AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 148:422–435 (2012)

Clan, Language, and Migration History Has Shaped Genetic Diversity in Haida and Tlingit Populations From Southeast Alaska

Theodore G. Schurr,1* Matthew C. Dulik,1 Amanda C. Owings,1 Sergey I. Zhadanov,1 Jill B. Gaieski,1 Miguel G. Vilar,1 Judy Ramos,2 Mary Beth Moss,3 and Francis Natkong4 and The Genographic Consortium

1Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398 2Yakutat Tlingit Tribe, Yakutat, AK 99689 3Huna Indian Association, Hoonah, AK 99829 4Hydaburg Cooperative Association, Hydaburg, AK 99922

KEY WORDS haplogroup; haplotype; lineage; SNP; STR; genealogy; founder; moiety

ABSTRACT The linguistically distinctive Haida and genetic variation in Haida and Tlingit populations; and Tlingit tribes of Southeast Alaska are known for their the impact of European entry into the region on the rich material culture, complex social organization, and genetic diversity of these indigenous communities. Our elaborate ritual practices. However, much less is known analysis indicates that, while sharing a ‘‘northern" about these tribes from a population genetic perspective. genetic profile, the Haida and the Tlingit are genetically For this reason, we analyzed mtDNA and Y-chromosome distinctive from each other. In addition, Tlingit groups variation in Haida and Tlingit populations to elucidate themselves differ across their geographic range, in part several key issues pertaining to the history of this due to interactions of Tlingit tribes with Athapaskan region. These included the genetic relationships of Haida and Eyak groups to the north. The data also reveal a and Tlingit to other indigenous groups in Alaska and strong influence of maternal clan identity on mtDNA Canada; the relationship between linguistic and genetic variation in these groups, as well as the significant influ- data for populations assigned to the Na-Dene linguistic ence of non-native males on Y-chromosome diversity. family, specifically, the inclusion of Haida with Athapas- These results yield new details about the histories of the kan, Eyak, and Tlingit in the language family; the possi- Haida and Tlingit tribes in this region. Am J Phys ble influence of matrilineal clan structure on patterns of Anthropol 148:422–435, 2012. VC 2012 Wiley Periodicals, Inc.

Additional Supporting Information may be found in the online (Institut Pasteur, Paris, France), Colin Renfrew (University of Cam- version of this article. bridge, Cambridge, UK), Daniela R. Lacerda (Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil), Ajay K. Genographic Consortium members include: Syama Adhikarla Royyuru (IBM, Yorktown Heights, New York, United States), Fabrı´- (Madurai Kamaraj University, Madurai, Tamil Nadu, India), Chris- cio R. Santos (Universidade Federal de Minas Gerais, Belo Hori- tina J. Adler (University of Adelaide, South Australia, Australia), zonte, Minas Gerais, Brazil), Himla Soodyall (National Health Labo- Elena Balanovskaya (Research Centre for Medical Genetics, Rus- ratory Service, Johannesburg, South Africa), David F. Soria Her- sian Academy of Medical Sciences, Moscow, Russia), Oleg Balanov- nanz (National Geographic Society, Washington, DC, USA), sky (Research Centre for Medical Genetics, Russian Academy of Pandikumar Swamikrishnan (IBM, Somers, New York, United Medical Sciences, Moscow, Russia), Jaume Bertranpetit (Universitat States), Chris Tyler-Smith (The Wellcome Trust Sanger Institute, Pompeu Fabra, Barcelona, Spain), Andrew C. Clarke (University of Hinxton, UK), Arun Varatharajan Santhakumari (Madurai Kamaraj Otago, Dunedin, New Zealand), David Comas (Universitat Pompeu University, Madurai, Tamil Nadu, India), Pedro Paulo Vieira (Uni- Fabra, Barcelona, Spain), Alan Cooper (University of Adelaide, versidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil), R. South Australia, Australia), Clio S. I. Der Sarkissian (University of Spencer Wells (National Geographic Society, Washington, DC, USA), Adelaide, South Australia, Australia), ArunKumar GaneshPrasad Pierre A. Zalloua (Lebanese American University, Chouran, Beirut, (Madurai Kamaraj University, Madurai, Tamil Nadu, India), Angela Lebanon), Janet S. Ziegle (Applied Biosystems, Foster City, Califor- Hobbs (National Health Laboratory Service, Johannesburg, South nia, United States). Africa), Asif Javed (IBM, Yorktown Heights, New York, United States), Li Jin (Fudan University, Shanghai, China), Matthew E. Grant sponsors: National Geographic Society, IBM, Waitt Family Kaplan (University of Arizona, Tucson, Arizona, United States), Foundation, University of Pennsylvania. Daniela R. Lacerda (Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil), Shilin Li (Fudan University, *Correspondence to: Theodore G. Schurr, Ph.D., Department of Shanghai, China), Begon˜ a Martı´nez-Cruz (Universitat Pompeu Anthropology, University of Pennsylvania, 3260 South Street, Phila- Fabra, Barcelona, Spain), Elizabeth A. Matisoo-Smith (University of delphia, PA 19104-6398, USA. E-mail: [email protected] Otago, Dunedin, New Zealand), Marta Mele´ (Universitat Pompeu Fabra, Barcelona, Spain), Nirav C. Merchant (University of Arizona, Received 9 October 2011; accepted 6 March 2012 Tucson, Arizona, United States), R. John Mitchell (La Trobe Univer- sity, Melbourne, Victoria, Australia), Laxmi Parida (IBM, Yorktown Heights, New York, United States), Ramasamy Pitchappan DOI 10.1002/ajpa.22068 (Madurai Kamaraj University, Madurai, Tamil Nadu, India), Daniel Published online 1 May 2012 in Wiley Online Library E. Platt (IBM, Yorktown Heights, NY, USA), Lluis Quintana-Murci (wileyonlinelibrary.com).

VC 2012 WILEY PERIODICALS, INC. GENETIC DIVERSITY IN HAIDA AND TLINGIT POPULATIONS 423 Southeast Alaska has long been known for its diver- sity of Native American communities. Prior to European contact, Eyak, Haida, Tlingit, and Tsimshian tribes lived in coastal and island portions of Southeast Alaska and northern British Columbia (Fig. 1). These groups are known for their distinctive totem poles, house carvings, masks and ceremonial garb, and material culture as well as their complex social organization and elaborate pot- latches (Garfield and Wingert, 1966; Kaplan and Bars- ness, 1986; Fairbanks, 1989; Kan, 1989; Halpin and Seguin, 1990; Emmons, 1991; MacDonald, 1994; Miller, 2000; Reid, 2002), and are considered to be part of a ‘‘Northwest Coast Culture.’’ However, while this region has been well studied from ethnographic (Swanton, 1905, 1908; Krause, 1956 [1885]; de Laguna et al., 1972; Oberg, 1973; Olsen, 1976; Emmons, 1991) and linguistic perspectives (Sapir, 1915; Krause 1979; Krause and Golla, 1980, 1981; Leer et al., 2001), much less is known about these tribes from a population genetic perspective. The ancestors of the Haida and Tlingit populations probably did not establish themselves in Southeast Alaska until after the end of the last glacial maximum. The ear- liest Paleoarctic sites, including Chuck Lake and Thorne River, Groundhog Bay in Icy Strait (Chichagof Island) and Hidden Falls on Baranof Island near Sitka, date to 10,000–6,500 years before present (YBP) and are marked by microblade and cobble stone tools (Carlson 1990; Davis, 1990; Ackerman, 1992, 1996; Moss, 1998; Ames and Maschner, 1999). During this period, the Northwest Coast developed into a distinct culture area (Davis, 1990; Acker- man, 1992, 1996; Moss, 1998; Ames and Maschner, 1999). Over the next 2,000 years, the culture and social organiza- tion associated with Northwest Coast peoples began to emerge (Davis, 1990; Ackerman, 1992). Around 5,000 years ago, the coastal art and aesthetic styles associated with the Northwest Coast began to appear (Davis, 1990; Ackerman, 1992). By 3,000 years ago, the cultures of the Northwest Coast were largely the same as those observed at the time of contact (Davis, 1990; Ames and Maschner, 1999). The indigenous populations living in the region Fig. 1. A map showing the historical territories of the Tlin- today are the direct cultural, and possibly biological, de- git and Haida in relation to neighbor tribes of Canada and Alaska (based on a map presented in Goddard (1996) and modi- scendants of these prehistoric Northwest Coast groups fied at en.wikipedia.org/wiki/File:Tlingit-map.png). (Davis, 1990; Ames and Maschner, 1999).

