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Animas River, Durango, Colorado

Animas River, Durango, Colorado

The fourth chapter of Crucible of Pueblos discusses the eastern portion of the Mesa Verde region, essentially the northern portion of the watershed of the San Juan River from the La Plata drainage east to the San Juan headwaters. This area has seen less research than some other parts of the Southwest, but several major salvage projects in recent decades have added a lot of data on Pueblo I period settlement in particular. The most important of these has been the Animas-La Plata Project associated with the inundation of Ridges Basin to create Lake Nighthorse south of Durango. These projects haven’t revolutionized our understanding of the Pueblo I period the way the Dolores Project did in the Central Mesa Verde region in the 1980s, but they have added large bodies of systematically collected data to broaden our understanding of the period.

The picture that emerges from this evidence shows the Pueblo I period to have been a dynamic, complex time in this region. Indeed, in some respects “chaotic” might be an appropriate descriptor. Population movement, both within the region and between it and other regions nearby, was frequent, sites were short-lived, and evidence for violence is abundant. The population fluctuated wildly but was never very large compared to other areas, but even this small population seems to have been culturally and perhaps ethnically diverse, which may have contributed to the instability and violence. Some of the earliest aggregated villages in the northern Southwest arose in this region during the eighth century AD, but they all appear to have been highly unstable: none lasted more than a few decades, and most appear to have met violent ends. Perhaps relatedly, these villages never held more than a small portion of the overall regional population, in contrast to early villages in some other regions. By the end of the Pueblo I period around AD 900 most parts of the region were largely depopulated, with the residents apparently moving primarily to the south, where many of them likely ended up at Chaco Canyon and were involved in the rise of the Chaco Phenomenon over the course of the tenth and early eleventh centuries.

The authors of this chapter divide their region into four “districts”: La Plata, Durango, Piedra, and Navajo Reservoir/Fruitland. While showing similarities in material culture suggesting connections with each other, the districts have markedly different demographic trajectories, and it seems clear that there was significant population movement among them over the course of the Pueblo I period.

Despite an earlier Basketmaker II occupation, Basketmaker III period settlement was limited to nonexistent in most of the districts, implying that the Pueblo I occupation was primarily the result of migration into the region. Only the La Plata district shows clear evidence for a small BMIII occupation, and even this is probably too small to account on its own for the larger population in the district during Pueblo I. It appears, then, that beginning in the AD 720s there was a migration of people into the La Plata and Durango districts, probably from the south. Site densities increased markedly around 750, especially around Durango, suggesting a further wave of migration, again from the south. It was at this time that the earliest villages began to develop in these areas, although most of the population continued to live in widely scattered hamlets and individual residences. These villages were short-lived and seem to have collapsed in the early 800s, in some cases with evidence for intense violence including, at Sacred Ridge in Ridges Basin, the earliest evidence for the sort of “extreme processing” (probably including cannibalism) of human remains that would recur periodically in later periods of Pueblo prehistory.

The collapse of the early villages in the Durango district appears to have coincided with a general depopulation of that district, with residents emigrating in multiple directions. Some went west and appear to have contributed to the rise of large villages in the Central Mesa Verde region, particularly in the Dolores area, where one large and well-documented community, Grass Mesa Village, shows evidence in its material culture for strong ties to the east. Other Durango people may have gone south into the Frances Mesa area in the lower Animas River valley, possibly mixing with other groups migrating north at the same time. This occupation was short-lived and may have ended with the people moving north into the Dolores area to join the villages there. Some Durango people may also have gone east to form the first Pueblo I occupation in the Piedra district, although this area has seen less research than others and the picture isn’t as clear. Recent surveys do suggest that the Piedra was somewhat marginal to developments elsewhere in the region during Pueblo I, and that its population was both smaller than had been thought and mostly limited to the late Pueblo I period. The fate of the La Plata population is less clear, but there is a definite decline in site numbers after AD 800 coinciding with an increased number of sites in the Mancos River drainage to the west, suggesting emigration to the west there as well.

Chimney Rock Great House

Chimney Rock Great House

As it turned out, the Dolores villages weren’t very stable either, and after their collapse in the mid- to late ninth century people seem to have migrated back into the eastern Mesa Verde region. A surge of immigration into the Fruitland/Navajo Reservoir district after about 880 contributed to the highest regional population of the whole Pueblo I period, although it still wasn’t very high (3,000 people at most regionwide, and likely more like 2,000). The Piedra district also saw a considerable increase in population at this time. The Fruitland/Navajo Reservoir occupation was short-lived, with more evidence of violent ends for some village sites, and it seems that most or all of the people moved south, with at least some of them joining the growing communities in and around Chaco Canyon. There may have been some migration south from the Piedra district as well, but it continued to be occupied into the Pueblo II period after 900. The Piedra people seem to have been somewhat isolated from developments elsewhere in the Pueblo world during early Pueblo II, which is unsurprising given that they were left quite isolated geographically by the depopulation of the Animas drainage and Navajo Reservoir area. They don’t seem to have been completely cut off, however, and ongoing contact with Chaco in particular is suggested by the development of the Chimney Rock great house with its remarkable astronomical alignments in the eleventh century.

