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Post by Admin on Apr 25, 2022 0:52:13 GMT
Genetic Dataset. We whole-genome sequenced 12 ancient individuals from two archaeological sites in the San Francisco Bay Area to a depth of 0.06 to 7.8× and mean 2.4×, after excluding two samples from the Rummey Ta Kuččuwiš Tiprectak site without sufficient genetic material (SI Appendix, Table S2 and Figs. S1–S3). Individuals from Síi Túupentak dated to 601 to 184 cal BP, and individuals from Rummey Ta Kuččuwiš Tiprectak dated to 1905 to 1826 cal BP. We also whole-genome sequenced eight present-day members of the Muwekma Ohlone tribe to high coverage, ranging from 18 to 25×. We assembled a dataset of relevant previously published samples. This dataset included 291 individuals from Asia, Europe, North America, and South America; it contained 68 ancient individuals and 223 modern individuals (SI Appendix, Table S3; Fig. 1A). After merging the new and previously published individuals, the dataset we analyzed contains 311 individuals, 80 ancient individuals and 231 present-day individuals, typed for 474,317 single-nucleotide polymorphisms (SNPs; see SI Appendix, Methods). Radiocarbon dates of the 12 newly sampled ancient individuals and those available for the previously published individuals are shown in Fig. 1B. Focusing on the ancient individuals from Nevada and California, we see that the dates fall into approximately three periods. The oldest group, from >4,000 cal BP, includes the individuals from Spirit Cave and those labeled Early San Nicolas. An intermediate group with ages between 2,000 to 1,500 cal BP includes the Lovelock Cave, Rummey Ta Kuččuwiš Tiprectak, and Barbara groups. The most recent set includes individuals from Síi Túupentak, North Channel Islands (in this study, San Miguel and Cruz), Late San Nicolas, and South Channel Islands (San Clemente and Catalina), mostly with dates <1,000 cal BP. Overview of Data Analysis. Using the sample of 311 present-day and ancient individuals, we performed principal components analysis (PCA) and model-based clustering analysis to identify genetic relationships among previously reported individuals, the newly sampled ancient individuals, and the present-day Muwekma Ohlone individuals. We then restricted attention to a subset of 165 individuals with ancestry relevant to the new individuals, and repeated the analysis, also analyzing identity-by-state (IBS) segment sharing (SI Appendix, Table S4). Whereas the PCA and model-based clustering analyses use the genotypes of the 474,317 SNPs directly, in order to identify IBS segments, we imputed genotypes from the ancient samples across the whole genome (Materials and Methods). In interpreting the results of the various analyses, we considered the relationships of the 12 newly sampled ancient individuals and eight present-day Muwekma Ohlone individuals to other individuals, as well as to each other.
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Post by Admin on Apr 25, 2022 17:48:23 GMT
The San Francisco Bay Area Individuals in the Context of Native American Genetic Diversity. First, using PCA and unsupervised model-based clustering, we explore the relationship between the San Francisco Bay Area individuals and previously published ancient and present-day individuals from surrounding regions. Fig. 2A shows a PCA plot of 311 individuals. European individuals cluster in the lower right corner of the plot, and the northernmost populations from Siberia, Alaska, and Greenland appear at the top of the figure. The lower left corner contains a cluster of individuals from California, Nevada, Mexico, and Central and South America. Fig. 2. PCA of all ancient and present-day individuals. (A) PCA of 311 individuals in the full dataset, including 231 modern and 80 ancient individuals. (B) An enlarged view of the cluster in the Bottom Left Corner of A. Clines are visible between these three corners of the plot. Three clines connect the left edge of the plot to the right corner of Europeans. Several Siberian individuals are placed along the upper right edge, a line of Pacific Northwest individuals connects the center of the left edge to the right corner, and a line of individuals from Mexico connects the lower left corner to the corner containing Europeans. These clines appear to reflect varying European admixture that aligns with principal component 1 (PC1). Present-day members of the Muwekma Ohlone tribe, who have a known history of admixture with European Americans, Mexicans, and Mexican Americans, fall along the lower edge, with variable values for PC1. Focusing on the cluster of individuals from California, Nevada, Mexico, and South America, Fig. 2B enlarges the lower left corner of Fig. 2A. In the enlarged view, individuals from South America appear in the bottom left corner, anchoring a south-to-north cline along PC2. At the top of Fig. 2B, the individuals from Lovelock Cave in Nevada, who are close in age to those from the Rummey Ta Kuččuwiš Tiprectak and Barbara sites (Fig. 1B), fall above the main cluster. The ancient individuals from the San Francisco Bay Area cluster with the ancient individuals from Southern California along the left edge of Fig. 2B. Model-based unsupervised clustering for K = 10 clusters, performed using NGSadmix, appears in Fig. 3. From Asia to South America, we first observe a cluster that appears largely in Mongolia and Siberia (dark blue) and a cluster that appears in Siberia, Greenland, and Alaska (light blue). Two clusters appear primarily in the Pacific Northwest and Alaska, with one centered on Stswecem’c and Splatsin (light green) and the other appearing in most other populations from the region (dark green). A sample of Europeans is assigned to a single cluster, which is seen in many populations in the plot (red). Among the remaining five clusters, three are centered on specific populations: Akimel O’odham (formerly termed Pima; light orange), Karitiana (pink), and Surui (light purple). One is centered on native populations of Mexico and South America (dark orange). PCA of all ancient and present-day individuals. (A) PCA of 311 individuals in the full dataset, including 231 modern and 80 ancient individuals. (B) An enlarged view of the cluster in the Bottom Left Corner of A. Clines are visible between these three corners of the plot. Three clines connect the left edge of the plot to the right corner of Europeans. Several Siberian individuals are placed along the upper right edge, a line of Pacific Northwest individuals connects the center of the left edge to the right corner, and a line of individuals from Mexico connects the lower left corner to the corner containing Europeans. These clines appear to reflect varying European admixture that aligns with principal component 1 (PC1). Present-day members of the Muwekma Ohlone tribe, who have a known history of admixture with European Americans, Mexicans, and Mexican Americans, fall along the lower edge, with variable values for PC1. Focusing on the cluster of individuals from California, Nevada, Mexico, and South America, Fig. 2B enlarges the lower left corner of Fig. 2A. In the enlarged view, individuals from South America appear in the bottom left corner, anchoring a south-to-north cline along PC2. At the top of Fig. 2B, the individuals from Lovelock Cave in Nevada, who are close in age to those from the Rummey Ta Kuččuwiš Tiprectak and Barbara sites (Fig. 1B), fall above the main cluster. The ancient individuals from the San Francisco Bay Area cluster with the ancient individuals from Southern California along the left edge of Fig. 2B. Model-based unsupervised clustering for K = 10 clusters, performed using NGSadmix, appears in Fig. 3. From Asia to South America, we first observe a cluster that appears largely in Mongolia and Siberia (dark blue) and a cluster that appears in Siberia, Greenland, and Alaska (light blue). Two clusters appear primarily in the Pacific Northwest and Alaska, with one centered on Stswecem’c and Splatsin (light green) and the other appearing in most other populations from the region (dark green). A sample of Europeans is assigned to a single cluster, which is seen in many populations in the plot (red). Among the remaining five clusters, three are centered on specific populations: Akimel O’odham (formerly termed Pima; light orange), Karitiana (pink), and Surui (light purple). One is centered on native populations of Mexico and South America (dark orange). Fig. 3. Model-based clustering of all 311 ancient and present-day individuals, with K = 10 clusters. The results represent a summary of 10 independent runs of unsupervised clustering. Each of the 10 clusters is represented by a color, and each individual is represented by a vertical bar. To aid interpretation, clustering results from a unified analysis are depicted over two rows. Ancient individuals are denoted by an orange horizontal line below the plot, and present-day individuals are denoted by a black horizontal line. The ancient individuals from the San Francisco Bay Area and Southern California both have majority membership in the same component (purple). As in the PCA, these two groups cluster together. We also observe, as seen by Scheib et al. (15), that the ancient individuals from Southern California separate into two groups: Individuals from San Nicolas and the Southern Channel Islands have membership primarily in a single component (purple), whereas individuals from Barbara and the North Channel Islands have more substantial membership in a second component as well (orange). As was seen by Moreno-Mayar et al. (16), we find that the individuals from Lovelock Cave in Nevada have noticeable membership in a component shared with those from the Pacific Northwest (light green, dark green), a similar signal to their separation in the PCA plot in Fig. 2B. The present-day Muwekma Ohlone are known to have European, Mexican, and Ohlone genealogical ancestors, consistent with the appearance of the red, orange, and purple components observed in these individuals.