LINGUISTIC DIVERSITY IN SOUTHEAST ALASKA Klawak, Stikine, Tongass, and Sanya (Supporting Infor- Efforts to understand the history of the indigenous mation Fig. S2). groups from this region have also involved the examina- By contrast, Eyak is essentially an extinct language, tion of linguistic evidence. Such research has revealed historically spoken in the Copper River region of south- that these groups speak languages belonging to the central Alaska (Krause and Golla, 1981; de Laguna, Athapaskan-Eyak-Tlingit (AET) family. The Tlingit lan- 1990b). According to linguistic evidence, even current guage, recognized as one of the oldest branches of the place names surrounding the Gulf of Alaska (including family, may have split from the Eyak-Athapaskan Yakutat) came from Eyak sources (de Laguna, 1972, branch about 5,000 years ago (Krause, 1979; Greenberg 1990a; Krause and Golla, 1981; Emmons, 1991). This et al., 1986; Krause and Golla, 1980) (Supporting Infor- evidence, and Tlingit oral history, suggests that Eyak mation Fig. S1). It is subdivided into Gulf Coast, North- was once more widespread in Southeast Alaska than at ern, Southern, and Inland dialects, which are largely the time of European contact (de Laguna, 1972, 1990a, mutually intelligible (Krause and Golla, 1980, 1981; de b; Krause and Golla, 1981; Emmons, 1991). Laguna, 1990a; Leer et al., 2001). Sixteen component Athapaskan is the youngest branch of the AET group- ‘‘tribes’’ (qwaan) comprise the three coastal subdialect ing within Na-Dene. Populations speaking Athapaskan regions. Each of these tribes is centered on a primary languages now occupy large areas of northern North village (Krause and Golla, 1981; Goldschmidt and Haas, America, with most living in Alaska and Canada (Sup- 1986; de Laguna, 1990a; Hope and Thornton, 2000). porting Information Fig. S1). Proto-Athapaskan itself These are, north to south, the Gulf Coast region with may have originated in the subarctic region of North Yakutat and Lituya Bay; the Northern region with Hoo- America some 3,000 years ago (Hoijer, 1956; Krause and nah, Chilkat, Auk, Sitka, Hutsnuwu, Taku, and Saw- Golla, 1981). The current distribution of Athapaskan dum; and the Southern region with Kake, Kuiu, Henya, languages in North America likely reflects a series of

American Journal of Physical Anthropology 424 T.G. SCHURR ET AL. migrations from this source area within the past 1,000 years (Greenberg et al., 1986; Ives, 2003, 2010; Matson and Magne, 2007). Most researchers also support the ‘‘Na-Dene hypothe- sis,’’ which asserts a distant ‘‘genetic" relationship between AET and Haida languages (Sapir, 1915; Krause and Golla, 1981; Ruhlen, 1998). According to this model, Haida and AET languages resemble each other because of sharing a common ancestry (Greenberg et al., 1986; Ruhlen, 1994, 1998; Manaster Ramer, 1996; Enrico, 2003). However, some have questioned the inclusion of Haida in the Na-Dene linguistic family, viewing it as a linguistic isolate (Krause, 1979; Levine, 1979). The Haida language itself is divided into Northern and Southern dialects, with Northern Haida being split into Alaskan (Kaigani) Haida and Masset (North Graham Island) Haida dialects (Enrico, 2003, 2005).

Tribal and clan structure Fig. 2. A map of southeast Alaska indicating the locations of study populations. All Northwest Coast groups have some form of an exogamous matrilineal clan system. In these systems, Research objectives clan status is passed from mothers to their children. Based on this status, individuals have access to specific To better understand the complex prehistory of South- clan territories for hunting and fishing, and can use east Alaska and the genetic relationships among North- clan-specific crests for decorating clothing and dwellings west Coast tribes, we undertook a genetic analysis of (Olson, 1967; Emmons, 1991; Kaplan and Barsness, Haida and Tlingit populations. We analyzed mtDNA and 1986; de Laguna 1990b). The clan system is comprised Y-chromosome variation to elucidate the maternal and by two moieties or reciprocating descent groups. For the paternal genetic histories of these indigenous popula- Tlingit and Eyak, clans are grouped into Raven (Ye´il) or tions and compared our findings to archeological, ethno- Eagle/Wolf (Ch’aak’/Gooch) moieties (Kaplan and Bars- graphic, and linguistic data for them. Our results shed ness, 1986; Emmons, 1991; de Laguna, 1990a, b). Tradi- light on the abovementioned aspects of Southeast Alas- tionally, moiety membership influenced marriage prac- kan prehistory and the history of Na-Dene speaking pop- tices, whereby persons belonging to Eagle clans would ulations in the region, as well as the influence of social marry those from Raven clans, and vice versa. organization on genetic diversity in Haida and Tlingit Like the Tlingit and Eyak, the Haida are grouped into populations. They further reveal the genetic impact of two moieties, although the clans belonging to the Haida European movement into the region over the past three Eagle moiety would belong to the Tlingit Raven moiety centuries. (Blackman, 1990). By contrast, the Tsimshian have four phratries instead of two moieties (Miller and Eastman, 1984; Halpin and Seguin, 1990; Miller, 2000). Thus, all METHODS Northwest Coast populations are organized into mater- Sample locations nally linked clans, grouped into exogamous units, which influence their social and ritual practices, and probably Between April 2009 and October 2011, we conducted also their genetic make-up. field research in the Tlingit communities of Yakutat and Hoonah, the city of Juneau (Tlingit), and the Haida com- munity of Hydaburg (Fig. 2). Based on ethnographic in- Historical period in Southeast Alaska formation, present day Tlingit communities may actually represent populations originating from 2 to 8 villages European entry into the region created new patterns within each Tlingit tribe (qwaan) that were consolidated of cultural and economic interactions in Southeast over the past 150 years (Goldschmidt and Haas, 1998). Alaska. In the mid-1700s, Russians began exploring the We also worked with several other Tlingit individuals region for exploitation of its natural resources (Frost, from other communities around the region (Angoon, 2003). By the late 18th century, Russian, Spanish, Eng- Sitka). lish, and French explorers had made contact with Tlingit populations (Fedorova, 1973; Tikhmenev, 1978; de La- guna 1990a; Wilber, 1993; Hope and Thornton, 2000; Yakutat. Eyak-speaking people from the Copper River Haycox, 2002; Black, 2004; Dauenhauer et al., 2008; Gri- area considered Yakutat to be part of their traditional nev, 2008). The American purchase of Alaska from Rus- homeland (de Laguna et al., 1964; de Laguna, 1972, sia in 1867 led to further settlement and exploitation of 1990b; Emmons, 1991). Shortly before contact with Euro- the region (Haycox, 2002; Borneman, 2004). The Klon- peans, the Tlingit moved into this area and began dike Gold Rush of 1898 opened Alaska to further natural absorbing Eyak groups. At that time, a number of Tlin- resource exploitation, including fishing, timbering, min- git and mixed Tlingit-Eyak settlements were present in ing and oil drilling, which continues today, along with the region, although only Yakutat has survived to the the influx of many people of non-native descent to find present day. Based on the 2010 US census, there are 662 work in these industries since that time (Berton, 1959; people living in the city and borough, with 35.8% of Borneman, 2004). them (237) being native by ancestry.