There are several noteworthy characteristics of this pattern of settlement and migration, which the authors of this chapter point out. One is the obvious importance of population movement, versus natural increase or decrease, in explaining the wild demographic swings both in the region as a whole and among its individual districts during this period. It was a very dynamic period, when people rarely lived in the same place for more than two or three generations. It’s not clear entirely why, but one reason is likely linked to one of the other noteworthy characteristics: widespread violence, including some of the most extreme violent incidents in the whole archaeological record of the Southwest. Interestingly, much of this violence, including the “extreme processing” incident at Sacred Ridge, appears to have been linked to internal conflicts within communities, especially the early villages. This may in turn explain why relatively few people in this region lived in villages, although it still leaves open the question of why anyone did. The authors suggest that one factor may have been the perception of safety in numbers in a chaotic era, although this ultimately proved to be illusory. It’s not clear to what extent warfare between communities was actually occurring, however, and the widespread popularity of a scattered settlement pattern suggests it may not have been that major a concern for most people. On the other hand, palisades around individual residents units are fairly common in the region, so it may be primarily a matter of different strategies for dealing with violence.

One other noteworthy thing about the violence is that the “extreme processing” phenomenon appears to have been exclusive to the eastern Mesa Verde region during this period. This is interesting because in later periods it occurs in other regions, most notably in the Central Mesa Verde region during the mid-twelfth century, where it is possibly associated with the collapse of the Chaco system. There has been much dispute and discussion about the occurrence of cannibalism as part of at least some of these assemblages, which I’ve discussed at length before. The fact that it appears earliest in the eastern Mesa Verde region during Pueblo I, when it appears to be limited to that region, adds an important piece of context for understanding the phenomenon. While the occurrence of ritual cannibalism in Mesoamerica has led some to look there for the roots of cannibalism in the Southwest, there are some important differences in the apparent practices behind the assemblages that make a Mesoamerican source difficult to document, and if the eastern Mesa Verde region was in fact the part of the Southwest where these practices originated that makes the Mesoamerican connection even more tenuous. While the exact connections between specific Basketmaker and Pueblo populations in different areas are hard to pin down, it’s generally thought that the eastern Basketmakers were both ancestral to later Pueblo populations in the same areas and descended from earlier Archaic populations. Importantly, these eastern groups generally show much less evidence for Mesoamerican influence than western groups, among whom “extreme processing” events are both much rarer and, when they do occur, much later than in the east. Obviously it’s not that there was no Mesoamerican influence among eastern groups, since they did have maize agriculture and so forth, but there’s much less evidence for specific, direct influence than in the west. This implies that “extreme processing,” including cannibalism, may actually have been a practice that developed indigenously in the eastern Mesa Verde region and spread to other parts of the northern Southwest as part of the widespread population movements following Pueblo I.

Finally, the violent and chaotic nature of the Pueblo I period in the eastern Mesa Verde region, whatever the underlying reasons for it, adds some context for the attractiveness of new social formations in other regions, such as the Pueblo I villages in the Dolores area and the emerging great-house communities of early Pueblo II in and around Chaco. While the Dolores villages were not ultimately able to deliver the kind of peace and stability that immigrants from the eastern Mesa Verde region may have been looking for, Chaco apparently was. Furthermore, once Chaco rose to regional prominence in the eleventh century it was able to extend that peace and stability over an unprecedentedly large area of the northern Southwest, including the eastern Mesa Verde region itself. Understanding how the system that emerged in Chaco Canyon was able to achieve this remarkable feat when no one had succeeded at anything like it before is one of the most important questions in Southwestern prehistory, and it is still very much an unanswered one. One important piece of the puzzle, however, is clearly the Pueblo I context in the Chaco area itself, and it is to this that we now turn.

Chaco Street in Aztec, New Mexico

Chaco Street in Aztec, New Mexico

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Utah Welcome Sign

Utah Welcome Sign

The third chapter of Crucible of Pueblos deals with the western part of the Mesa Verde or Northern San Juan region, which basically corresponds to what is now the southeastern corner of Utah. In this context the area is bounded by Cedar Mesa on the west and the Abajo Mountains on the north, as well as by the borders with Colorado and Arizona on the east and south. This is a fairly standard way to define this area archaeologically except that the western boundary is more restrictive than usual, which appears to mainly be a decision based on the near-total lack of sites dated to the Pueblo I period west of the eastern edge of Cedar Mesa. (There are actually Pueblo sites dating to this period much further west in southwestern Utah and southern Nevada, the so-called “Virgin Anasazi,” but they aren’t included in this book at all for some reason.)

The authors divide their study area into a series of physiographic sub-regions based primarily on elevation, which is a useful way to track changes in occupation patterns over the course of the period they discuss. It’s also a different approach to defining sub-regions than most of the other chapters in the book use. These sub-regions are important because the differences in precipitation and growing season length among them seem to have been important factors behind shifting settlement patterns during the period of interest. These shifts seem to have mainly taken place across the region rather than separately in spatial sub-regions such as drainages, as was the case in some other regions.

