Examining the Pro to-Algonquian Migration: Analysis of mtDNA

BETH A. SCHULTZ, RIPAN S . MALHI AND DAVID G. SMITH University of California, Davis

The study of Algonquian history is of interest to both linguists and archaeologists who have formulated hypotheses regarding the time and place of their homeland. With recent advances in genetic technology and the examination of mitochondrial DNA of Native Americans in the north­ eastern portion of North America, we can test the likelihood of these pre­ viously suggested hypotheses. 1 Sapir (1913) first suggested the term Ritwan to denote the California languages Wiyot and Yurok, and later (1916) suggested a distant genetic relationship with the Algonquian languages of the East, and named this language family Algic. This relationship is significant primarily because of its wide geographic spread. In 1929, Sapir subdivided Native American languages into six major groups, one of which was Algonkin-Wakashan (Almosan). The similarities he noted between the West Coast Wakashan language (and other Mosan languages) and the Algonquians in the East strengthened his hypothesis for a western homeland for Proto-Algonqui­ ans. Further linguistic evidence has since provided support for the Algon­ quian-Ritwan connection and is regarded by most historical linguists as proven (Haas 1960, 1965; Goddard 1975). While the Almosan grouping has been scrutinized, no strong linguistic evidence has emerged for this grouping (Haas 1965). Most recently, Campbell (1997) regarded Sapir's classification as controversial, with a "- 75 % probability" of sharing a common ancestor; in other words, Campbell believes there is a strong likelihood that there is not a common ancestor for Almosan. Although there is little evidence for a strong genetic relationship between the Algonquian and Mosan languages, independent evidence suggests that Proto-Algonquians originated in the Northwest. The linguis­ tic diversity within Algonquian groups is lower in the East than in the West, and thus provides evidence of a West to East migration (Goddard 1994). Haas (1965) has shown cognate and sound correspondences for

I. Beth A. Schultz and Ripan S. Malhi contributed equall y to the research and analysis included in this paper. PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 471

Kutenai and Algonquian, as well as further relationships between Kutenai and Salishan. Denny (1989) highlights additional linguistic similarities between Kutenai, Salishan, and Algonquian. Rhodes (personal communi­ cation, 1999) suggests that the Algonquian languages may have been located on the Plateau before they began to diversify, which is why there are typological similarities among Algonquian, Salishan, Kutenai, and Wakashan. It is possible that this proposed spread of the Algonquian lan­ guage from West to East was a linguistic spread that did not involve the movement of people. In addition to linguistic evidence for a western homeland for Proto­ Algonquians, archaeological connections link prehistoric people of the Plateau to those of the East. The Western Idaho Archaic burial complex, dated between 4000 and 6000 ybp, shares many similarities with the Red Ocher and Glacial Kame traditions in the East (Pavesic 1985). These buri­ als are primarily found in sandy knolls with bodies in a flexed position, often covered with generous amounts of red ocher, and occasionally are alongside canine burials. Burial artifacts include marine shell beads (the Olivella type in western Idaho), cache blades (large, unnotched, bifacially chipped forms found primarily in graves), and the distinctive "turkey-tail" projectile point (Pavesic 1985). The "turkey-tail" projectile point is a large ceremonial type common to the Eastern Woodlands, and is morpho­ logically similar to those points found in the Western Idaho complex. When diagnostic features of the Red Ocher complex are compared to those of the Western Idaho complex, the features appear remarkably con­ gruent (Denny 1991). Based on the distribution in time and space of these similar burial complexes, Denny (1991) proposed that the people of the Western Idaho complex were Proto-Algonquian speakers, and they migrated to the Great Lakes approximately 4000 ybp.

MITOCHONDRIAL DNA Using mitochondrial DNA (mtDNA), we can examine genetic rela­ tionships between modern and ancient peoples in North America. This allow u to determine whether or not modem Algonquian-speaking peo­ ple are genetically similar to ancient peoples of the Glacial Kame and/or We tern Idaho Archaic burial complexes, or to other modem people of the Pacific Northwes t. We can also investigate, assuming a pre-historic Proto­ Algonquian migration from the West, whether the Algonquian expansion wa pri marily one of people or of language and culture. 472 BETH A. SCHULTZ, RIPAN S. MALHI AND 0AVID G. SMITH