American Journal of Physical Anthropology GENETIC DIVERSITY IN HAIDA AND TLINGIT POPULATIONS 425 Hoonah. Hoonah is located on the north shore of Chi- Haida and Tlingit clan history chagof Island, one of the larger islands of the Inner Pas- sage. It is the principal village for the Huna Tlingits. We obtained information about clan history of each Forced to leave their traditional home at Glacier Bay community and its members to assess whether the 200 years ago because of advancing glaciers, they relo- mtDNA data corresponded with the matrilineal clan sta- cated to Hoonah 20 miles to the south of this area (de tus of the participants. This information was also impor- Laguna 1990a; Emmons, 1991). Based on the 2010 US tant because the different clans in the Haida and Tlingit census, there are 760 people living in the city, with clans often have distinct histories and geographic ori- 52.5% of them (399) being native by ancestry. gins. Juneau. Juneau is located on the Gastineau Channel in Yakutat Tlingit. There are several major clans in the Southeast Alaska, and faces the town of Douglas across Yakutat area. Among them, the Teikweidı´ (Brown Bear) the channel, with which it forms the current municipality and Galyax Kaagwaantaan (Beaver/Wolf) are subunits of of Juneau. It is also close to Auke Bay to the north and the the Eagle/Wolf moiety, while the L’unax.a´di (Silver Taku River to the south. Prior to European arrival in the Salmon) and Kwa´ashk’ikwa´an (Humpback Salmon) are late 18th century, Tlingit belonging to the Auke and Taku subunits of the Raven moiety (de Laguna, 1972, 1990a; tribes fished in the Gastineau Channel (Emmons, 1991; Emmons, 1991; Goldschmidt and Haas, 1998). Goldschmidt and Haas, 1998). Since becoming the capital Hoonah Tlingit. As seen in Yakutat, the Hoonah Tlin- of Alaska in 1906, Juneau has been a cultural center for git have clans belonging to both the Eagle and Raven Tlingit, Haida, and Tsimshian groups living in Alaska. moieties. The Eagle moiety contains three clans, includ- ing Wooshkeetaan (Shark), Chookaneidi (Brown Bear), Hydaburg. The Haida first arrived on the Prince of and Kaagwaantaan (Wolf), while the Raven moiety con- Wales Island in the 1700s from Graham Island in British sists of two main clans, the T’akdeintaan (Kittywake) Columbia. By doing so, they pushed the Tongass Tlingit and L’uknax.a’di (Coho Salmon) (Swanton, 1908; Krause, into the northern portion of the Prince of Wales Island. 1956 [1885]; Goldschmidt and Haas, 1998; Dauenhauer Hydaburg was formed in 1912 through the consolidation et al., 2008). of the Kaigani Haida communities of Howkan (Dall Island), Klinkwan, and Sukkwan that were located along Haida. Ethnographic information indicates that the Cordova Bay on the western side of the Prince of Wales Haida are divided into two moieties also called Raven Island (Blackman, 1990). According to the 2010 US cen- and Eagle, with each having numerous lineages sus, there are 376 people living in the city, with 77.1% of (Swanton, 1905; Blackman, 1990). Haida villages on the them (290) being native by ancestry. Prince of Wales Island historically contained representa- tives of several different lineages, and most contained Sample and data collection members of both moieties. Based on oral histories, Swan- ton (1904, 1905) also speculated that the Eagle moiety During our work in Southeast Alaska, we obtained might have come from a different tribe. buccal samples from a total of 97 individuals following informed consent, of whom 64 were women and 33 were Mitochondrial DNA analysis men. We also collected oral histories and genealogical data from Tlingit and Haida participants and community To elucidate the maternal genetic ancestry of the members, and examined archival materials, primary and Native Alaskan individuals, we examined mtDNA varia- secondary historical sources, and ethnological informa- tion in both male and female participants through direct tion from the region. This information provided a crucial sequencing of the control region (CR), and analysis of genealogical and historical context with which to inter- single nucleotide polymorphisms (SNPs) in the coding pret the genetic data. All samples and genealogical data region of the mtDNA genome. The SNP analysis were obtained with approval from the University of involved screening the samples for markers that identi- Pennsylvania IRB, the Alaska Area IRB, and Alaska fied the basal structure of the mtDNA phylogeny using Native governments. TaqMan1 assays (Applied Biosystems). All assays were Tlingit and Haida samples were characterized for vari- read on an ABI 7900HT Fast Real-Time polymerase ation in the mitochondrial DNA (mtDNA) and the non- chain reaction (PCR) system. Once assigned to one of recombining portion of the Y-chromosome (NRY) using these basal lineages, the samples were screened for addi- the methods outlined below. All DNA test results were tional SNPs that define specific haplogroups and their returned to the participants. For the purpose of this subbranches using both custom TaqMan assays and po- analysis, we reduced the mtDNA and NRY data sets to lymerase chain reaction - restriction fragment length include only tribal members from each location. Accord- polymorphism (PCR-RFLP) analysis (Zhadanov et al., ingly, we excluded five of the participants because they 2010; Gaieski et al., 2011). All haplogroup assignments were not Native Alaskans or tribal members. Based on were made using the nomenclature presented in Phylo- genealogical information, we also excluded the mtDNAs Tree.org (mtDNA Tree Build 12; 07-20-12; van Oven and of eight other individuals because they were maternally Kayser, 2009). related to other participants, and three additional Y- In addition, for each sample, the entire mtDNA CR chromosomes because they were paternally related to (1121 bp), encompassing hypervariable regions I and II other participants. In addition, the data from individuals (HVS1 and HVS2), was sequenced using previously pub- sampled in Hoonah and Juneau were combined, since lished methods (Zhadanov et al., 2010; Gaieski et al., individuals from each sampling location had clan and 2011). All sequences were read on an ABI 3130XL Gene familial relationships. We were thus left with 84 tribal Analyzer, and aligned and edited with the Sequencher members (female and male) for the analysis of mtDNA 4.9 software tool (Gene Codes Corporation). The SNP variation, and 28 male tribal members for the Y-chromo- assays and CR sequencing defined the maternal hap- some analysis. logroup and haplotypes, respectively, for each individual.