One way this region differs from others, and especially from the Central and Eastern Mesa Verde regions, is that there has been a relative lack of large-scale salvage excavation projects to provide large amounts of detailed archaeological data. Instead, most data is from surveys and small-scale excavations, and detailed chronological information in particular is missing for most sites that have been recorded. Rough dating of sites to Pecos Classification period at best based on frequencies of a few ceramic types is the norm here, which limits the comparability of data on trends in settlement over time. Nevertheless, the authors of this chapter do their best to come up with a coherent narrative of settlement during the Basketmaker III and Pueblo I periods in this area, which seems to have been an important one for understanding the cultural development of early farming populations and the origins of aggregated villages.

The most striking pattern in the population dynamics of this region in the Basketmaker III and Pueblo I periods is of apparent cycles of population growth and decline on the scale of decades and of greater magnitude than can be explain by internal demographic processes, implying migration into and out of the region multiple times. Most interestingly, these cycles appear to be largely complementary to similar cycles in other nearby regions, especially the Central Mesa Verde region just to the east. This strongly implies that one of the major factors in population changes in both these regions was movement between them.

To go into greater detail, the story told in this chapter begins in the seventh century AD with the expansion of Basketmaker III populations across the region from the narrow area of Basketmaker II settlement along the San Juan River and its major tributaries. The authors attribute this expansion in part to the introduction of beans and pottery, which freed farming populations from dependence on outcrops of limestone to cook with their corn for nitrogen-fixing purposes. Population spread especially into the upland areas with deep soils well-suited to dry farming. Over the course of the Basketmaker III period scattered hamlets began to consolidate into “proto-villages” with public architecture such as oversized pit structures surrounded by scattered households. The authors note the similarity of this pattern to the later Pueblo II great house communities, which is indeed an interesting parallel.

There appears to have been a regional population decline in the early eighth century, although this may be an artifact of the limited data set and difficulty assigning sites to precise time periods. In any case, there is evidence of a noticeable population increase after AD 750, with several villages of tightly clustered households containing public architecture appearing, along with a considerable number of smaller residential sites and a few sites in highly defensive locations, especially at the western edge of the region near Cedar Mesa. The population increase was accompanied by the introduction of a strikingly different type of pottery, Abajo Red-on-orange, which shows many similarities to pottery from the Mogollon region far to the south and likely reflects long-distance migration of some sort. There were still many continuities in architecture and other aspects of material culture, however, which suggests that these migrants combined with local populations rather than replacing them.

The largest and most famous of the villages that developed during this early Pueblo I period is Alkali Ridge Site 13, excavated by J. O. Brew in the 1940s. This site consisted of a series of long, continuous arcing roomblocks, made up of “room suites” of one “habitation” room backed by two smaller “storage” rooms. This is a pattern that would become standard for Pueblo I villages at a slightly later date, and would endure in various forms for centuries. Site 13 consists of six of these arcs, four of which were excavated by Brew. Three of the arcs excavated by Brew also had oversized pit structures with highly formalized features suggesting possible use as public architecture of some sort.

There were other village-sized sites that were established at this time, although few have been excavated. These are among the earliest sites of this size and level of organization in the northern Southwest, and continuities with later sites in other regions suggest they may have been very influential on later developments.

In addition to the early village sites, defensive sites on high, inaccessible promontories began to appear during the early Pueblo I period. These sites have not been studied in any depth, and little is known about them. Some appear to have evidence of extensive residential populations and/or public architecture, while others don’t. One intriguing pattern is an apparent line of them at the western edge of the region along the eastern margins of Cedar Mesa. This, combined with the lack of Pueblo sites to the west, has suggested to some researchers that there was a buffer area or “no-man’s-land” between the Pueblo population in southeastern Utah and early Fremont populations northwest of the Colorado River during this period. It’s worth noting, however, that there were also a few of these apparent defensive sites well within the Mesa Verdean Pueblo region, including the Fortified Spur site near the Colorado-Utah border, so tensions may have been internal as well as external at this point.

During the middle Pueblo I period from AD 825 to 880 there appears to have been a regional population decline, although again this may be due in part to data gaps. It is noteworthy, however, that this is the period of a major population increase in the Central Mesa Verde region to the east, including the formation of the well-known cluster of aggregated villages in the Dolores River Valley, some of which show some striking similarities to earlier Utah villages such as Site 13. It is reasonable to postulate that a pattern of emigration from southeast Utah into southwest Colorado led to this pattern. Southeast Utah wasn’t completely depopulated, however. In addition to scattered small sites throughout the region, there are a very few larger communities firmly dated to this period, including an intriguing site on Elk Ridge called the Pillars that has extensive evidence for middle Pueblo I residential architecture and some tentative evidence for public architecture as well. There are several other sites in the same general area that have more tentative evidence for occupation during this time, and it seems this may have been one of a handful of population clusters in the region during a time of otherwise low population.