The mitochondrial genome is small, circular and located outside the nucleus in the cell, and is characterized by features that make it ideal for addressing these questions. First, because it is extra-nuclear, mtDNA does not undergo meiosis and thus is passed on only from mother to offspring, without recombination (Giles et al. 1980); the only source of variation in mtDNA is from mutation, allowing us to directly trace relationships between maternally related individuals. Second, this genome contains non-coding regions as well as loci coding for proteins used in cellular res­ piration that occurs in the mitochondria. Little selection acts upon the non-coding regions so mutations that appear here will not affect the sur­ vival of the individual (Avi se 1994, Stoneking 1990). With minimal selec­ tion, the environment will not play a directional role in the frequency of genotypes in a population. Third, mtDNA rapidly evolves at a rate from one to ten times as fast as nuclear DNA, with the non-coding regions accumulating mutations at the fastest rate (Stoneking 1990, Brown et al. 1979, Stoneking et al. 1986). This rapid rate of mutation accumulation is useful for evolutionary studies of groups with a recent common ancestor, and particularly for studies comparing human populations (Stoneking 1994, Johnson et al. 1983). Finally, the high copy number of mtDNA cre­ ates a higher probability of extracting DNA from ancient samples that have degraded over time (results are seen in Stone and Stoneking 1993, Kaestle 1997, 1998). Studies of multiple regions of the mitochondrial genome for varia­ tions, or polymorphisms, have revealed there to be five distinct lineage clusters, or haplogroups, of Native Americans (Schurr et al. 1990, Forster et al. 1996). Each maternally descended Native American belongs to one of these five haplogroups, referred to as haplogroup A, B, C, D, and X. While all of these haplogroups are widely represented throughout the Americas, haplogroup analysis has revealed a clear pattern in North America. Haplogroup A has a high frequency in the North, whereas hap­ logroup B is frequent in the Southwest. Haplogroup D is common in the Western interior, and haplogroups C and X are highest in frequency in the East (Lorenz and Smith, 1996, Mahli et al. 2001). The gain or loss of specific restriction sites (in the case of haplo­ groups A, C, D, and X) or the presence of a nine base-pair deletion (in the case of haplogroup B) in the mtDNA defines each of the five haplo­ groups. Restriction fragment length polymorphism (RFLP) analysis may be performed by adding a restriction enzyme to a particular sample of PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 473

DNA and allowing the enzyme to cut, or digest, the fragment as illus­ trated in Figure 1. The enzyme will only digest the fragment if it recog­ nizes a particular nucleotide sequence in the fragment; if there is a variation in that sequence, the enzyme will not digest it. Samples can then be run out on a polyacrylamide gel. DNA is negatively charged so it migrates to the anode of an electrical field, sorting the fragments by size. The digested sample of DNA appears as two small bands, and the undi­ gested sample as one large band, as Figure 2A illustrates. The restriction sites diagnostic of haplogroups A, C, D, and X are given in Table 1. The nine base-pair deletion can be detected by running out a specific fragment from region V of the mitochondrial genome on a polyacrylamide gel; individuals of haplogroup B will have a fragment that is nine base-pairs shorter than non-haplogroup B individuals, as shown in Figure 2B . A higher resolution analysis can be conducted by characterizing point mutations in the control region (largest of the non-coding regions) of the mtDNA. All control region sequences in our analysis are expressed as divergences from the Cambridge Reference Sequence (Anderson et al. 1981 ). Specific mutations in this sequence correspond with each of the five haplogroups and are shown in Table 2; together with additional muta­ tions unique to the individual, these mutations form an individual's haplo­ type. For example, individuals of haplogroup A can be identified by ancestral mutational changes at nucleotide positions (nps) 16223 (cytosine to thymine transition), 16290 (cytosine to thymine transition), and 16319 (guanine to adenine transition), but an individual may also have markers specific to their maternal lineage (i.e. the Cheyenne/Arap­ aho individual in Table 2 has cytosine to thymine transition markers at nps 16111 and 16192). Current data suggest that the Americas were colonized by at least one member of each haplogroups A, B, C, D, and X (Brown et al . 1998, Schurr et al. 1990, Torroni et al. 1992). These five haplogroups may be the result of a ingle group migration, or they may have come in various migrations each bringing in different haplogroups, potentially with multiple migra­ tion bringing in different types of these five haplogroups. Haplogroups A, B, C, and D have been found in East Asia, but haplogroup X has not (Torroni et al. 1993). Haplogroup X is found in central and western Asia and in Europe; however, in most cases the European and Asian versions of haplogroup X differ from the Native American haplogroup X by a CR marker (the ab ence of a tran ition at np 16213, Brown et al. 1998). Since 474 BETH A. SCHULTZ, RIPAN S . MALHI AND DAVID G. SMITH the initial peopling of the Americas, these founding haplotypes have diversified, and in modern Native Americans, we can find variations of haplotypes that are specific to regional areas.