American Journal of Physical Anthropology 426 T.G. SCHURR ET AL. Y-chromosome analysis moiety membership were also examined as variables shaping the mtDNA diversity in the Tlingit and Haida, We investigated the paternal genetic ancestry of the latter being comprised of 16 Haida individuals (11 Native Alaskans by screening the male samples for phy- Eagle, 5 Hydaburg Raven) with indigenous haplotypes. logenetically informative SNPs in the non-recombining To compare our Y-STR data with other published data portion of the Y-chromosome (NRY) that define major pa- sets from Native American populations, we reduced the ternal haplogroups and their sub-branches. Biallelic number of analyzed Y-STR loci to 10 of the 11 recom- markers defining each of the major NRY haplogroups mended by the Scientific Working Group on DNA Analy- were tested in all men, and classification into smaller, sis Methods, namely, DYS19, DYS385a, DYS385b, more refined haplogroups was accomplished using a DYS389I, DYS389II, DYS390, DYS391, DYS392, hierarchical approach following published information DYS393, and DYS439. In the published data sets, (Y Chromosome Consortium, 2002; Karafet et al., 2008) DYS385 was used in the diversity estimates, and the and methods (Zhadanov et al., 2010; Gaieski et al., shorter repeat allele was consistently associated with 2011). In addition, each sample was screened for seven- DYS385a, although the assignment of the two-repeat al- teen short tandem repeats (STRs) using the multiplex leles cannot be made accurately without further genotyp- AmpFlSTR Y-filer PCR Amplification Kit (ABI), and six ing. Data sets were restricted to only indigenous Y-chro- additional fragment length polymorphisms and two addi- mosomes. All participants who claimed Tlingit or Haida tional Y-STRs (M17, M60, M91, M139, M175, M186, paternal ancestry were included in the statistical analy- DYS388, and DYS426) through a separate multiplex sis, whereas those participants who claimed paternal reaction (Zhadanov et al., 2010; Gaieski et al., 2011). ancestry tracing back to other populations were not. A The combination of SNP and STR data defined paternal haplogroup predictor (http://www.hprg.com/hapest5/) lineages in these individuals. (Athey, 2007) was used to assign Y-STR haplotypes from Zlojutro (2008) into Y-chromosome haplogroups. After Comparative population data making the data sets comparable, we estimated haplo- type diversity and MPDs from the Y-chromosome STR For statistical and phylogenetic analyses, we compared haplotypes using Arlequin 3.11. Haida and Tlingit mtDNA and Y-chromosome data with Mitochondrial DNA CR sequences were used to con- those from other indigenous populations in the region struct a network of A2 haplotypes using NETWORK (Supporting Information Fig. S3). These populations 4.6.0.0 (www.fluxus-engineering.com; Bandelt et al., included Bella Coola (Ward et al., 1993), Greenland Inuit 1995, 1999). The weighting scheme suggested by Bandelt (Salliard et al., 2000), Alaskan Athapaskans (Shields et et al. (2002) was used with slight modifications. Accord- al., 1993), Apache and Navajo (Budowle et al., 2002), ing to this scheme, fast-evolving sites were given lower Yakima (Ward et al., 1993), Aleuts (Rubicz et al., 2003; weights relative to other less mutable sites. Networks Zlojutro et al., 2006; Zlojutro, 2008), Haida (Ward et al., were created using both median joining and reduced me- 1993), and Nuu-chah-nulth (Ward et al., 1991). In addi- dian joining approaches with MP processing (Polzin and tion, we compared our Y-chromosome STR data with Daneschmand, 2003). other data sets (Bolnick et al., 2006; Redd et al., 2006; The time to most recent common ancestor (TMRCA) Zlojutro, 2008) to assess haplotype diversity in paternal for each paternal haplogroup was estimated from Y-STR lineages from indigenous populations of North America. data using the calculation of rho statistics with Network 4.6.0.0, where the founder haplotype was inferred as in Statistical and phylogenetic analysis work by Sengupta et al. (2006). Networks were gener- ated as described by Dulik et al. (2011). The evolutionary Pairwise FST genetic distances between the Haida, Tlingit, and comparative populations were estimated mutation rate was used to estimate coalescence dates with HVS1 sequence data using the Tamura-Nei model with a generation time of 25 years. of sequence evolution (Tamura and Nei, 1993) in Arle- quin v.3.11 software (http://cmpg.unibe.ch/software/arle- RESULTS quin3/) (Excoffier et al., 2005). The inter-population FST mtDNA diversity in Southeast Alaska genetic distances were then represented in two dimen- sions through multi-dimensional scaling (MDS) using Our analysis of mtDNA variation in Southeast Alas- SPSS 17.0 (SPSS 2009). In addition, haplotype diversity, kan populations provided a number of insights into the nucleotide diversity, MPDs, Tajima’s D and Fu’s FS were maternal history of these groups. Haida and Tlingit pop- calculated from mtDNA HVS1 sequences, using Arlequin ulations had mtDNA profiles that resembled those of 3.11. other northern populations from Alaska and Canada We also conducted a hierarchical analysis of molecular (Starikovskaya et al., 1998; Schurr et al., 1999; Rubicz variance (AMOVA) to evaluate the extent of population et al., 2003, 2010; Schurr and Wallace, 2003; Zlojutro, et genetic structure in the data sets from Tlingit and al., 2006; Crawford et al., 2010; Raff et al., 2011). The Haida. For the Tlingit tribes, all indigenous mtDNA hap- vast majority of individuals had mtDNAs belonging to lotypes were sorted by geographic location and clan Native American haplogroup A2, while most of the rest membership. Any clan made up of a single individual belonged to haplogroups C and D, which are also indige- was excluded from the analysis. All of the remaining nous in origin (Supporting Information Tables S1 and clans were specific to a single moiety and geographic S2; Fig. S4). None of these populations possessed hap- location, except for the L’uknax.a´di (Coho) clan of the logroup B2 or X2a mtDNAs, which appear in Amerin- Raven moiety, which was found in the Hoonah and Yak- dian populations to the south. Several individuals had utat regions. This analysis thus involved data from 52 mtDNAs belonging to West Eurasian (e.g., H, T, U) or Tlingit (38 Hoonah [16 Eagle, 22 Raven]; 14 Yakutat [0 East Eurasian (E1a1a) haplogroups. These persons ei- Eagle, 14 Raven]) individuals for whom we had both ther had Tlingit or Haida fathers and non-native moth- moiety and clan information. Similar comparisons using ers or had been adopted into the tribe.