After AD 880 population rapidly increased again, and many large villages were built between this point and AD 950. This was a period of rapid depopulation in the Central Mesa Verde region, again suggesting a complementary pattern of migration between the two regions. Many of these new village sites were in highly defensive locations, including some that were nowhere near the frontiers of the region. There is also an intriguing pattern of continuity in location between these early villages and later Pueblo II great house communities from the eleventh century. This pattern is made even more intriguing by two phenomena:

  1. Some of these sites, such as Red Knobs and Nancy Patterson Village, have evidence for masonry roomblocks similar to the “proto-great houses” known from many sites in New Mexico in and around Chaco Canyon during this same time.
  2. There seems to have been another depopulation of southeastern Utah around AD 950, implying that population at these sites was not actually continuous despite these similarities.

It has long seemed to me that southeastern Utah is a crucial area for understanding Chaco. There are several lines of evidence suggesting that at least some people living in Chaco Canyon and involved in its rise to regional dominance had strong ties to Utah, and I suspect those ties were more important in the emergence of the Chaco system than has been generally recognized. This chapter adds some much-needed context on the earlier history of Pueblo populations in Utah, and to me it strongly reinforces those ideas about the importance of Utah to Chaco. The exact nature of these relationships and their importance is still unclear, and the relatively sketchy data available make it harder to figure out, but it still definitely seems like there is something important here.

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McPhee Reservoir and Mesa Verde Escarpment from McPhee Campground

McPhee Reservoir and Mesa Verde Escarpment

The second chapter of Crucible of Pueblos discusses the Central Mesa Verde region, which is defined as basically the southwestern corner of Colorado, bounded on the west and south by the modern borders with Utah and New Mexico, on the east by the La Plata River valley, and on the north by the highlands north of the Dolores River. This is the region where Pueblo I period villages have been most extensively studied, primarily by the Dolores Project during the construction of McPhee Reservoir in the 1980s and in subsequent research by archaeologists building on that work. As a result, there’s not a whole lot that’s new in this chapter for someone who has been following the literature on this topic, although it does make a good introduction to the subject for someone who hasn’t. It also discusses some parts of the area, especially the northern and eastern fringes, that have seen much less research than the well-studied Great Sage Plain (including the Dolores sites) and Mesa Verde proper. Overall, the data assembled here is among the most detailed and reliable available to analyze demographic trends and population movements during the Pueblo I period in the northern Southwest.

Among the key factors that the authors discuss are the inherent attractiveness of this region to early farmers because of its good soil and relatively favorable climatic conditions compared to other nearby areas. Indeed, this is the only part of the northern Southwest that has seen extensive dry farming in modern times, and it is still primarily agricultural in use. This makes it unsurprising that early farmers would have concentrated here, as indeed they did, starting in the Basketmaker III period ca. AD 600 and increasing steadily in population through about 725. These early sites generally consisted of scattered hamlets presumably housing individual families. Villages, which in this context means clusters of multiple residential roomblocks in close proximity, began to appear around 750, often in association with great kivas, which had previously been rare in this region for reasons that are unclear.

Villages to both the west and east, discussed in subsequent chapters, date to the same period as these early ones in the Central Mesa Verde villages, and there was a striking variety in community organization and layout across the broader region. The dissolution of the eastern and western villages seems to have contributed to an influx of population into the Central Mesa Verde area in the early ninth century, resulting in the largest and densest concentration of population seen to that date. Village layout also became more standardized, with two main patterns dominating, one associated with great kivas and another including U-shaped roomblocks that were likely ancestral to later “great houses.” These villages, most extensively documented at Dolores, were however short-lived, and by the early tenth century the area was almost completely depopulated, with the former inhabitants apparently moving primarily to the south, into the southern part of the San Juan Basin, where they seem to have played a key role in the developments that led to the rise of Chaco Canyon as a major regional center in the eleventh century.

As I said before, none of this is groundbreaking information at this point, and I’ve discussed some of the implications of the Dolores data before. It is however useful to have a synthesis of this region during this important period to refer to, and this chapter works well for that purpose.

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McPhee Reservoir, Dolores, Colorado

McPhee Reservoir, Dolores, Colorado

A few years ago I did a series of posts called “Aftermath” that consisted of short commentaries on the chapters in The Prehistoric Pueblo World, a volume edited by Michael Adler that synthesized information on the archaeology of the Pueblo III period (AD 1150 to 1350) in various regions of the Southwest. This period postdated the decline of Chaco Canyon as a major regional center, and understanding it is important for understanding the relationship between Chaco and the modern Pueblos, as well as for understanding some aspects of Chaco itself.

Another period that is of perhaps even greater interest for understanding Chaco is the Pueblo I period (generally defined as AD 750 to 900, but see below), which immediately predates Chaco’s rise to regional dominance. I was therefore pleased to see the publication in 2o12 of Crucible of Pueblos: The Early Pueblo Period in the Northern Southwest, a volume synthesizing information on the Pueblo I period along the same lines as Adler’s effort for Pueblo III. It’s edited by Rich Wilshusen, Gregson Schachner, and James Allison, all of whom have made important recent contributions to understanding of this under-researched period. I’m just now getting around to reading it, and I decided to do a similar series of posts commenting on the chapters as I read them. I’m entitling the series “Foreshadow” to indicate the way developments during this period seem to, well, foreshadow later developments at and involving Chaco.