MoDERN MTDNA ANALYSIS For this study, we analyzed mtDNA samples from modern and prehis­ toric Native American groups shown in Figure 3, from northeastern North America and from the proposed Algonquian homeland in the Pacific Northwest. In the Northwest, we examined the Bella Coola (Salishan­ speakers), Nuu-Chah-Nulth (Wakashan-speakers), and Yakima (Sahaptin­ speakers). We also analyzed proto-historic samples from the Snake River and Memaloose Island dated to about 200 ybp. In the Northeast, we stud­ ied Algonquian-speaking populations, including the Turtle Mountain Chippewa, Northern Ontario Ojibwa, Wisconsin Chippewa, Manitoulin Island Ojibwa, Micmac, and Cheyenne or Arapaho individuals. We also examined neigh boring populations including the Sisseton-Wapheton Sioux, the Mohawk, and a pre-historic Oneota population from Norris Farms (approx. 700 ybp). The pre-historic Oneota and the proto-historic Northwest samples give a more accurate genetic representation of Native Americans in those regions at the time of contact. Sources of these sam­ ples are listed in Table 3. We tested the hypothesis that the ancestors of Algonquian speakers migrated into the Northeast from a western homeland on the Columbia Plateau and attempted to determine whether the Algonquian expansion was primarily a linguistic and cultural one, or a genetic one. If there were an Algonquian migration and a genetic expansion, we would expect to find similar haplogroup frequencies in both regions, as well as shared haplotypes between modern Algonquians and the Pacific Northwest Indi­ ans as illustrated in Figure 4.

Haplogroup analysis The haplogroup distributions of modern and prehistoric groups in the Northeast are shown in Figure 5. The Northeast is relatively homoge­ neous with respect to haplogroup frequency distributions; there is a high representation of haplogroups A and C, and a significant amount of haplo­ group X with respect to other regions across North America (Smith et al. 1999, Malhi et al. 2001). The distribution of haplogroup X is very high PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 475

(50%) in the Micmac, but this high frequency may be due to a small, non­ random sample. The Algonquian-speaking groups genetically resemble their modern neighbors, as well as the Norris Farms pre-historic popula­ tion, thus indicating regional continuity of haplogroups A, C, and X for at lea t the last 700 years. The only population without haplogroup X is the Iroquoian-speaking Mohawk, who, because of the absence of haplogroup X and a high frequency of haplogroup B, resemble the Cherokee- also Iroquoian speakers (Malhi et al. 2001). The haplogroup frequency distribution in groups from the Pacific Northwest, given in Figure 5B, shows a divergence between the groups located on the coast and those located more inland on the Plateau. The coastal Bella Coola and Nuu-Chah-Nulth have high frequencies of haplo­ groups A and D, as well as a significant amount of haplogroup C, but the frequency of haplogroup B in these populations is very low. The Yakima, Memaloose Island, and Snake River populations, located further inland, have a higher representation of haplogroup B, but relatively little haplo­ group A and C. Haplogroup A in the Memaloose Island sample is slightly larger than the Yakima and Snake River populations, perhaps because these Chinookan-speakers maintained close ties to groups along the Northwest Coast. Results of the principal component (PC) analysis, illustrated in Figure 6, further support the division of the Northwest populations into Coastal and Plateau groupings. PC analysis is a way of mapping multivariate data, in our case haplogroup frequency data, on a multi-dimensional scale. The fir t (horizontal) PC captures the greatest amount of variation, and should be given the most amount of attention, while the second (vertical) PC pro­ vide additional information on the variation between populations. In Fig­ ure 6 the Memaloose Island, Yakima, and Snake River populations form a di tinct group. The Nuu-Chah-Nulth group together with the Bella Coola, and also with populations of the Northeast. Modern haplogroup frequency distributions differ between the Coa tal and Plateau populations, with the Coastal groups more closely re embling Algonquian of the Northea t. To further inve tigate this and other po ible relation hip , we compared haplotype between the North­ we t Coa t/Plateau and Northea t populations. 476 BETH A. SCHULTZ, RIPAN S. MALHI AND DAVID G. SMITH