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Post by Admin on Apr 25, 2022 19:39:07 GMT
Population Structure Within Western North American Populations. Next, we consider a subset of 165 individuals to more closely examine population structure within western North America. For this subset, we perform PCA, model-based clustering, and analysis of IBS segment sharing. Fig. 4A shows the first two principal components. The ancient individuals from San Nicolas and the South Channel Islands cluster are in the top left corner, with the remaining Southern California individuals from Barbara and the North Channel Islands appearing below them along the left side. The European individuals cluster on the right side. Most remaining individuals cluster in the bottom left corner, including those from Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak. Muwekma Ohlone and MXL (Mexican in Los Angeles) individuals fall along a cline connecting the lower left corner to the cluster containing Europeans, the same cline observed in Fig. 2A. Fig. 4. PCA of a subset of ancient and present-day individuals, considering 165 samples with ancestry relevant to newly sampled individuals from the San Francisco Bay Area. (A) PCs 1 and 2. (B) PCs 2 and 3. We plot PC2 with PC3 in Fig. 4B. In this plot, the individuals from Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak separate from the large cluster that appeared in the lower left corner of Fig. 4A. In the top left corner, the individuals from Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak cluster together. Populations placed near these individuals in Fig. 4A, including several Indigenous populations from Mexico, appear in the center and lower left corner. Inferences with unsupervised model-based clustering for K = 4 and 5 appear in Fig. 5. At K = 4, we observe four clusters that are largely similar to four of the clusters seen in the K = 10 analysis shown for the larger dataset in Fig. 3. The European individuals are placed in one cluster (red), the Akimel O’odham individuals are assigned primarily to a second cluster (light orange), a third cluster is centered on individuals from Mexico (dark orange), and a fourth is centered on the ancient individuals from California (purple). Fig. 5. Model-based clustering of a subset of ancient and present-day individuals, considering 165 samples with ancestry relevant to newly sampled individuals from the San Francisco Bay Area. Separately for K = 4 and K = 5, the results represent a summary of 10 independent runs of unsupervised clustering. Coloring is the same as described in Fig. 3. Increasing K to 5 splits the purple cluster into two, with the purple cluster remaining centered on the individuals from Southern California and the new blue cluster centered on the ancient individuals from the San Francisco Bay Area. A small amount of membership is seen in this blue cluster in other populations, including the individuals from Barbara and the North Channel Islands, the Spirit Cave and Lovelock Cave samples, the North American samples, the Lagoa sample from South America, and the modern Muwekma Ohlone. To further understand population structure in western North America, we evaluate IBS genomic sharing between pairs of individuals, focusing on 53 ancient individuals from Nevada, California, and Mexico and employing genome-wide imputed genotypes (Fig. 6). The individuals from the oldest site, Spirit Cave in Nevada, share segments broadly, potentially reflecting ancestral haplotype sharing with many more recent individuals because of their increased ages. To some extent, a similar pattern is seen for individuals from the next oldest site, Early San Nicolas.