This post addresses the introduction, which is by the three editors of the volume along with Kellam Throgmorton, who is not otherwise a familiar name (at least to me) but who is thanked in the acknowledgments for his work “reimagining” this chapter. He was apparently a graduate student at the University of Colorado at the time, and has since graduated and is now “doing contract archaeology work in New Mexico.” The introduction as it stands is very engaging and readable, so if that was Throgmorton’s doing I can see why the volume editors took care to thank him specifically.

This introductory chapter is primarily a history of archaeological research on the Pueblo I period in the Southwest, but it also situates that history in the context of archaeological understanding of that period and how it relates to others, which has changed markedly over time. It also explains the reasoning for this volume’s use of “Early Pueblo” rather than “Pueblo I” to describe the period of interest, which is defined more broadly than Pueblo I has traditionally been. As with so much else in Southwestern archaeology, the issues here go back to the classification developed at the first Pecos Conference in 1927. As this chapter makes clear, this was initially primarily a developmental sequence rather than a chronological one, and the Pueblo I period in particular has been misunderstood on this account. This volume therefore uses a more general “Early Pueblo” period of circa AD 650 to 950 to frame the developments in the regions it discusses, which covers the various definitions that have been used for Pueblo I in different areas, as well as parts of Basketmaker III in some because of the importance of immediately preceding events for understanding Pueblo I.

The bulk of this chapter relates the history of understanding of the Pueblo I period by archaeologists. This history follows the familiar sequence of culture history/classification followed by processualism/environmental determinism followed by post-processualism/neohistoricism, but with an emphasis on how the Pueblo I period tended to be subsumed by larger theoretical constructs until the rise of large cultural resource management projects in the 1970s and 1980s massively increased the data available and forced a reevaluation of the period. The most influential of these efforts was the Dolores Project, which happened to occur in an area that was one of the most important centers of Pueblo I village development. The massive scale of this project, the largest ever in the US at the time, led to a much more detailed understanding of the Pueblo I period and the recognition that, rather than a brief interlude in the sequence of development from small hamlets to large pueblos, this was a time of rapid formation of the first major agricultural villages in the northern Southwest, followed by their equally rapid dissolution and a massive outmigration of people from the region. The precision of tree-ring dating allowed for very fine-grained understanding of the chronology, and the results of the project showed a level of dynamism in population movement and culture change that was totally unexpected and hard to fit in the gradual progression paradigm underlying the traditional Pecos classification.

Furthermore, certain aspects of the short-lived Dolores villages were strikingly reminiscent of the well-known Chacoan communities that emerged to the south shortly afterward, which led to the increasingly accepted idea that the formation and dissolution of villages during Pueblo I in the Dolores area were events that directly influenced the rise of Chaco. Indeed, it is now considered quite likely that many of the people who were involved in the development of early great houses at Chaco had moved there from Dolores.

So that’s the main message in this chapter, which also serves as an introduction to the volume itself and the other chapters in it. The next few chapters cover the specifics of settlement patterns in several parts of the northern Southwest, including not just the Mesa Verde region (the focus of most Pueblo I research so far) but also Chaco and its surroundings as well as areas further south and east. The latter two areas are often not addressed very well in research on this period, so I’m very interested in seeing the information on them presented here. The next few chapters cover a few broad thematic issues of interest for understanding this period across all the regions, then there are concluding chapters by Steve Lekson and John Kantner putting all this in a larger perspective. Overall this seems like a well-designed and desperately needed synthesis of an important but poorly understood period in Southwestern prehistory, and I’m eager to dive into the details.

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Great Kiva at Chetro Ketl in the Snow

Great Kiva at Chetro Ketl in the Snow

This post is mainly just a list of the posts I’ve done in the “Tracing the Connections” series over the past few months. Here they are:

Introduction

The Lay of the Land

The Evidence from Linguistic Relationships

The Evidence from Linguistic Contact

The Evidence from Oral Traditions

The Evidence from Skull Measurements

The Evidence from DNA: Introduction

The Evidence from DNA: Southwest-Specific

Overall, the evidence from all these different sources is very consistent in indicating that the modern Pueblos of New Mexico and Arizona are clearly the descendant communities of the ancient Pueblos in a general sense, but that tracing a line of descent between any specific ancient site and any specific modern Pueblo is not currently possible. With further research, however, I think there is a lot of potential for identifying more specific connections using multiple lines of evidence.