Haplotype analysis With sequence, or haplotype, data accumulated from Northeast popu­ lations we performed more specific analyses, including a mismatch distri­ bution analysis. Mismatch distributions are histograms of the number of sequence differences between each possible pair of individuals in the pop­ ulation. From the pattern of the histogram, we can infer population history (Harpending et al. 1998). If there has been continuous expansion and growth, resulting in a homogeneous population, we expect to see a smooth, unimodal distribution centered on the average number of pair- wise differences (Figure 7). If population size has remained relatively constant over a long period of time or if the population has been impacted by gene flow, however, we expect to see an uneven or multimodal distri­ bution. The mismatch distribution from the hypervariable region of Algon­ quians belonging to haplogroup A forms a unimodal distribution, given in Figure 7A. Sequences from Algonquians belonging to haplogroup C, shown in figure 7B, however, form a multimodal distribution. It appears that haplogroup A among Algonquians has undergone a significant expan­ sion. Haplogroup C, being multimodal, indicates that there are multiple C haplotypes represented, probably a result of admixture between two groups, one with haplogroup C but in which haplogroup A is absent or rare, the other group having both haplogroups A and C. Networks were constructed from DNA sequences within haplogroups A and C. Networks display the number of mutational differences among haplotypes in a graphic manner, highlighting any possible reticulations. The haplogroup A network, given in Figure 8A, is complex, possibly due to a rapid population expansion, which is consistent with the results of the mismatch distribution for haplogroup A. There is one shared haplotype within the Northeast, between Siouan and Algonquian speakers. The Bella Coola and the Nuu-Chah-Nulth also share one haplotype, but there are no shared lineages between the Northeast and the Northwest. The hap­ logroup C network, Figure 8B, clearly shows the differences between the Northeast and the Northwest, and again, no haplotypes are shared between these two regions.

Conclusions from modern mtDNA An examination of modern samples provides no clear evidence of a Proto-Algonquian migration involving female movement from the North- PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 477 west. Similar haplogroup frequencies exist between the Indigenous peo­ ples of the Pacific Coast and the Northeast, but these alone do not provide enough evidence for a genetic relationship. Upon further examination, there were no shared haplotypes between the Northeast and the Northwest Coast/Plateau. However, since the Algonquians are a heterogeneous group with respect to the diversity within haplogroup C, if a Proto-Algon­ quian migration did occur, it genetically absorbed some of the surround­ ing non-migrating population's variations of haplogroup C. It is possible that the specific populations chosen for study are far more genetically dis­ tant than other groups in the areas and, if studied, these populations might exhibit shared haplotypes between the two regions.

ANCIENT MTDNA ANALYSIS To better understand the genetic relationship between the Northwest Coast/Plateau and the Northeast, it is helpful to know the genetic compo­ sition of prehistoric populations, before and after the proposed Proto- Algonquian migration. We examine three of these prehistoric sites: 1) the Braden and DeMoss sites, part of the Western Idaho Archaic burial com­ plex located on the Snake River in the Plateau (approx. 6000 ybp); 2) the Congdon site near the Columbia River in the Plateau (approx. 3000 ybp) and 3) the Hind Site, a Glacial Kame site in southern Ontario (approx. 3000 ybp) (Figure 3). Modern haplogroup frequency distributions from the Northeast, the Plateau, and the Northwest Coast were collected into regional groupings as shown in Figure 9, due to the haplogroup continuity of these three regions, and were compared with the haplogroup frequencies of the ancient populations cited above, also shown in Figure 9. The Braden and DeMoss, Congdon, and Hind sites all had high (>40%) frequencies of haplogroup B, similar to the modern indigenous peoples of the Plateau. These ancient samples also exhibited little (<15%) haplogroup A, creating a clear differentiation from the Northeast and the ancient populations. Braden and DeMoss exhibits only haplogroups B and D, while the Cong­ don also exhibits a relatively low frequency of haplogroup C. The Hind site, although located in the Northeast, appears more similar to the groups on the Plateau than to modern Northeast groups. However, the small sam­ ple size of these ancient populations imposes a significant margin of error on the estimation of frequency distributions. 478 BETH A. SCHULTZ, RIPAN S. MALHI AND DAVID G. SMITH

