A South American Prehistoric Mitogenome: Context, Continuity, and the Origin of Haplogroup C1d

<div><p>Based on mitochondrial DNA (mtDNA), it has been estimated that at least 15 founder haplogroups peopled the Americas. Subhaplogroup C1d3 was defined based on the mitogenome of a living individual from Uruguay that carried a lineage previously identified in hypervariable region I sequences from ancient and modern Uruguayan individuals. When complete mitogenomes were studied, additional substitutions were found in the coding region of the mitochondrial genome. Using a complete ancient mitogenome and three modern mitogenomes, we aim to clarify the ancestral state of subhaplogroup C1d3 and to better understand the peopling of the region of the Río de la Plata basin, as well as of the builders of the mounds from which the ancient individuals were recovered. The ancient mitogenome, belonging to a female dated to 1,610±46 years before present, was identical to the mitogenome of one of the modern individuals. All individuals share the mutations defining subhaplogroup C1d3. We estimated an age of 8,974 (5,748–12,261) years for the most recent common ancestor of C1d3, in agreement with the initial peopling of the geographic region. No individuals belonging to the defined lineage were found outside of Uruguay, which raises questions regarding the mobility of the prehistoric inhabitants of the country. Moreover, the present study shows the continuity of Native lineages over at least 6,000 years.</p></div

TMRCA estimates for the putative common ancestors of haplogroup C1d and subhaplogroup C1d3.

<p>BSP: Bayesian skyline plot. See Tables A and B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141808#pone.0141808.s004" target="_blank">S2 Text</a> for further details.</p><p>TMRCA estimates for the putative common ancestors of haplogroup C1d and subhaplogroup C1d3.</p

Map showing the location of the Uruguayan samples belonging to subhaplogroup C1d3 with the five complete mitogenomes used in this study.

<p>The locations of the living individuals (circles) correspond to their mothers’ birthplace. The archaeological site where the prehistoric sample was recovered is marked with a square.</p

Ancient DNA Analysis of Mid-Holocene Individuals from the Northwest Coast of North America Reveals Different Evolutionary Paths for Mitogenomes

<div><p>To gain a better understanding of North American population history, complete mitochondrial genomes (mitogenomes) were generated from four ancient and three living individuals of the northern Northwest Coast of North America, specifically the north coast of British Columbia, Canada, current home to the indigenous Tsimshian, Haida, and Nisga’a. The mitogenomes of all individuals were previously unknown and assigned to new sub-haplogroup designations D4h3a7, A2ag and A2ah. The analysis of mitogenomes allows for more detailed analyses of presumed ancestor–descendant relationships than sequencing only the HVSI region of the mitochondrial genome, a more traditional approach in local population studies. The results of this study provide contrasting examples of the evolution of Native American mitogenomes. Those belonging to sub-haplogroups A2ag and A2ah exhibit temporal continuity in this region for 5000 years up until the present day. Of possible associative significance is that archaeologically identified house structures in this region maintain similar characteristics for this same period of time, demonstrating cultural continuity in residence patterns. The individual dated to 6000 years before present (BP) exhibited a mitogenome belonging to sub-haplogroup D4h3a. This sub-haplogroup was earlier identified in the same general area at 10300 years BP on Prince of Wales Island, Alaska, and may have gone extinct, as it has not been observed in any living individuals of the Northwest Coast. The presented case studies demonstrate the different evolutionary paths of mitogenomes over time on the Northwest Coast.</p></div

Phylogeny of complete mitochondrial genomes sequenced in this study.

<p>Mutations are transitions unless specified. Transversions are indicated by an A, G, C, or T after the nucleotide position. Insertions are indicated by an “i”, deletions are indicated by a “d”, recurrent mutations are underlined, and mutations back to the rCRS nucleotide are designated by a “@”. The C stretch length polymorphism in region 303–315 was disregarded in the tree. The sample “Haida 9″ was analyzed in Schurr et al. (2012). All other samples were analyzed in this study.</p