Back Wall of Hungo Pavi Showing Two Stories

Back Wall of Hungo Pavi Showing Two Stories

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Old Bonito from Above

Old Bonito from Above

Having introduced the basics of archaeological use of DNA evidence, and discussed some other applications of DNA studies in archaeology, let’s take a look at the data relevant to the Southwest specifically. For modern populations in North America overall, there are some broad trends that have been identified in mitochondrial haplogroup distribution by region, as first elucidated by Joseph Lorenz and David Glenn Smith of UC Davis in 1996. They only looked at haplogroups A, B, C, and D, since haplogroup X had not yet been identified as a founding haplogroup at that time. Their results showed that there are definite patterns in haplogroup distributions by region. For the Southwest specifically, they found most groups showed very high levels of B and low levels of A, despite the fact that A was the most common haplogroup in their sample overall. The main Southwestern groups that showed high levels of A were the Athabascan-speaking tribes (Navajo and Apache), which is unsurprising since northern Athabascan groups, along with most other groups in the Arctic and Subarctic, are almost exclusively A, and it’s well established that the southern Athabascans immigrated into the Southwest from the north relatively recently. Some other Southwestern groups show some representation of A as well, which Lorenz and Smith attribute to intermixing with the Athabascans (although as I’ll discuss below this doesn’t seem to be the whole story). Similarly, the Navajos and Apaches showed substantial representation of B and C, unlike their northern cousins, and this is probably due to intermixing with the Pueblos and other Southwestern populations.

A subsequent study by Smith, Lorenz, and some of their students at Davis looked specifically at haplogroup X, which had been identified in both modern and ancient Native American samples by then and was established as a founding haplogroup. They found it widely distributed among modern populations speaking a variety of languages but particularly among speakers of Algonquian and Kiowa-Tanoan languages. The Kiowa-Tanoan connection is of particular interest for Southwestern purposes, of course, as this is one of the main language families spoken by the eastern Pueblos in New Mexico. In this case, haplogroup X was found in the Kiowa and Jemez samples. This is very interesting since the Jemez are Pueblo and the Kiowa are not, and the relationship between the Kiowa and the Tanoan-speaking Pueblos is a longstanding mystery. It’s hard to know how to interpret the haplogroup X data in this connection. Since X is so rare overall the fact that it is so concentrated in certain groups seems meaningful somehow, but since it’s still pretty rare in those groups and little follow-up research on this has since been done it remains quite mysterious.

Turning to the ancient evidence, the first work in the Southwest was associated mostly with the University of Utah. In 1996 Ryan Parr, Shawn Carlyle, and Dennis O’Rourke published a paper reporting on aDNA research on the remains of 47 Fremont individuals from the Great Salt Lake area, 30 of which could be assigned to a haplogroup. The Fremont have always been something of a mystery, with many Southwestern cultural features but living on the northern fringes of the Southwest and having some notable differences from Pueblo cultures to the south. What the Utah researchers found, however, seemed to show the Fremont patterning genetically with the Pueblos rather than with other groups in the Great Basin or Plains. Haplogroup A was completely missing from their sample, while B was by far the most common haplogroup and C and D were also present in small numbers. This seems to clearly rule out one theory about the Fremont, which is that they were composed in part of Athabascans on their way south from the Subarctic, and also casts in serious doubt other theories linking them to later cultures on the Plains (where haplogroup A is also very common). It’s true that there is internal cultural variation within the construct “Fremont” and it’s quite possible there was genetic variation as well, but the Great Salt Lake Fremont were the furthest north of the identified subdivisions and the closest to the Plains, so if even they show more genetic similarities to the Southwest that is strong evidence against theories associating them with areas to the north and east.

It’s also noteworthy that the Fremont distribution is in contrast to what Lorenz and Smith found among modern Numic peoples who now occupy the Fremont’s Great Basin home. The Numic Paiute/Shoshone sample that Lorenz and Smith looked at lacked haplogroup A, but it showed a very high proportion of haplogroup D (the highest in their whole study, in fact) and a low proportion of B and C. This doesn’t totally rule out some Fremont contribution to Numic ancestry, but it makes it seem unlikely that there was substantial genetic continuity between Fremont and Numic populations, which supports the “Numic Expansion” hypothesis for the late prehistory of the Great Basin. Smith and his student Frederika Kaestle later published a paper making this exact argument, using not only the Fremont data but additional ancient remains from the western Great Basin to argue that the differences in haplogroup frequencies supported a replacement of the earlier Basin inhabitants by the Numa.

Following up on this research, a subsequent paper by the same Utah researchers added in data from the Anasazi. They successfully assigned 27 Anasazi samples to haplogroups. Of these, 12 were from southeastern Utah, 9 were from Canyon del Muerto, 4 were from Canyon de Chelly, and 2 were from Chaco Canyon. Of the Chaco remains, one came from the debris in Room 56 at Pueblo Bonito, a part of the north burial cluster in Old Bonito which was very crudely worked over by Warren K. Moorehead in the 1890s. The other I can’t seem to find any specific information on. All of the Anasazi remains analyzed in this study were from the collections of the American Museum of Natural History, which makes me surprised that only two Chaco samples were involved. It’s possible that more were analyzed but only these two produced enough DNA to work with. In any case, if in fact there are more Chaco remains at the AMNH that have not yet been analyzed for DNA it would be very helpful to analyze them.

The results of this analysis were consistent with the standard archaeological understanding that the modern Pueblos are the descendants of the Anasazi. B was the most common haplogroup, with smaller levels of A and C. D wasn’t present at all, and two of the specimens didn’t fall into any of the four haplogroups, implying that they might have belonged to X. (The two Chaco samples belonged to haplogroups B and C; the sample from Room 56 belonged to haplogroup B.) Note that A is present here in populations dating well before any likely admixture with Athabascans, which is evidence against Lorenz and Smith’s contention that the presence of A in modern Pueblos can be attributed entirely to mixture with Athabascans.

