Post by Admin on May 25, 2020 4:39:45 GMT
Discussion
These data support a shared ancestry for the indigenous peoples of the Northwest Coast dating back to at least ∼10,300 cal y B.P. The individual supporting this scenario is Shuká Káa, who belongs to mtDNA haplogroup D4h3a. Although both Anzick-1 and 939 also belong to this mtDNA haplogroup, later ancient and modern individuals of the Northwest Coast do not (13, 22). Despite belonging to different mtDNA haplogroups, Shuká Káa exhibits a close nuclear DNA relationship with 302 (∼2,500 cal y B.P.) and 443 (∼1,750 cal y B.P.), both of whom belong to mtDNA haplogroup A2, which is observed today at high frequencies among modern Northwest Coast populations (22). Thus, based on the limited mtDNA data alone, the hypothesis of a change in the genetic composition of the Northwest Coast appearing by the time of 302 and 443 might be plausible. However, our more extended genome-wide analysis does not support a change in the genetic composition of the Northwest Coast appearing by the time of 302 and 443, both of whom form a sister clade with the Tsimshian (Fig. S5). Instead, we observe a trend of genetic continuity through time, which is exemplified by individual 939 who displays affinities with both the more recent Northwest Coast ancient individuals and Shuká Káa. Individual 939 shares the same mtDNA haplogroup D4h3a as Shuká Káa while belonging to the predominant North American ancestry component observed in 443 and 302 (Fig. 2D). Furthermore, previously published complete mitochondrial genome data from individual 938 (13), who is similar in age and found on the same island site as 939, exhibit an A2 mtDNA haplogroup. These results indicate that the two haplogroups were already present in the ancestral population and are not the result of later gene flow into the area.
Also of interest is the evidence for the placement of Shuká Káa on different lineages than Anzick-1 and Kennewick Man (Fig. S9D). Despite their shared North American geographies and time periods as well as evidence that a single peopling event occurred in the late Pleistocene (23), our analyses show that population structure existed in the late Pleistocene of North America. These data are concordant with the late Pleistocene archaeological record documenting distinct contemporaneous archaeological cultures in different regions of North America (24).
We find that the placement of Shuká Káa (based on D-statistic simulations) is consistent with residing on a branch with modern day indigenous people from the Northwest Coast, whereas Anzick-1 fits separately on a branch that leads to the southern lineage, including populations from Central and South America (Fig. 4). Our result suggests that Shuká Káa was part of a population closely related to the ancestors that gave rise to the current populations of the northern Northwest Coast.
Fig. 4.
Shuká Káa in relation to other Native American groups. Schematic showing Shuká Káa placed on the branch leading to North Americans, which is supported by simulation-based D statistics.
On a broader scope, ADMIXTURE analysis revealed a component that dominates contemporary North American populations, which increases over time regarding the Northwest Coast (Fig. 2D and Fig. S10). We also observe a small fraction of this component in the 24,000-y-old MA-1 individual from Siberia (19) (Fig. 2D). This result suggests that the North American component reflects an early ancestral lineage that has drifted through time to high frequency on the Northwest Coast.
Fig. S10. Cluster analysis generated by ADMIXTURE. Set includes indigenous populations from the Americas, Siberia, and the Arctic, Greenland and the Anzick-1, Kennewick, S
It should be noted that, because of the highly degraded nature of the DNA extracted from Shuká Káa sample, the autosomal analyses had less than the optimal number of overlapping sites (Table 2). This outcome is likely the cause for the lack of significance in both the ranked f3 and D statistics when regarding Shuká Káa. In light of these observations, projections that consider missing data and contamination corrections were used to help mitigate the low number of sites available (SI Text). Despite these limitations, the analyses presented here, taken as a whole and compared with higher-depth samples, paint a sensible and convincing picture of the peopling of the Northwest Coast.
We conclude that the Northwest Coast exhibits an ancestral lineage that stems from the initial peopling of the region. The observed temporal change of mtDNA haplogroups in the area was probably caused by sampling, and no clear signs of gene flow into the area after the first settlement have been identified. Shuká Káa, who lived some 10,300 y ago, was part of an ancestral population that may have first populated the region but was distinct from ancestral populations related to Anzick-1. Although we cannot use our data to identify the specific ancestral location of this coastal lineage, the facts that Shuká Káa lived over 10,000 y ago and that Anzick-1 is related to the South American lineage suggest that the ancestral population likely existed north of the continental ice before the deglaciation of the interior corridor sometime after 12,600 y B.P. (23). This inference is supported by both the ADMIXTURE analysis showing a large component of ancestry of Shuká Káa shared with Siberian populations (the yellow component) and previous analysis by Verdu et al. (25) that suggests a closer relationship to Northeast Asian groups by Pacific Northwest populations than Central and South American populations.
The collaborative approach of this study shows an example of how indigenous community members and scientific researchers can work together in a positive and mutually beneficial way. In addition, the results presented here reveal the power of regional studies to elucidate demographic complexities, shedding light on the peopling of the Northwest Coast and the early ancestral lineages of North America.