American Journal of Physical Anthropology GENETIC DIVERSITY IN HAIDA AND TLINGIT POPULATIONS 427 A comparison of CR haplotypes in the Haida and Tlin- et al., 2003; Zlojutro et al., 2006). However, D4h3 haplo- git also revealed intriguing similarities between them types were not observed in any of these populations, de- (Supporting Information Table S2). All three groups spite their presence in an ancient sample from the shared two A2 haplotypes, the first being the founder Northwest Coast and modern populations from south- HVS1 haplotype (#1) and the second having additional western North America (Kemp et al., 2007; Perego et al., 16129 and 16311 mutations (#3). Two other A2 HVS1 2009). haplotypes (#2 and #4) were observed in Hoonah and The network of A2 haplotypes confirmed these obser- Hydaburg, although the Hydaburg individuals bearing vations (Fig. 3; Supporting Information Fig. S5). The these haplotypes had maternal Tlingit ancestry. These Haida and Tlingit shared several haplotypes, including observations suggested that the founder A2 mtDNAs #3, although Haida HVS1 haplotype #9 was clearly dis- were originally present in both the Tlingit and the tinctive relative to others in Tlingit populations. Indeed, Haida, but that the derived HVS1 haplotypes (#2, #3, the whole mtDNA genome sequence for HVS1 haplotype #4) arose in the Tlingit and were then later spread into #9 was quite distinctive relative to any other A2 haplo- the Haida. type that has been characterized in the same way (Sup- A2 haplotypes possessing the 16129 mutation have porting Information Table S3). Athapaskan HVS1 haplo- previously been observed in North, Central, and South type #7, Inupiaq HVS1 haplotype #5, and Tsimshian American populations (e.g., Ward et al., 1991, 1993; Tor- HVS1 haplotype #6 were also clearly delineated in the roni et al., 1993; Starikovskaya et al., 1998; Johnson and network (Supporting Information Fig. S5). Interestingly, Lorenz, 2006; Tamm et al., 2007). If all of these haplo- the latter three haplotypes lacked the mutation at np 64, types belong to the same maternal lineage, then this dis- which occurs just before the start of the HVS2 region, tribution suggests that it likely arose in founding Native and which was present in all of the A2 mtDNAs from American populations and was spread with initial settle- the Haida and most of those from the Tlingit. The phylo- ment of the Americas. However, given the polymorphic genetic significance of this mutation is not entirely clear. nature of the 16129 site (Bandelt et al., 2002; Ruiz- It has been reported as being hypervariable in A2 Pesini et al., 2007; Achilli et al., 2008; van Oven and mtDNAs throughout the Americas (Tamm et al., 2007; Kayser, 2009), the haplotypes bearing this mutation Achilli et al., 2008; Perego et al., 2009), although it could appear similar because of the recurrence of this might possibly delineate two sets of founding A2 haplo- site in the HVS1, hence, would have only distant genetic types, one with and one without the mutation (Vilar et relationships. al., 2011). Interestingly, there were differences in the patterns of The statistical analysis of Haida and Tlingit HVS1 A2 variation between the two Tlingit populations and sequence data also yielded new insights into the genetic between the Tlingit and Haida populations. For example, diversity within the region. Comparisons of the Haida HVS1 haplotype #7 only appeared in Yakutat Tlingit. and Tlingit mtDNA data with those from published data This haplotype represents an Athapaskan-specific subli- sets showed that populations in Southeast Alaska were neage of A2 that has been found in Alaska and Canada, generally less diverse than populations from other regions and other areas where Athapaskan populations (Supporting Information Table S4). The Nuu-chah-nulth, expanded (e.g., US Southwest) (Shields et al., 1993; Tor- Bella Coola, and Yakima had greater haplotype diver- roni et al., 1993; Starikovskaya et al., 1998; Budowle et sities than the two Tlingit and two Haida populations. al., 2002; Rubicz et al., 2003; Schurr and Wallace, 2003). Aleuts and Greenlandic Inuit also had lower diversity In addition, HVS1 haplotype #9, which is characterized estimates, although the Alaskan Athapaskans by Shields by the 16355 mutation, was observed in only the Haida. et al. (1993) had a higher value, probably because the It appears to have arisen in this tribe, as it occurs in no samples were collected from various tribes in Alaska. other population in the Northwest Coast region, aside The MDS plot of these FST estimates further illus- from the neighboring Bella Coola, in which similar hap- trated the genetic relationships among populations from lotypes has been observed (Ward et al., 1993). the circumarctic region (Supporting Information Table Native Americans of different ethnic backgrounds also S5; Fig. 4). Haida from Hydaburg and Queen Charlotte contributed several other A2 haplotypes to the Haida Island clustered tightly together and separately from and Tlingit communities. For example, HVS1 haplotype Tlingit groups, and were genetically close to Bella Coola, #5 represented an Inuit individual from Hoonah, while a Northwest Coast Amerindian population. The Yakutat HVS1 haplotype #8 belonged to an Inupiaq individual and Hoonah Tlingit were also genetically distant from from Yakutat. These A2 mtDNAs are commonly seen in each other, with Yakutat being closer to Alaskan Atha- Yupik and Inupiaq populations (Starikovskaya et al., paskans, Apache and Navajo, in part due to sharing 1998; Schurr et al., 1999; Saillard et al., 2000; Helgaon Athapaskan A2 haplotypes with these groups, and Hoo- et al., 2006; Gilbert et al., 2008). Likewise, the unique nah showing some similarities to both NW Coast Amer- HVS1 haplotype #6 occurred in a Haida individual with indians and the Haida. The Greenland Inuit, Yakima, Tsimshian maternal ancestry. and Aleuts were all positioned at some distance from the By contrast, haplogroup C and D haplotypes appeared general cluster of Northwest Coast populations. Overall, mostly in the Yakutat Tlingit. These included a unique the FST values were generally high, indicating substan- version of C1 (#11) in a Hispanic/Mexican individual tial population differentiation. who traced her maternal ancestry to Chihuahua, Mexico, and a C1b type (#10) in a Haida individual that differed Influence of social organization on mtDNA from the founder C1 by two steps. In addition, a Tlingit diversity individual from Yakutat had a D1 haplotype (#12), while another with Alaskan Athapaskan maternal ancestry When mtDNA data were sorted according to the had a D2 haplotype (#13) similar to those commonly descent groups of Tlingit and Haida individuals, we seen in Chukchi, Siberian Yupik, and Aleut populations noted a strong correspondence between mitochondrial (Starikovskaya et al., 1998; Schurr et al., 1999; Rubicz haplotype and maternal moiety affiliation (Supporting

American Journal of Physical Anthropology 428 T.G. SCHURR ET AL.

Fig. 3. A reduced-median network of HVS1 sequences from Tlingit and Haida populations. The nodes are shaded to indicate the Alaskan Native population(s) in which an HVS1 sequence appears, with the key appearing in the upper left corner of the figure.

Similar to those for the Yakutat Tlingit, the Hoonah mtDNA data showed a clear distinction between the Eagle and Raven moiety members. Aside from those per- sons adopted into an Eagle clan, all but one of its mem- bers had only the A2 founder HVS1 haplotype #1. The remaining mtDNA haplotypes belonged to Raven clan members. Among these, L’uknax.a´di (Coho Salmon) and T’akdeintaan (Kittywake) members had A2 HVS1 haplo- type #3, Kaach.a´di (Land Otter) members had HVS1 haplotype #2, and L’eeneidi (Dog Salmon) had HVS1 haplotype #4. Thus, judging from the clan and mtDNA data, the Eagle and Raven individuals shared virtually no specific mtDNA haplotypes. In Hydaburg, the Eagle and Raven moieties were also genetically distinguishable from each other. Aside from the A2 founder HVS1 haplotype #1, they shared no other maternal lineages. In fact, based on full CR sequences, Fig. 4. A MDS plot of FST estimates for Tlingit, Haida and comparative indigenous populations. even the A2 founder haplotypes in Raven and Eagle individuals differed by the presence or absence of the 189 mutation in the HVS2. Thus, members of the Raven Information Table S6). In the Yakutat Tlingit, there and Eagle moieties in the Kaigani Haida actually shared were striking differences between the Eagle and Raven no specific haplotypes. members, and between clans within each of these moi- Comparison of the mtDNA sequence data at the moi- eties. All individuals from the Kwa´ashk’ikwa´an clan had ety level for Haida and Tlingit populations hinted at A2 haplotype #7, those from the L’uknax.a´di clan had A2 deeper connections between them. In both the Hoonah haplotype #3, and an individual with Eyak maternal and Yakutat, A2 HVS1 haplotype #3 occurred in Raven ancestry who belonged to the Galyax Kaagwaantaan clan members, suggesting a common source for these clan (Raven moiety) had D1 haplotype #12. Within the mtDNAs. By contrast, these kinds of A2 haplotypes Eagle moiety, individuals adopted into the Teikweidi belonged to Haida Eagle moiety members. This was an clan included those having Koyukon Athapaskan (haplo- intriguing finding in light of the hypothesized ‘‘foreign" type #13), Inupiaq (haplotype #8), and non-native (haplo- origin of the Eagle moiety in the Haida (Swanton, type #16) maternal ancestry. 1905).

American Journal of Physical Anthropology GENETIC DIVERSITY IN HAIDA AND TLINGIT POPULATIONS 429