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Post by Admin on Apr 25, 2022 22:03:00 GMT
Fig. 6. The highest levels of IBS sharing occur along the diagonal between individuals from the same population. The analysis suggests four clusters—Nevada, San Francisco Bay Area, North Channel Islands together with Barbara, and South Channel Islands—for which pairs within a cluster possess elevated IBS sharing relative to pairs from distinct clusters. Segment sharing decreases for pairs from distinct clusters, with the exception of the sharing between individuals from the North Channel Islands and the Late South Channel Islands, who are close in age. The clustered pattern of IBS sharing mirrors observations seen in Figs. 4 and 5. Because the highest levels of sharing occur within these population clusters and because the individuals in a cluster have a range of ages, the IBS sharing within each cluster suggests population continuity over space and over time, in the sense that subsequent populations possess ancestry in prior populations. Focusing on the San Francisco Bay Area, the elevated sharing between the individuals from the older Rummey Ta Kuččuwiš Tiprectak site and the more recent Síi Túupentak site and the relatively low sharing of these individuals to others suggest a notable level of genetic continuity in time between the two sites and that at both of the time periods they represent, their populations possessed distinct ancestry from contemporaneous individuals in Nevada and Southern California. Present-day Muwekma Ohlone and Ancient Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak Individuals. Present-day members of the Muwekma Ohlone tribe are known to possess European, Mexican, and Ohlone genealogical ancestors, and we observe this history of admixture in many of our analyses. In Figs. 2A and 4A, the Muwekma Ohlone lie along a cline on PC1, reflecting European and Mexican admixture. In Figs. 3 and 5, the largest cluster memberships for the Muwekma Ohlone appear in the cluster centered on the European individuals (red) and the cluster centered on Indigenous individuals from Mexico (dark orange). Despite this signal of admixture, the analyses consistently suggest shared ancestry between the Muwekma Ohlone and the individuals from the Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak sites. In Fig. 3 and in the analysis with K = 4 in Fig. 5, the Muwekma Ohlone share membership with the ancient individuals from California, both those from the San Francisco Bay Area and those from Southern California (purple). In Fig. 5, at K = 5, we also see that the cluster centered on the individuals from Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak is visible in the Muwekma Ohlone (blue). By excluding membership corresponding to European admixture, we can compare the shared membership that the Muwekma Ohlone possess with the cluster centered on Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak to corresponding shared membership that other modern populations possess with this cluster. In Fig. 7, for various modern populations, we consider the relative proportion that appears in the blue component in the K = 5 plot in Fig. 5 in modern individuals, as a fraction of total membership excluding the red component centered on the European individuals. This analysis reveals that the Muwekma Ohlone possess a larger relative proportion of the blue component than do other populations; Mann-Whitney tests for the eight Muwekma Ohlone produce P = 5.6 × 10−4 for a comparison with 22 MXL individuals, P = 3.0 × 10−5 with 12 Akimel O’odham individuals, and P = 4.0 × 10−6 with 21 Maya individuals (with small sample sizes of two individuals each, P = 0.09 with Mixtec, P = 0.02 with Mixe, and P = 0.04 with Zapotec). Hence, despite the admixture history of the Muwekma Ohlone, so that the population possesses multiple membership components, one membership component shared between the Muwekma Ohlone and the ancient individuals from the Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak sites—a component suggestive of a partial shared ancestry—can be observed. This sharing between the present-day and ancient individuals is further supported in additional tests using the f4 statistic, by which greater similarity is observed between the Muwekma Ohlone and the Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak sites than between the Muwekma Ohlone and ancient individuals from surrounding regions (SI Appendix, Table S5). Fig. 7. Membership in the blue cluster in the K = 5 cluster analysis in Fig. 5, divided by one minus membership in the red cluster, for present-day populations from California and Mexico. For each individual, the proportion is calculated as the membership fraction in the blue cluster divided by the total fraction of membership in the blue, purple, light orange, and dark orange clusters. Individual values and boxplots are shown.