Using PC analysis the Northwest Coast populations again cluster with the Northeast, and the Plateau populations separate out as illustrated in Figure 10. The Braden and DeMoss population clusters with the modem Plateau populations, indicating regional continuity on the Plateau span­ ning the last 7,000 years. The Hind and the Congdon sites also cluster together despite their geographic distance from each other. Because of the apparent similarities within these ancient populations, as well as between them and the Plateau populations, it is critical we look more closely at haplotype data in the future to determine if there are any shared lineages. Due to the preliminary status of this report, the results we have currently are suggestive but do not provide any statistically significant conclusions.

CONCLUSIONS From the comparisons of the modern and ancient data in this paper, neither the Hind nor the Braden DeMoss populations can be hypothesized to be genetic ancestors of the Algonquian people. However, the haplo­ group analysis reveals clear regional continuity on the Plateau from the time of the Western Idaho Archaic burial complex (the Braden and DeMoss sites) to the present. We also recognize regional continuity in the Northeast from the late pre-historic time of the Norris Farms population to modern times. However, the Hind site does not share genetic continuity with the other Northeast populations; rather, it clusters with the popula­ tions on the Plateau. Due to the preliminary status of this report, our results, while suggestive, do not provide statistically significant conclu­ sions. The Hind site may represent a population that did not make signifi­ cant genetic contributions to modern populations of the Northeast, and therefore appears genetically different. The Hind site may also be a popu­ lation that has since undergone significant genetic drift, or whose descen­ dants were absorbed into neighboring populations and, for reasons undetermined, were genetically different. The similarity between the Hind site and both ancient and modern populations of the Columbia Pla­ teau, and their difference from modern Algonquian groups might indicate those at the Hind Site were recent emigrants from the Plateau whose descendants experienced a considerable level of admixture with women from neighboring groups which contributed high frequencies of haplo­ groups A, C, and X. We must also consider the small sample size of the Hind site; with additional analysis, the frequency distribution might look PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 479 more similar to the modern populations of the Northeast. To select among these alternative hypotheses, it will be helpful to examine other ancient populations from geographically, temporally, and culturally contiguous areas. Continued research of modern populations as well as on ancient sam­ ples will clarify our understanding of the relationships between these peo­ ples. A broader geographic sampling from Algonquian tribal groups will also provide a more accurate picture of haplotype variation, and better indicate the probability of an Algonquian expansion. More samples from neighboring tribal groups will help us understand if the proposed Proto- Algonquian emigrants were genetically absorbed by the original people of the area, or if there is a distinction between Algonquians and individuals from other language families. An increased sample size from the ancient populations, and confirmation extractions performed on the Hind site samples, will provide a larger, more significant database with which to work. Sequence data will be especially important in determining if there are shared haplotypes across temporal and geographic space, indicating a prehistoric Algonquian migration, and any potential ancestral populations to the modern Algonquian people.

ACKNOWLEDGEMENTS We are indebted to the Native Americans who authorized the use of both modern and ancient samples, as well as to numerous personnel of Indian Health Service Facilities where most of the modern samples stud­ ied were obtained. We would like to acknowledge Dr. Max Pavesic, Dr. Frederika Kaestle, Dr. Robert Yohe, Dr. James Chatters, Dr. Steve Hack- enberger, and Dr. Susan Pfeiffer for providing ancient samples, and Mr. Chad Shook for assistance with the maps and figures. We would also like to thank Dr. Peter Denny for a testable hypothesis and continual advice. This study was supported by grants RR00169 and RR05090 from the National Institutes of Health, a dissertation improvement grant provided by the National Science Foundation, and a Wenner-Gren Foundation grant. 480 BETH A. SCHULTZ, RIPAN S. MALHI AND DAVID G. SMITH

APPENDIX: FIGURES AND TABLES Figure 1: Restriction Fragment Length Polymorphism (RFLP) Analysis ...GTTGAC...... GTCGAC...... CAACTG...... CAGCTG...