TABLE 1. Results of Tlingit and Haida AMOVAs and moiety. Both moiety and ethnicity produced consid- Groups % variation P-value erable Between Population–Within Group estimates, while geography generated the highest Among Group (a) AMOVA of Hoonah and Yakutat Tlingit mtDNA value. Interesting, in all analyses, there were never sig- diversity nificant Among Group differences at the 5% significance Moiety level [Table 1(c)]. These results could have been influ- Among group 0.17 0.519 Between population within group 97.60 0.000 enced by the small sample sizes of the populations as Within Group 2.23 0.000 well as the relative lack of Eagle moiety members in Geography Yakutat. Among group 44.50 0.143 Between population within group 53.79 0.000 Within Group 1.71 0.000 Y-chromosome diversity in Southeast Alaska (b) AMOVA of Hoonah Tlingit mtDNA diversity by moiety The analysis of NRY variation in these same popula- Among group 71.68 0.101 tions using SNPs defined a variety of paternal haplo- Between population within group 22.29 0.000 types in male individuals (Supporting Information Within Group 6.03 0.000 Tables S7 and S8; Fig. S4). Some of these haplotypes (c) AMOVA of Tlingit and Haida mtDNA diversity belonged to haplogroups C3*, C3b, Q1a*, and Q1a3a*, Moiety which have been observed in various Native American Among group 29.39 0.900 populations (e.g., Karafet et al., 2001; Lell et al., 2002; Between population within group 55.30 0.000 Bortolini et al., 2003; Zegura et al., 2004; Bolnick et al., Within Group 54.09 0.000 2006). Others belonged to haplogroups E1b1b1, I1, I2b, Geography Among group 27.94 0.200 J1e and R1b1b2, which are common among European Between population within group 23.46 0.000 populations (Rosser et al., 2000; Karlsson et al., 2006), Within Group 48.60 0.000 or O3a3*, which is common in Southeast and East Asia Ethnicity groups (Shi et al., 2005; Xue et al., 2006; Zhong et al., Among group 212.63 1.000 2011). Haplogroups C and Q were found in participants Between population within group 57.23 0.000 claiming Tlingit or Haida paternal ancestry, with the Within Group 55.41 0.000 exception of a single C3* lineage (Y-STR haplotype #1). All other haplogroups were found in men claiming a non-indigenous paternal ancestor. Comparison of haplogroup C and Q haplotypes with When assessing the distribution of mtDNA haplotypes those present in other Native American communities in Haida and Tlingit relative to geography and moiety revealed a distinct pattern of male genetic diversity in status using AMOVA, a more complex picture of mater- Southeast Alaska. As noted above, we identified two nal genetic variation emerged. The first AMOVA branches of haplogroup Q in Southeast Alaskans, these involved Hoonah and Yakutat Tlingit, with each clan being Q1a*, defined by the MEH2 SNP, and its deriva- being grouped into its respective moiety. The resulting tive Q1a3a*, defined by the M346 and M3 SNPs. Q1a* is Within Group variation was very low Table 1(a), reflect- a paragroup made up of only a handful of individuals, ing low levels of diversity within each maternal clan. with all other Native Americans falling into the more When the clans were grouped by moiety, the Between derived Q1a3* (M346) and Q1a3a* haplogroups (Borto- Population–Within Group component rose dramatically, lini et al., 2003; Zhadanov et al., 2010; Bisso-Machado et indicating significant differences between at least two of al., 2011; Gaieski et al., 2011). In Southeast Alaska, the clans in one of the moieties. When the clans were Q1a* appeared in only the Tlingit, while Q1a3a* was grouped by geography, a significant portion of the varia- present in both the Haida and Tlingit. tion was shifted into the Among Group component, The Q1a* and Q1a3a* haplotypes were quite diverse although the differences were not significant (P-value [ when considering their STR profiles. The differences 0.1). between the two Q1a* haplotypes were remarkable, as The most likely candidate for the clan influencing the they varied at 12 out of 19 STR loci, while the Q1a3a* AMOVA results was the Humpback Salmon clan from haplotypes differed amongst themselves at 6–8 STR loci, Yakutat. As noted above, this clan belongs to the Raven on average. In fact, based on these data, every single Q moiety and has primarily the Athapaskan A2 haplotypes haplotype in the Haida and Tlingit was found to be (#7) that is very different from the others present in the unique. This level of diversity suggested that these Q Y- Hoonah and Hydaburg areas. These results were also chromosomes might represent paternal lineages that consistent with the large FST value between the Hoonah have persisted and diversified in the region for thou- and Yakutat Tlingit (Supporting Information Table S5). sands of years. Consistent with this view, the TMRCA To further assess the effects of the Yakutat samples on for the Q1a3a* Y-chromosomes present in the Tlingit these results, data from only the Hoonah region Tlingit and Haida was 10,120 years 6 2,200, using rho statistics clans were subjected to AMOVA. They were grouped and the evolutionary mutation rate, a date consistent only by moiety. This AMOVA produced a very low Within with earlier estimates for the age of the M3 mutation in Group, a moderate Between Population–Within Group, the Americas (Zegura et al., 2004). and also a very large Among Group value [Table 1(b)]. In addition, we detected haplogroup C3* (M217) and These results confirmed the genetic differences between C3b (P39) haplotypes in the Tlingit. These findings the Eagle and Raven moieties in the Hoonah Tlingit, were consistent with other studies that have shown while also pointing to the skewing of the earlier Between haplogroup C to be present in Athapaskan and Algon- Population–Within Group estimate by another clan. quian populations from North America (Bortolini et al., A third AMOVA was conducted with both Haida and 2003; Zegura et al., 2004; Bolnick et al., 2006; Malhi Tlingit samples, grouping them by geographic region et al., 2008). However, previous studies did not analyze a

American Journal of Physical Anthropology 430 T.G. SCHURR ET AL.

TABLE 2. Y-STR haplotype diversity of indigenous Y-chromosomes in Haida, Tlingit and Aleut Hoonah Tlingit Yakutat Tlingit Haida Aleuts Sample number 10 2 1 21 Haplotype number 9 2 1 12 Haplotype diversity 0.978 6 0.054 1.000 6 0.500 1.000 6 0.000 0.924 6 0.035 Mean pairwise differences 6.000 6 3.125 9.000 6 6.708 0.000 6 0.000 4.771 6 2.429

sufficient number of SNP markers to delineate the differ- all, indigenous Y-chromosomes in the Aleut villages, ent kinds of C haplotypes that were present in their which represented only 15.3% of Aleut men (Zlojutro, study populations. 2008). The indigenous Y-chromosomes from Southeast Approximately half of the NRY haplotypes were non-in- Alaska made up approximately 50% of the total, which digenous in origin. Of these, haplogroups I1 and I2b is similar to frequencies of indigenous Y-chromosomes in occurred only in Hydaburg. This observation was consist- eastern North America (Bolnick et al., 2006). ent with a number of Haida families having male ances- tors who, over the past several generations, came to the DISCUSSION region from Scandinavia or northern Europe, where such haplogroups are common (Rosser et al., 2000; Karlsson Genetic variation in Southeast Alaska et al., 2006). The other West Eurasian haplogroups Our analysis of mtDNA and Y-chromosome variation in appeared largely in individuals from Hoonah and Haida and Tlingit individuals provides new insights into Yakutat. Haplogroup R1b1b2 was especially common in the genetic history of indigenous populations from South- these tribes, which was not surprising given that the east Alaska. Although the sample sizes for these popula- male ancestors of these families traced their roots directly tions are small, the resulting data, viewed in the context to Denmark, Germany, Ireland, Netherlands, Norway, of ethnographic and genealogical evidence, appear to be Russia, Spain, or Sweden, where this paternal haplogroup generally representative of the communities in which we is ubiquitous (Balaresque et al., 2010; Myres et al., 2010). worked, thereby allowing us to make reasonably strong Interestingly, one Tlingit man from Yakutat possessed inferences about their population histories. a Y-chromosome from haplogroup O3a3, which is typi- A primary objective of this study was to assess the cally seen in Southeast and East Asia. Although he self- genetic affinities of Haida and Tlingit populations with identified as a Tlingit (having a Tlingit mother), he had other native communities in North America. Overall, the a Filipino father. In fact, a number of Tlingit men and Haida and Tlingit show a mostly ‘‘northern’’ genetic pro- women had Filipino grandparents on the maternal or pa- file similar to that of circumarctic populations. This pro- ternal sides of their families based on their genealogies, file is marked by the high frequency of haplogroup A2 particularly in Yakutat. In such cases, women who had and the presence of haplogroup D2. Yet, specific A2 hap- Filipino ancestry traced it through their paternal grand- lotypes differed. For example, A2b lineages that are com- fathers, or men traced it through their paternal grand- mon in Arctic populations were not found in Tlingit and mothers. Thus, given the inheritance patterns of mtDNA Haida. The Southeast Alaskan groups also lack hap- and Y-chromosomes, the Filipino genetic lineages from logroup B2 and X2a mtDNAs and exhibit very low fre- these family members were not sampled. quencies of C1 and D1 haplotypes. These haplogroups To further explore Y-chromosome diversity in circum- are commonly seen in Amerindian populations such as arctic populations, we compared our data with those the Nuu-chah-nulth, Bella Coola, Yakima, and other from other native North American populations for which tribes located south of this region (Ward et al., 1991, core Y-STR data were available. Our results revealed 1993; Shields et al., 1993), and are also present in the that Y-STR diversity in the Tlingit and Haida was rela- Navajo and Apache due to their intermarriage with tively similar to that seen in other Native American pop- Puebloan and other Amerindian population since enter- ulations (Table 2). The diversity value for the Hoonah ing the American Southwest some 500–1,000 years ago Tlingit was 0.978, whereas that for the Yakutat Tlingit (e.g., Budowle et al., 2002). and Hydaburg Haida was 1.000 because of small sample In addition, while observed in certain Amerindian pop- sizes. Diversity estimates for Aleuts (Zlojutro, 2008) ulations living in mainly coastal areas in southwestern were recalculated without non-indigenous haplotypes. North America and western South America (Rickards et The resulting diversity estimate for Aleut haplogroup Q al., 1999; Schurr, 2004; Perego et al., 2009), D4h3 haplo- lineages was 0.924 instead of 0.990, well below the esti- types are not present in either the Haida or Tlingit, de- mates seen in Southeast Alaska. The Tlingit and Haida spite its presence in the prehistoric On Your Knees Cave values fell in the range of estimates for indigenous east- male from Prince of Wales Island (Kemp et al., 2007). ern North American populations (Bolnick et al., 2006) as This pattern of mtDNA diversity suggests that the hap- well as those from Native Americans analyzed by Redd logroups initially brought to the Northwest Coast have et al. (2006). It is likely that estimates from the latter been replaced by those ancestral to the Haida, Tlingit, are inflated, as recent admixture was not accounted for and other Northwest Coast tribes in the region. in this analysis. To conduct a comparable analysis with the Aleut data Tlingit population history from Zlojutro (2008), we had to run the Aleut Y-STR haplotypes through a haplogroup predictor to identify Our genetic data provide new insights into the popula- the indigenous paternal lineages to which they belonged tion history of Tlingit populations from Southeast (Athey, 2007). Overall, this haplogroup predictor worked Alaska. In some respects, the Hoonah and Yakutat tribes well, although a few of the Y-STR haplotypes seemed to are genetically similar to each other, with both having be misclassified. Nevertheless, we identified most, if not two of the most common HVS1 haplotypes present in the