Based on the dominance of B and low levels of other haplogroups, these researchers concluded that the Anasazi remains they analyzed were not significantly different from the Fremont remains they had analyzed earlier, adding further support to their contention that the Fremont pattern with the Pueblos. Note, however, that the Fremont hadn’t shown haplogroup A at all, while the Anasazi had it at a low but still respectable level (22%). Also, the Fremont showed a low level of haplogroup D, which the Anasazi didn’t have at all. These differences don’t necessarily mean the Fremont and Anasazi weren’t related, of course, but they do show how much that similarity is a judgment call supported by questionable statistics. In this case one big problem with the statistical analysis was treating the haplogroup frequencies as ratio-level data, which implies that they are meaningfully representative of the underlying populations despite the very small and non-random samples. This is highly implausible. This problem means that the authors’ conclusions about whether differences between samples were “significant” or not in a statistical sense is not really meaningful since it can’t reasonably be expected to generalize to the populations, which are what we really care about.

In addition, as Connie Mulligan pointed out in the general paper on aDNA that I discussed previously, the differences that the Davis researchers found between the haplogroup frequencies of the Fremont and Numic samples, which they used as evidence of a lack of population continuity, were actually quite similar statistically to the differences the Utah researchers found between the Fremont and Anasazi, which they interpreted as not being significant! This disconnect goes to show that there’s actually quite a bit of subjective judgment in interpreting results like this, despite the superficial impression of “objective” statistical data.

One way to overcome this confusion would be to increase the number of samples analyzed and try to make them as close to representative of the underlying populations as possible. That would certainly help, but the fundamental problem of defining the ancient population of interest, and the apparent impossibility of analyzing a sample from it that could be assumed to be truly representative, are daunting challenges. A more productive approach, which subsequent research has in fact been following, is to do more in-depth analysis of available samples, so that more detailed data than crude haplogroup assignments are possible.

One way to do more in-depth analysis would be to move away from relying exclusively on haplogroup assignments and look instead at the nuclear genome. Sequencing the whole nuclear genome provides vastly more, and more statistically robust, information than mitochondrial haplogroup assignment, as commenter ohwilleke pointed out in response to my initial DNA post. Most of the studies mentioned in my previous post in other parts of the world have used this methodology, with very informative results. This type of analysis has, however, not been done on ancient remains from the American Southwest to my knowledge. I’m not sure why exactly, but there are various reasons including cost and level of preservation of remains that could account for this lacuna.

Instead, Southwestern researchers have mostly doubled down on mitochondrial haplotype analysis and extended its reach by looking at further mutations within the defined haplogroups to identify sub-haplogroups that can further narrow down genetic relationships. This has been a productive line of investigation, as exemplified by a very interesting paper from 2010 dealing with Chaco-era sites in the area of Farmington, New Mexico.

B-Square Ranch, Farmington, New Mexico

B-Square Ranch, Farmington, New Mexico

The paper, by Meradeth Snow and David Glenn Smith of Davis and Kathy Durand of Eastern New Mexico University, analyzed human remains from two sites on the B-Square Ranch, a large ranch that includes most of the land south of the San Juan River in Farmington. The ranch is owned by the Bolack family, which has long been prominent in local and statewide affairs. Its patriarch for many years was Tom Bolack, who was governor of New Mexico for a brief period in the 1960s and was also well known for his elaborate produce displays at the State Fair. His son Tommy Bolack, who took over management of the ranch when Tom died, has long had an interest in archaeology and did his own excavations in various of the many archaeological sites on the ranch. In recent years rather than continuing his own excavations he has worked with Linda Wheelbarger, a professional archaeologist who teaches at San Juan College in Farmington, to conduct field schools in the summers for SJC students as well as analyses of artifacts and human remains from both these recent excavations and his own earlier amateur work.

Among these analyses was the aDNA analysis of remains that Bolack excavated from the Tommy and Mine Canyon sites, two small-house sites on the ranch dating to the Chaco era. The Tommy site is slightly earlier, dating to approximately AD 800 to 1100, while the Mine Canyon site dates to approximately AD 1100 to 1300. Since the Tommy site seems to have been abandoned at approximately the same time the Mine Canyon site was founded, one obvious interpretation is that the Mine Canyon site was founded by the same people who had previously lived at the Tommy site. The DNA evidence, however, challenges this interpretation and suggests a more complicated story.

For this study, 73 samples were sent to Davis for aDNA analysis. This included a mix of tooth and bone samples. Of these samples, 48 (65.7%) could be assigned to a mitochondrial haplogroup. Of these, 26 were from the Tommy site and 12 from the Mine Canyon site.