These data support a shared ancestry for the indigenous peoples of the Northwest Coast dating back to at least ∼10,300 cal y B.P. The individual supporting this scenario is Shuká Káa, who belongs to mtDNA haplogroup D4h3a. Although both Anzick-1 and 939 also belong to this mtDNA haplogroup, later ancient and modern individuals of the Northwest Coast do not (13, 22). Despite belonging to different mtDNA haplogroups, Shuká Káa exhibits a close nuclear DNA relationship with 302 (∼2,500 cal y B.P.) and 443 (∼1,750 cal y B.P.), both of whom belong to mtDNA haplogroup A2, which is observed today at high frequencies among modern Northwest Coast populations (22). Thus, based on the limited mtDNA data alone, the hypothesis of a change in the genetic composition of the Northwest Coast appearing by the time of 302 and 443 might be plausible. However, our more extended genome-wide analysis does not support a change in the genetic composition of the Northwest Coast appearing by the time of 302 and 443, both of whom form a sister clade with the Tsimshian (Fig. S5). Instead, we observe a trend of genetic continuity through time, which is exemplified by individual 939 who displays affinities with both the more recent Northwest Coast ancient individuals and Shuká Káa. Individual 939 shares the same mtDNA haplogroup D4h3a as Shuká Káa while belonging to the predominant North American ancestry component observed in 443 and 302 (Fig. 2D). Furthermore, previously published complete mitochondrial genome data from individual 938 (13), who is similar in age and found on the same island site as 939, exhibit an A2 mtDNA haplogroup. These results indicate that the two haplogroups were already present in the ancestral population and are not the result of later gene flow into the area.
Also of interest is the evidence for the placement of Shuká Káa on different lineages than Anzick-1 and Kennewick Man (Fig. S9D). Despite their shared North American geographies and time periods as well as evidence that a single peopling event occurred in the late Pleistocene (23), our analyses show that population structure existed in the late Pleistocene of North America. These data are concordant with the late Pleistocene archaeological record documenting distinct contemporaneous archaeological cultures in different regions of North America (24).
We find that the placement of Shuká Káa (based on D-statistic simulations) is consistent with residing on a branch with modern day indigenous people from the Northwest Coast, whereas Anzick-1 fits separately on a branch that leads to the southern lineage, including populations from Central and South America (Fig. 4). Our result suggests that Shuká Káa was part of a population closely related to the ancestors that gave rise to the current populations of the northern Northwest Coast.
Fig. 4.
Shuká Káa in relation to other Native American groups. Schematic showing Shuká Káa placed on the branch leading to North Americans, which is supported by simulation-based D statistics.
On a broader scope, ADMIXTURE analysis revealed a component that dominates contemporary North American populations, which increases over time regarding the Northwest Coast (Fig. 2D and Fig. S10). We also observe a small fraction of this component in the 24,000-y-old MA-1 individual from Siberia (19) (Fig. 2D). This result suggests that the North American component reflects an early ancestral lineage that has drifted through time to high frequency on the Northwest Coast.
Fig. S10. Cluster analysis generated by ADMIXTURE. Set includes indigenous populations from the Americas, Siberia, and the Arctic, Greenland and the Anzick-1, Kennewick, S
It should be noted that, because of the highly degraded nature of the DNA extracted from Shuká Káa sample, the autosomal analyses had less than the optimal number of overlapping sites (Table 2). This outcome is likely the cause for the lack of significance in both the ranked f3 and D statistics when regarding Shuká Káa. In light of these observations, projections that consider missing data and contamination corrections were used to help mitigate the low number of sites available (SI Text). Despite these limitations, the analyses presented here, taken as a whole and compared with higher-depth samples, paint a sensible and convincing picture of the peopling of the Northwest Coast.
We conclude that the Northwest Coast exhibits an ancestral lineage that stems from the initial peopling of the region. The observed temporal change of mtDNA haplogroups in the area was probably caused by sampling, and no clear signs of gene flow into the area after the first settlement have been identified. Shuká Káa, who lived some 10,300 y ago, was part of an ancestral population that may have first populated the region but was distinct from ancestral populations related to Anzick-1. Although we cannot use our data to identify the specific ancestral location of this coastal lineage, the facts that Shuká Káa lived over 10,000 y ago and that Anzick-1 is related to the South American lineage suggest that the ancestral population likely existed north of the continental ice before the deglaciation of the interior corridor sometime after 12,600 y B.P. (23). This inference is supported by both the ADMIXTURE analysis showing a large component of ancestry of Shuká Káa shared with Siberian populations (the yellow component) and previous analysis by Verdu et al. (25) that suggests a closer relationship to Northeast Asian groups by Pacific Northwest populations than Central and South American populations.
The collaborative approach of this study shows an example of how indigenous community members and scientific researchers can work together in a positive and mutually beneficial way. In addition, the results presented here reveal the power of regional studies to elucidate demographic complexities, shedding light on the peopling of the Northwest Coast and the early ancestral lineages of North America.