American Journal of Physical Anthropology GENETIC DIVERSITY IN HAIDA AND TLINGIT POPULATIONS 431 region (#1 and #3). This finding suggests that these A2 mtDNA A2 founder haplotypes (#1), which, interestingly, mtDNAs could have been part of the original maternal are more diverse at the HVS2 level than those in the gene pool for Tlingit populations, and is consistent with Tlingit, as well as others that were obtained through ethnographic evidence for the origins of certain Yakutat intermarriage with Tlingit groups (#2 and #4), based on clans in Hoonah (de Laguna, 1972, 1990b). They both genealogical information. They also possess a haplotype also have Q1a, Q1a3a*, and C3* Y-chromosome haplo- (#9) that is not seen in the Tlingit or other Northwest types, suggesting they could potentially have a common Coast populations, aside from the geographically adja- or similar paternal ancestry, although no specific STR cent Bella Coola (Ward et al., 1993), and also have a haplotypes are shared between them. Q1a3a* haplotype distinct from those seen in the Tlingit. At the same time, while being linguistically and cul- In addition, the Haida from Hydaburg are genetically turally similar, the two Tlingit tribes are genetically dis- closest to Haida from Queen Charlotte Island in Canada. tinctive from each other. The Yakutat Tlingit show stron- This is not a surprising finding because the Haida only ger maternal genetic ties to Athapaskan groups from in- began expanding into the Prince of Wales Island during terior Alaska than do the Hoonah Tlingit, and is the the past few centuries, displacing the Tongass Tlingit only population with the Athapaskan-specific A2 haplo- groups living there. type (#7). A single Yakutat individual with Koyukon Furthermore, genetic distance estimates based on Athapaskan maternal ancestry also has a D2 haplotype mtDNA HVS1 data show the Haida to have greater (#13), which appear mostly in Alaskan Aleut, Athapas- genetic affinities with Northwest Coast Amerindian than kan, and Inupiaq groups, as well as the Siberian Chuk- Athapaskan tribes. In this regard, Ward et al. (1993) chi (Starikovskaya et al., 1998; Saillard et al., 2000; believed that the similarities between the Haida and Rubicz et al., 2003; Zlojutro et al., 2006; Gilbert et al., Bella Coola were due to a recent shared origin of the two 2008). In addition, as previously noted, a number of Yak- populations, despite the fact that the Haida speak a Na- utat participants have parents or grandparents who Dene language and the Bella Coola an Amerind one. By were born in the Alsek River or Dry Bay area, while contrast, Lorenz and Smith (1997) asserted that the sim- others were noted to have Eyak maternal grandparents. ilarities between the Bella Coola and the Haida were not Thus, the Yakutat haplotype distribution likely reflects due a recent common origin of both populations, but extensive interactions with Athapaskan populations rather reflected recent gene flow between them after the from interior of south-central Alaska, and possibly also Bella Coola migrated into the area. Given the lack of the assimilation of smaller ethnic groups like the Eyaks haplogroup B2 and D1 mtDNAs in the Haida and the (de Laguna, 1972, 1990b; Emmons, 1991). distribution of the A2 haplotypes described above, our The Hoonah Tlingit, on the other hand, exhibit mainly data support the view that recent gene flow has pro- A2 founder haplotypes (#1) and those derived from it (#2 duced the observed patterns of mtDNA diversity in the and #3), one of which is also seen in the Yakutat Tlingit Haida and Bella Coola. Furthermore, based on the cur- (#3). They also lack the A2 sublineage that is observed in rent genetic evidence, the Haida appear not to be closely many other Athapaskan-speaking tribes. As a conse- related to adjacent Tlingit populations, with the pattern quence, they show greater genetic similarities to the of genetic diversity in this population reflecting some Haida and Northwest Coast Indian populations than to degree of isolation from neighboring tribes. the Yakutat Tlingit. These affinities might possibly reflect the sharing of mtDNA haplotypes with the Haida and Genetic and linguistic diversity in the Na-Dene Tsimshian, with whom they have exchanged marital part- ners in the recent past, and which are mirrored by cultural linguistic family influences on Tlingit populations from these neighboring Another goal of this study was to investigate the rela- tribes in the form of iconography and clan name identifica- tionship between linguistic and genetic diversity for pop- tion (de Laguna, 1972, 1990a; Blackman, 1990; Emmons, ulations assigned to the Na-Dene linguistic family, spe- 1991). This pattern also generally supports evidence sug- cifically, the inclusion of Haida in the family with Atha- gesting that certain Tlingit clans originated in the area paskan, Eyak, and Tlingit. As noted above, we observe defined by the Nass River in British Columbia and Stikine differences in mtDNA composition between the Haida River in Southeast Alaska (de Laguna, 1990b). and the Tlingit. In addition to their distinct mtDNA pro- Such differences could also possibly reflect more an- file, the Haida lack A2a haplotypes (#7) seen in many cient population subdivisions that resulted from cultural other Athapaskan tribes (Shields et al., 1993; Torroni et and geographic isolation. Previous linguistic studies al., 1993; Starikovskaya et al., 1998; Budowle et al., noted several distinct dialect groups in Southeast 2002; Schurr and Wallace, 2003), although this is also Alaska, with the Yakutat belonging to the Gulf Coast true for the Hoonah Tlingit. The Q1a3a* Y-chromosome group and Hoonah belonging to the Northern group (de observed in the Haida (#20) is also distinctive compared Laguna, 1990a). This linguistic divergence would imply to those in Tlingit groups, although it represents a single that Tlingit groups underwent regional genetic differen- male lineage in this population. Together, these data tiation within Southeast Alaska. Under this scenario, suggest that the Haida do not share a recent common the Tlingit emerged from a common Northwest Coast ancestry with the Tlingit. gene pool that had developed by 5,000 years ago, and Thus, we observe only modest genetic evidence for the then diverged from each other linguistically and geneti- composition of the Na-Dene stock as originally proposed cally as they expanded throughout the region, while also by Sapir (1915), in which Haida and AET populations being influenced by neighboring indigenous populations. share a common genetic ancestry. However, this inter- pretation is not supported by previous analyses of Haida Haida population history and AET languages. While linguistically influenced by Tlingit tribes as they expanded northward from their Our data indicate that the Haida are genetically dis- Canadian homeland, the Haida are viewed as speaking tinctive from Tlingit populations. They have mostly a Na-Dene language by a number of Native American