+ Hind II enzyme

...GTTGAC...... GTC GAC...

...CAACTG...... CAG CTG... Restriction fragment length polymorphism analysis uses enzymes to recognize whether a particular sequence exists in a chosen fragment of DNA. Each restriction enzyme will rec­ ognize one specific pattern, for example, the Hind II enzyme recognizes the nucleotide pattern: guanine-thymine-cytosine-guanine-adenine-cytosine (GTCGAG), and will cut or digest it between the C and G in this short sequence. If there has been a mutation, thus changing the pattern, the enzyme will not recognize nor digest that DNA fragment. We can run these fragments out on a polyacrylamide gel to determine if there are two small fragments (digested DNA) or one large fragment (undigested DNA).

Figure 2: Gels displaying RFLP Analysis and nine Base Pair Deletions

DNA fragments can be run out on polyacrylamide gels to separate the fragments by size. A positive current is run across the gel, causing the negatively charged DNA fragments to run down the gel. The smallest fragments move the fastest, and are therefore near the bot­ tom. (A) RFLP analysis was conducted on multiple samples, in this gel the first lane con­ tains no DNA, a test negative, lanes 2, 4, and 5 are negative for the restriction site, and lane 3 contains a digested sample. (B) In another gel, the samples being tested for the 9- base pair deletion were run out. Lane 1 is a negative control, lanes 2 and 3 have samples containing the 9-base pair deleted fragment (haplogroup B), and lanes 4-6 do not. Table 1: Restriction Sites for Native American mtDNA Studies

Haplogroup Restriction Site Restriction Digested Not Digested A np 633 Hae Ill A not A c np 13259 Hinc IT not C c ""0 D np5176 Alu I not D D ~ X np 14465 Ace I X not X d r> Four haplogroups can be determined by restriction analysis, A, C, D, and X. They are listed 0 with their corresponding nucleotide position on the mitochondrial genome, restriction enzyme, 0z .0 and whether a digested product or undigested product determines the haplogroup. c :; Table 2: Native American Haplotypes (Sequences) z

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ~ 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 1 1 1 1 2 2 2 2 2 6 6 9 Sample 1.0. Haplogroup language Ethnicity 0 1 1 1 1 1 1 1 1 I 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 4 5 5 4 4 5 9 0 3 4 9 9 4 3 ~ 9 1 1 5 6 7 8 8 8 8 1 1 2 5 6 7 7 9 9 1 2 2 5 5 6 8 1 1 3 6 3 5 0 5 9 0 1 -l 3 1 4 1 2 3 3 4 8 9 3 7 3 0 4 4 s 0 s 9 5 7 5 7 2 2 2 9 0 CRS T c c A c C A c c T G T c c c G c c T G T c c T T A T T c A G T A T A A A A A z FOX11 A AJgonqu1an Sac&Fox T T T T A c c T G c 0 G SW037 A A19onqU1an Ch1ppewa T T A c G c T c 0 >z 66VLS 8 Caddoan Pawnee c c c c c )> OY001 8 Siouan Oua11aw c c T c r lr:NIA32 c Siouan Iowa T T c c T c c c -< Vl PONCA60 c S1ouan Ponca T c T c v; SHA62 D AlaonqUian Shawnee T T c c N N N N N N N N N N N 0 16RN D lrogoUian ~h erokee, OK RC 0 T T T c T A c c N N N N N N N N N N N, ., SIS 49 X AJgonqUian 81a ckfool G T A T c A 0 C G I CH 20 X Algonqu1an W_Ch1ppewa c C A T T A 0 C G :s: c I b Ten examples of Native American sequences are listed. These sequences are aligned against the Cambridge reference sequence (CRS, Anderson z et al. 1981) and all differences marked. Each haplogroup has corresponding markers in the control region sequence (highlighted above in gray). > For example, haplogroup A can be recognized by the majority of markers in nucleotide positions (nps) 16223, 16290, 16319, 64, 146, and 153. Ind ividuals are also identifiable by additional sequence markers, for example the Sac and Fox individual has markers at nps 16111 , 16250, 16362, 16519, 93 and 235. Deletions are represented by (-) and N indicates sequence unknown. ,J:. 00 ~ Tabl e 3: Hapl ogroup Frequencies and Sample Sources 00 N

Samples: Haplogroup Frequen cy:

Population Region Language Time Classification A B c D X N= Reference to tTI -l Hind Site Northeast Unknown Ancient (-3000 ybp) 0.125 0.625 0.188 0.062 0 16 in prep, Schultz et al. :I: Lorenz and Smith 1996; Smith et >- Micmac Northeast Algonquian Modern 0.333 0 0.167 0 0.5 6 al. 1999; Malhi et al. 2001 (/)n :I: Manitoba Island Ojibwa Northeast Algonquian Modern 0.333 0.091 0.273 0.03 0.273 33 Scozzari et al. 1997 c r Northern Ontario Ojibwa Northeast Algonquian Modern 0.63 0.037 0.074 0 0.259 27 Scozzari et al. 1997 -l _,N Turtle Mountain Ojibwa Northeast Algonquian Modern 0.571 0.179 0.179 0 0.071 28 Malhi et al. 2001 C? ""0 Wise . Chippewa Northeast Algonquian Modern 0.274 0.048 0.355 0.032 0.29 62 Malhi et al. 2001 >z Lorenz and Srnith 1996; Smith et (/) Cheyenne Ara pah o Northeast Algonquian Modern 0.343 0.114 0.343 0.143 0.057 35 al. 1999· Malhi et al. 2001 ~ Norris Farms Northeast Unknown Pre-Historic (-700 ybp) 0.315 0.12 0.426 0.083 0.056 108 Stone and Stoneking 1998 r> Lorenz and Smith 1996; Smith et ::s Sisseton Wah peton Sioux Northeast Siouan Modern 0.556 0.2 0.178 0.044 0.022 45 al. 1999; Malhi et al. 2001 >z Mohawk Northeast lroquoian Modern 0.577 0.171 0.236 0.016 0 123 Merriwether and Ferrel1996 0 0 Nuu-Chah-Nulth Northwest Coast Wakashan Modern 0.4 0.067 0.133 0.267 0.133 15 Ward et al. 1991 >:s Bella Coola Northwest Coast Salishan Modern 0.5 0.083 0.167 0.25 0 36 Ward et al. 1991 0 0 Braden DeMoss Plateau Unknown Ancient (- 3000 ybp) 0 0.429 0 0.571 0 7 in prep, Malhi et al. (/) 3:: Congdon Plateau Unknown Ancient (- 6000 ybp) 0 0.5 0.375 0.125 0 8 in prep, Malhi et al. ::j :I: Memaloose Island Plateau Chinookan Proto-Historic (-200 ybp) 0.185 0.593 0 0.222 0 27 in prep, Malhi et al. Snake River Plateau Salishan Proto-Historic (- 200 ybp) 0.1 0.3 0 0.5 0.1 10 in prep, Malhi et al. I Yakim a Plateau Sahaptin Modern 0.071 0.619 0.071 0.167 0.071 42 Shields et al. 1993 PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 483

Figure 28: Populations Studied: (A) The Northeast

(B) the Northwest 484 BETH A. SCHULTZ, RIPAN S. MALHI AND DAVID G. SMITH

Figure 4: Gene Flow Model

Northwest Northeast Time

r •' • t r t t Present »V"^|* Continental • Divide This model graphically represents the pattern of expected gene flow across temporal and geographic space, assuming a prehistoric West to East migration. Time approaches the present at the bottom of the figure, and the geographic regions are listed at the top. Haplo­ types common to the ancient Northwest are in gray, and haplotypes common to the ancient Northeast are in black. Gene flow is expected within geographic regions due to interbreed­ ing with neighboring groups. If a migration occurred sometime in prehistory, the ancient Northwest haplotypes would be carried to the Northeast. Over time, due to regional gene flow, we would expect to find ancient Northwestern haplotypes throughout modern North­ eastern populations.