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Post by Admin on Apr 26, 2022 17:11:54 GMT
Discussion In this study, we sequenced genomes of 12 ancient individuals from two archaeological sites in the San Francisco Bay Area and eight present-day members of the Muwekma Ohlone tribe. To study population structure within California and western North America more broadly, we compared these individuals to previously published genomes of ancient and present-day Indigenous individuals. We also compared the 12 ancient individuals and eight modern individuals from the San Francisco Bay Area. Continuity of Ancient and Modern Populations in the San Francisco Bay Area. We first performed analyses of the newly sampled ancient individual genomes with a broad sample containing individuals from North America, South America, Europe, and Siberia. In these analyses, the ancient individuals from the Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak sites clustered most closely with the ancient individuals from Southern California. Using PCA, the individuals from these groups overlap (Fig. 2), and with model-based clustering, we see that a shared cluster is centered on them (Fig. 3, purple). Next, we focused our analysis on a subset of populations with ancestry relevant to the newly sequenced ancient individuals. In finer-scale analysis, the ancient individuals from the San Francisco Bay Area and Southern California, who cluster together in the larger dataset, are split into separate clusters. With PCA, the individuals from Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak cluster together (Fig. 4), and with model-based clustering, at K = 5, a cluster is centered on the ancient individuals from the San Francisco Bay Area (Fig. 5, blue). In an analysis of IBS sharing, we find elevated sharing among the ancient San Francisco Bay Area individuals from the two archaeological sites relative to the sharing with individuals from Mexico, Nevada, and Southern California. Finally, we considered the relationship between the ancient individuals from Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak and their relationship to the present-day Muwekma Ohlone. Although the present-day individuals also possess recent European and Mexican ancestry, we find that they also share ancestry with the ancient individuals. In particular, considering fractions of individual genomes estimated to have Indigenous ancestry, we found in Fig. 7 that the Muwekma Ohlone share a relatively high proportion of a cluster shared with the ancient individuals from the San Francisco Bay Area (blue cluster in Fig. 5). The shared ancestry components provide support for genetic continuity between the individuals from the Rummey Ta Kuččuwiš Tiprectak and Síi Túupentak archaeological sites and between the two sites and the present-day Muwekma Ohlone. This continuity, in the sense of a possible genealogical descent relationship connecting the more ancient and more recent populations, would then extend from the Rummey Ta Kuččuwiš Tiprectak individuals, dated to 1905 to 1826 cal BP, through the Síi Túupentak individuals, who date to 601 to 184 cal BP, to current tribal members. The two archaeological sites represent substantially longer time periods than the dates associated with the particular individuals sampled; Rummey Ta Kuččuwiš Tiprectak was inhabited 2440 to 175 cal BP, most actively during 2440 to 1610 cal BP, and Síi Túupentak spans 605 to 100 cal BP. The genetic connections between the two archaeological sites and between the sites and the present-day Muwekma Ohlone individuals suggest that the present-day Muwekma Ohlone share continuity with peoples who have inhabited the San Francisco Bay Area for at least two millennia, since the genetic sampling period for Rummey Ta Kuččuwiš Tiprectak, 1905 to 1826 cal BP, and potentially to the earliest dates of the site, around 2440 cal BP. These results suggest that models in which ancestral Ohlone populations are posited to have migrated to the region 1,500 to 1,000 y ago (3, 37, 38) provide underestimates of the continuity of the population. They are compatible with reconstructions that posit Ohlone population continuity in this portion of the San Francisco Bay Area extending back to 2,500 y ago or possibly earlier (39–41). We note that the population continuity we have observed between the archaeological sites and the current Muwekma Ohlone takes the form of a continuity of genetic ancestry components and a noteworthy sharing of genomic segments. This form of genetic continuity does not provide formal evidence that the modern individuals are directly descended from the individuals studied from these archaeological sites, but it is compatible with a view that the modern population is descended from those in the archaeological sites or from genetically similar contemporaneous populations. That this continuity is detectable is perhaps surprising, considering the extreme disruption and increase in deaths of the Ohlone caused by Spanish occupation. Mission records document substantial intermixture with neighboring non-Ohlone groups that began after other tribal groups (notably Coast Miwok, Bay Miwok, Plains Miwok, and Yokuts) from neighboring areas were brought to the same missions because of the rapid decline of Bay Area Ohlone mission populations (9, 42). As a result, for example, some descendants of marriages between Ohlone and non-Ohlone individuals identified culturally as Ohlone, spoke the language, and maintained key cultural traditions (28, 30, 43). Genetic continuity with the archaeological sites is detectable despite this intermixture of Indigenous populations from locations relatively distant from