American Journal of Physical Anthropology 432 T.G. SCHURR ET AL. linguists (Greenberg et al., 1986; Manaster Ramer, 1996; mation, clans belonging to the Haida Eagle moiety would Ruhlen, 1998; Enrico, 2003). Thus, if the Haida share be placed in the Tlingit Raven moiety (Blackman, 1990) deeper linguistic ties with AET speaking populations, and might even have originated in a different tribe then they have since diverged from them genetically, (Swanton, 1905). Hence, judging from this evidence, albeit with some gene flow due to interactions with these Tlingit and Haida subdivisions might possibly neighboring populations. have deeper genetic connections between them than indicated here.

mtDNA diversity and clan status Historical admixture As noted previously, ethnographic studies indicated The genetic data from the Haida and Tlingit confirm that clan status in the Haida and Tlingit is based on genealogical and historical evidence of intermarriage matrilineal descent. Traditionally, a member of the Eagle with non-indigenous persons. A number of Tlingit Clan married someone from the Raven clan, and vice women have married men of non-native descent over the versa. However, the strictness of this practice has waned past several generations. These men, who have paternal somewhat over the past century, partly due to intermar- Swedish, Danish, German, Scotch-Irish-English, and Fil- riage with non-native persons. For this reason, we were ipino descent, came to Alaska to fish commercially, hunt uncertain as to whether the mtDNA data would show whales, work in mines, timber forests, or serve at Ameri- any correspondence with the clan status of the partici- can military bases in Alaska. In the case of the O3a3* pants. haplotype in the Tlingit, this finding is consistent with In fact, there was a strong association between the the economic history of Southeast Alaska where, during maternal clan status and mtDNA haplotype background the early to mid-1900s, mostly male Filipinos were hired of individuals from Yakutat, Hoonah, and Hydaburg. In to work in Alaskan salmon canneries. These men subse- general, it was possible to distinguish members of the quently established ties with members of such Alaska Tlingit Eagle and Raven moieties from each other based Native tribes as the Tlingit, Haida, Aleut, and Tsim- on the mtDNA haplotype composition of each social shian, and often married into these communities (Cor- grouping. Members of the Raven moiety in Yakutat had dova, 1983; Bacho, 1988; Bucholdt, 1996; Barton, 2011). ´ either #2 and #3 haplotypes (L’uknax.adi clan) or Atha- In addition, some Haida and Tlingit men have married ´ ´ paskan-specific A2 haplotypes (#7) (Kwaashk’ikwaan non-native women, most of whom having been formally clan) because of previous interactions with Ahtna Atha- adopted into their respective communities. Regardless of paskan populations, with another Raven individual from their non-native ancestry, these individuals are consid- ´ the Gaanax.adi clan having D1 haplotype (#12). Because ered members of Haida and Tlingit tribes. all of the Eagle clan members involved in this study had been adopted into the Tekiweidi clan, they exhibited a CONCLUSIONS mixture of different maternal haplotypes. We observed the same pattern for Eagle and Raven In summary, our genetic data reinforce perspectives on moieties in the Hoonah Tlingit. The Eagle and Raven Haida and Tlingit history that come from archeological, members shared no mtDNA haplotypes, except for #4. ethnographic, and linguistic studies. The Tlingit are ge- This was an intriguing finding because, while many of netically different from the Haida, are themselves genet- their clans apparently arose in the Hoonah region, the ically subdivided, and have distinct genetic affinities ancestors of a number of tribal members came from with surrounding Athapaskan and Northwest Coast pop- clans originating in other parts of the traditional Tlingit ulations. The limited sharing of certain mtDNA haplo- territory that encompassed the Northern and Southern types by Haida and Tlingit populations suggests only in subdialect regions (de Laguna, 1990a). Furthermore, recent times has there been population interactions lead- both the Hoonah and Yakutat A2 haplotypes #3 occurred ing to intermarriage, hence, gene flow, between them. In only in Raven clan members, suggesting a common addition, we observed considerable diversity in the Q1a* source for these mtDNAs, and the genetic divergence of and Q1a3a* paternal haplotypes in the Tlingit, implying these two moieties some time ago. These results are con- their antiquity in the region and possibly greatly diver- sistent with information obtained through ethnographic sity in founding Y-chromosome haplogroups than previ- studies of Tlingit tribes (de Laguna, 1972, 1990a; ously appreciated. In this regard, our estimates of Q-M3 Emmons, 1991) and recent genealogical data, and indi- diversity were consistent with those obtained from other cate that matrilineal kinship and clan-based marriage Native American populations. Additional details about practices continue to shape mtDNA variation in the Tlin- the history of Haida and Tlingit peoples will emerge git today. from comparative studies with other Alaskan Native Similarly, we observed genetic differences by moiety in populations, such as Yupik, Inupiaq, and Athapaskan the Kaigani Haida from Hydaburg. Accordingly, Raven groups from Alaska and Canada, and through whole and Eagle moiety members did not share any haplotypes mtDNA genome sequencing, expanded NRY SNP geno- when considering the entire CR sequences of the partici- typing and analysis of autosomal loci in these popula- pants. However, the correspondence between moiety sta- tions. tus and specific mtDNA haplotypes is not as strong as seen in the Tlingit populations. This pattern might ACKNOWLEDGMENTS reflect the mixing of lineages from formerly separated groups that resulted from the consolidation of smaller The authors express their gratitude for the participa- Haida communities in the early 20th century. In addi- tion by Tlingit and Haida individuals in this study, and tion, whereas A2 haplotype #3 occurred in Tlingit Raven the support of this study by the Huna Indian Associa- clan members, these kinds of mtDNAs appeared in tion, the Huna Totem Corporation, the Huna Heritage Haida Eagle clan members. This observation is intrigu- Foundation, the Yakutat Tlingit Tribe, and the Hyda- ing in light of the fact that, based on ethnographic infor- burg Cooperative Association. The authors also thank

American Journal of Physical Anthropology GENETIC DIVERSITY IN HAIDA AND TLINGIT POPULATIONS 433

Kathy Miller and Kathryn Hurtley, past and present Ex- Bortolini MC, Salzano FM, Thomas MG, Stuart S, Nasanen SP, ecutive Directors of the Huna Heritage Foundation, and Bau CH, Hutz MH, Layrisse Z, Petzl-Erler ML, Tsuneto LT, Grace Villareal and Robert Starbard from the Huna In- Hill K, Hurtado AM, Castro-de-Guerra D, Torres MM, Groot dian Association, for their facilitation of our research in H, Michalski R, Nymadawa P, Bedoya G, Bradman N, Labuda Southeast Alaska. In addition, they thank Merritt D, Ruiz-Linares A. 2003. Y-chromosome evidence for differing ancient demographic histories in the Americas. Am J Hum Ruhlen for his constructive comments on the manu- Genet 73:524–539. script, and Janet Ziegle from Applied Biosystems for pro- Bosch E, Calafell F, Rosser ZH, Nørby S, Lynnerup N, Hurles viding technical assistance with the DNA analysis. ME, Jobling MA. 2003. 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