Figure 6: Principal Components (PC) Analysis of Modern Populations

z.o- W Chippewa • 15 • Ml < )|l JH.i Snake River 1.0 •

04 Nuu-aiah-Nullh 5- Yakima 3_ • Northern Ojibwa • Chey/Arap m 0.0 • • Norris Farms -.5" Meir.atoose Island Bella Coola • TM Chippewa -10- • SW Sioux • -1.5 • MohnwL

PC1 Haplogroup variation exists primarily along the X (PCI) axis, and secondarily along the Y (PC2) axis. There are two clusters, the Northeast and Northwest Coast on the right side of the diagram, and the Plateau groups on the left side. Figure 5: Haplogroup Frequency Distributions (A) Populations from northeastern North America (continued overleaf)

100.. '"c:l ~ 90 .. d > eo .. 5 0 z 70'!(, !:) c > 60'J. z ~ Ci 50'!(, s: -l 40'!(, i5z

30'!(, >z > r 20% en-< Ci) 0 10% .., ~

O'J. Mic mac N=6 Manlloba Island Northern Turtle hlounlaln Wisconsin Cheyenne Norris Farms Sisselon Mohawk N=123 ~ Oilbwa N=JJ Onlar1o Ojlbwa O)lbwa N=28 Chlppewa Arapaho N=35 N=1 08 Wahpelon > N=27 N=62 SiouxN=45

~ 00 Vl -"'- Figure 5 (continued): Haplogroup Frequency Distributions 00 0\ (B) from the Pacific Northwest.

100% to m -1 90% ::r:: > (/) 80% n ::r:: c r 70% +--f~~(f!'!(4 ~ -1 J"l C? 60% -o )> z (/) 50% ~ )> r 40% ::r:: )> z 30% CJ t:J )> 20% < CJ 0 10% (/) $: -1 0% _, r- - ....~- ::r:: YaK1ma N=42 Memaloose Island N=27 SnaKe R1ver N=l 0 Nuu-Chah-Nulth N=15 Sella Coola N=36 PROTO-ALGONQUIAN MIGRATION: ANALYSIS OF MTDNA 487

Figure 7: Mismatch Distributions for Haplogroups A and C

0.35

0.3

0.25

> g 0.2 9 •Algonquian V * 0.15

0.1

0.05

3 4 5 6 Pairwise Differences

(A) The frequency of pairwise differences between individuals within haplogroup A result in a unimodal distribution.

•Algonquian!

3 4 5 6 7 8 9 10 11 12 13 14 15 Pairwise Differences

(B) There is a multimodal distribution for individuals belonging to haplogroup C. ~ 00 Figure 8: Haplogroup Networks 00 0 Hypothetical 0 Hypothetical 0 Yakima 0Yakima 0 Nuu-Chab-Nullh 0 Nuu-Chah-Nulth 0 BellaCoola to 0 BcllaCoola m 0 Algonquian -l 0 Algonquian :c • Siouan • Ea!llem Neighbon >­ nCI.l :c c r -l j'J C? -c )> z Cl.l Snake River ~ Memaloose lsd. )> r NCN :c )> z 0 t:l )> < 0 C) Cl.l:s: -l :c

These networks for (A) haplogroup A and (B) haplogroup C graphically display the multiple lineages within these haplogroups. The clear circles represent hypothetical lineages that must have existed in order for the current lineages to have evolved. Each line segment represents one nucle­ otide difference between the lineages. Figure 9: Haplogroup Frequency Distribution of Modem and Ancient Groups

10~ '"0 90'1. ~ d eo-. +------¥~1tJ ~ m!m11!m I r> 0 0 z 70'11. I ~m;?J y ,0 c ;; 60'1. z ~ Ci ~ -l 0z z> >r -< ~ Cll .,0 :s:: tj z Nortttwsst Coast N=51 Plateau N=79 Braden DeMoss N=7 Congdon N=S 3000ybp Hind S1te N=16 Northeast N=467 > 6000ybp 3000ybp Modern populations of the Plateau , the Northwest Coast, and the Northeast were consolidated into groups due to their regional similarities to be compared to the ancient populations. +>- 00 \0 490 BETH A. SCHULTZ, RIPAN S. MALHI AND DAVID G. SMITH

Figure 10: Principal Components Analysis of Modern and Ancient Populations 2" Snake River N Ojibwa • a • Nuu-Chah-Nulth 1 - •

m Bella Coola Memaloose TM Chippewa " MI Ojibwa • a Cs.0- Island * a SW Sioux " W Chippewa o Yakima Chey/Arap " Mohawk _1 - • Norris Farms Site -2" Congdon # Site

-3 -2 -1

PC1 Principal components (PC) analysis, using haplogroup frequencies of modern (small b ack dots) and ancient (large gray dots), shows a Northeast-Northwest Coast cluster and a Plateau cluster.

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