the sites. Interpretations in Relation to the Penutian Language Family. Attempts to explain the complex mosaic of California languages and language families at European contact have given primacy to historical linguistic reconstructions that posit successive precontact migrations and displacements of various language groups and approximate timings of language divergence within families (44–46). Archaeologists have then looked for changes in the precontact archaeological record that would test these models. As a result, precontact California history is often framed as possessing linguistic and archaeological cultural concordance (40, 47). With respect to the San Francisco Bay Area, this view holds that speakers of Hokan languages initially occupied central California. Subsequently, Hokan speakers were then pushed to geographic peripheries by Penutian speakers entering California in a series of migrations and inhabiting the Central Valley and Bay Area (3, 13, 40, 48). Proto-Penutian speakers in California are hypothesized to have originated in the Great Basin or possibly on the Columbian Plateau. This hypothesis has been based on historical linguistic reconstructions, archaeological investigations, and recent mitochondrial DNA research (3, 40, 49)—notably including similarities in material culture (projectile point types, stone pipes, extensive bone tool industry with distinctive types, and basketry techniques) between the Lovelock Culture of western Nevada and the appearance of the Windmiller Pattern in central California during the Late Holocene (40, 48, 50). The Ohlone language falls within the geographically extensive Penutian language family, most closely related to the neighboring Miwok and Yokuts languages (44–48). The four ancient Lovelock Cave individuals are clustered to some extent with ancient individuals from the San Francisco Bay Area and Southern California (Fig. 2). They also share two ancestry clusters with ancient and modern individuals from the Pacific Northwest (Fig. 3, light green, dark green). Four ancient Pacific Northwest Coast individuals, along with the ancient Big Bar individual also from the Pacific Northwest, possess a small amount of membership in a cluster shared with the ancient individuals from Nevada and California (Fig. 3, purple). These patterns are compatible with a view that the Lovelock Cave individuals share similarities with Penutian groups that spread both into the Pacific Northwest and into California (48). In this view, the shared ancestry component could represent a signature of a spread of the Penutian languages, with the Lovelock Cave individuals and the Pacific Northwest Coast and Big Bar individuals both descended from ancestors in the Great Basin region (Fig. 3, purple). Despite this similarity to the ancient individuals from Lovelock Cave, both the ancient San Francisco Bay Area individuals and the present-day Muwekma Ohlone individuals clustered more closely with ancient individuals from Southern California, where the Penutian language family is absent, than with the (possibly Penutian-speaking) Lovelock Cave individuals associated with Lovelock Culture. Because our analyses do not cluster individuals associated with putative regions of Penutian speakers together (e.g., Lovelock Cave, Pacific Northwest, San Francisco Bay Area), we can conclude that if Penutian languages did spread from the Great Basin into California, then either the spread might have involved linguistic rather than demic diffusion or a shared genetic signal of an initial migration has been eroded by subsequent demographic processes. In both scenarios, genetic and linguistic histories in California are not coupled, so that a history of the spread of cultures in the region is unlikely to always align with the spread of languages. This perspective is consistent with the challenges archaeologists have noted in trying to link historical linguistic models of migrations of populations speaking specific languages with clear changes in the archaeological record, resulting in widely divergent suggestions for the timing of these migration events (13, 14, 51). We note that in Southern California, we observed a consistent separation of South Channel Islands and San Nicolas individuals from individuals from the North Channel Islands and Barbara, amplifying a pattern visible in figure S11 in Scheib et al. of ref. 15. The ancient individuals from Barbara and the North Channel Islands cluster with the ancient San Francisco Bay Area samples, separating from the individuals from the South Channel Islands, including the individuals from San Nicolas Island. This separation accords with a language boundary at the time of European contact: Individuals from Barbara and the North Channel Islands spoke Chumash languages (considered either part of the Hokan group or an ancient linguistic isolate), whereas individuals from the South Channel Islands (plus San Nicolas) spoke Takic languages of the Uto-Aztecan group (45, 46). Takic language speakers are hypothesized to have migrated from the Great Basin into Southern California during the last 5,000 y, with uncertain timing of their arrival on the coast and the South Channel Islands (1, 40, 45, 52). The genetic clustering of Early San Nicolas Island individuals (dated from 5,000 to 4,000 cal BP) with Late San Nicolas Island individuals (dated to 2,000 cal BP or later) but separate from individuals from the North Channel Islands and Barbara suggests population continuity on San Nicolas during this time span and is compatible with the reconstruction that posits an early arrival of Takic language speakers on San Nicolas.
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