheet during the Last Glacial Maximum (18,000 years before present [YBP]); after the glacier retreated, ice patches remained on the island until ca. 9,000 calibrated (cal) YBP [1]. Nevertheless, indigenous peoples, whose ancestors had trekked some 5,000 km from the west coast, arrived approximately 10,000 cal YBP in Labrador and ca. 6,000 cal YBP in Newfoundland [2, 3]. Differential features in material culture indicate at least three settlement episodes by distinct cultural groups, including the Maritime Archaic, Palaeoeskimo, and Beothuk. Newfoundland has remained home to indigenous peoples until present day with only one apparent hiatus (3,400-2,800 YBP). This record suggests abandonment, severe constriction, or local extinction followed by subsequent immigrations from single or multiple source populations, but the specific dynamics and the cultural and biological relationships, if any, among these successive peoples remain enigmatic [4]. By examining the mitochondrial genome diversity and isotopic ratios of 74 ancient remains in conjunction with the archaeological record, we have provided definitive evidence for the genetic discontinuity between the maternal lineages of these populations. This northeastern margin of North America appears to have been populated multiple times by distinct groups that did not share a recent common ancestry, but rather one much deeper in time at the entry point into the continent.

Quantitative Phylogenomics of Within-Species Mitogenome Variation: Monte Carlo and Non-Parametric Analysis of Phylogeographic Structure among Discrete Transatlantic Breeding Areas of Harp Seals (Pagophilus groenlandicus)

Phylogenomic analysis of highly-resolved intraspecific phylogenies obtained from complete mitochondrial DNA genomes has had great success in clarifying relationships within and among human populations, but has found limited application in other wild species. Analytical challenges include assessment of random versus non-random phylogeographic distributions, and quantification of differences in tree topologies among populations. Harp Seals (Pagophilus groenlandicus Erxleben, 1777) have a biogeographic distribution based on four discrete trans-Atlantic breeding and whelping populations located on "fast ice" attached to land in the White Sea, Greenland Sea, the Labrador ice Front, and Southern Gulf of St Lawrence. This East to West distribution provides a set of a priori phylogeographic hypotheses. Outstanding biogeographic questions include the degree of genetic distinctiveness among these populations, in particular between the Greenland Sea and White Sea grounds. We obtained complete coding-region DNA sequences (15,825 bp) for 53 seals. Each seal has a unique mtDNA genome sequence, which differ by 6 ~ 107 substitutions. Six major clades / groups are detectable by parsimony, neighbor-joining, and Bayesian methods, all of which are found in breeding populations on either side of the Atlantic. The species coalescent is at 180 KYA; the most recent clade, which accounts for 66% of the diversity, reflects an expansion during the mid-Wisconsinan glaciation 40~60 KYA. FST is significant only between the White Sea and Greenland Sea or Ice Front populations. Hierarchal AMOVA of 2-, 3-, or 4-island models identifies small but significant ΦSC among populations within groups, but not among groups. A novel Monte-Carlo simulation indicates that the observed distribution of individuals within breeding populations over the phylogenetic tree requires significantly fewer dispersal events than random expectation, consistent with island or a priori East to West 2- or 3-stepping-stone biogeographic models, but not a simple 1-step trans-Atlantic model. Plots of the cumulative pairwise sequence difference curves among seals in each of the four populations provide continuous proxies for phylogenetic diversification within each. Non-parametric Kolmogorov-Smirnov (K-S) tests of maximum pairwise differences between these curves indicates that the Greenland Sea population has a markedly younger phylogenetic structure than either the White Sea population or the two Northwest Atlantic populations, which are of intermediate age and homogeneous structure. The Monte Carlo and K-S assessments provide sensitive quantitative tests of within-species mitogenomic phylogeography. This is the first study to indicate that the White Sea and Greenland Sea populations have different population genetic histories. The analysis supports the hypothesis that Harp Seals comprises three genetically distinguishable breeding populations, in the White Sea, Greenland Sea, and Northwest Atlantic. Implications for an ice-dependent species during ongoing climate change are discussed.