The successfully analyzed samples from the Tommy site showed a typical distribution of haplogroups for a Southwestern population: 3% A, 69% B, 14% C, and 14% D. (This study didn’t look for haplogroup X, and all successfully analyzed samples fell into one of the other founding haplogroups.) The Mine Canyon sample, however, showed a very unusual distribution: 58% A, 33% B, 8% C, and 0% D. This is an exceptionally high proportion of haplogroup A, which is generally fairly rare in the Southwest except in Athabascan groups which are generally thought to have arrived in the region well after these sites were abandoned. Haplogroup A is also very common in Mesoamerica, which makes its dominance in a Chaco-associated site particularly intriguing given the evidence for contact with Mexico seen at Chaco Canyon itself and some outlying Chacoan sites.

The authors are careful to note that these are very small sample sizes, which makes sampling bias a very real possibility to account for this sort of striking result. They compare these distributions to several other ancient and modern Southwestern and Mesoamerican populations using Fisher’s exact test and find, unsurprisingly, that the Tommy site sample isn’t significantly different from other ancient Southwestern populations but is significantly different from all the modern populations as well as the ancient Mesoamerican ones. The Mine Canyon sample, on the other hand, was found to be significantly different from all the ancient Southwestern samples as well as all the modern Southwestern ones except the Athabascan Navajo and Apache, while it wasn’t significantly different from any of the ancient or modern Mesoamerican samples. This result is clearly driven primarily by the unusually high proportion of haplogroup A at Mine Canyon, which means it doesn’t really add much to the paper. Although Fisher’s exact test does take into account the small sample sizes, it doesn’t address the more fundamental problem with this sort of use of statistics on this type of data which can’t really be trusted to be representative of the underlying population of interest. This is the sort of thing I was talking about in the earlier post under the somewhat tongue-in-cheek label of “elaborate statistical techniques” on data that don’t necessarily fit the necessary requirements for their use. This sort of technique is not actually very elaborate compared to more sophisticated statistical analyses used for studies of whole genomes, where the number of data points is immense and they can actually be assumed to be representative of the analyzed individual’s full ancestry. Calculating P-values for differences between two samples based on four data points for each, when neither sample is necessarily representative of its underlying population of interest, is not very useful, but very common in mtDNA studies at least in the Southwest. To their credit, the authors of this paper are well aware of the weaknesses of this part of it and are careful to downplay the significance of the statistical analysis.

With these intriguing preliminary results, the researchers attempted further sequencing to identify more specific mutations that might define sub-haplogroups and clarify relationships on a more granular scale. Of the 48 samples that could be assigned to haplogroups, 23 were successfully sequenced for mutations in a region of the mitochondrial genome known to be highly variable. (Note how small the sample gets with subsequent levels of analysis.) Poor preservation was a major problem at this point, and there wasn’t enough genetic material remaining to construct the sort of network diagram that is often included in papers like this, showing specific mutations and the relationships they imply between specific ancient and modern samples.

The most interesting results from this further sequencing were with haplogroup A. Of the 8 samples initially identified as belonging to this haplogroup, 6 samples from the Mine Canyon site showed two distinctive mutations that are otherwise known only from 3 modern Zuni samples, along with one Tohono O’odham and one Chumash sample. Importantly, this set of mutations is unknown from both Mesoamerican and Athabascan groups. This is strong evidence that the dominance of haplogroup A at the Mine Canyon site does not indicate either migration from Mesoamerica or an early Athabascan presence in the Southwest; instead, it seems that this site just happens to have had an unusually high proportion of a rare but natively Southwestern lineage which survived into modern times at Zuni (and may have had some connections further west). The samples belonging to haplogroup B similarly showed the dominance of a sub-haplogroup distinctive to the Southwest and unknown in Mesoamerica.

The differences between the Tommy site and the Mine Canyon site in haplogroup frequencies, while they may well be a function in part of the small sample sizes, may also provide evidence for complex population movements within the late prehistoric Southwest. The exact parameters of these movements can’t be defined until more evidence is available from other areas, however, especially Chaco Canyon and the Mesa Verde region.

Overall, despite the poor preservation of the samples involved, this study provides important support for a finding that has come out consistently across all lines of evidence relating ancient to modern Pueblo people: there is a lot of evidence for continuity over time on a regional scale with complex movements within the Southwest, but little to no evidence of significant population movement into or out of the Southwest in recent centuries. (There is a whole other debate about the extent of population movement into the Southwest much earlier, at the time when agriculture was first introduced, which I haven’t discussed much in these posts and which isn’t of much importance for the specific issue I’m addressing here.) I think there is a lot of potential for more detailed reconstruction of movement within the Southwest based on a combination of lines of evidence, but we’re certainly not there yet.

I’ve gotten some questions about how the DNA evidence relates to the issue of hierarchy at Chaco. I’ll have a more extensive post on the evidence for social hierarchy, which I think is extensive, but the short answer is that DNA doesn’t really provide any evidence one way or the other on this point. Since all evidence points to a general pattern of population continuity in the Southwest at least since the introduction of agriculture, the genetic patterns of any elites that arose wouldn’t be likely to differ in any noticeable way from those of the commoners they rose from. Indeed, the one sample to be analyzed for mitochondrial DNA that is very likely to come from an elite Chacoan context, the sample from Room 56 at Pueblo Bonito, belonged to haplogroup B, the most common in both ancient and modern Southwestern populations. It’s theoretically possible to imagine an elite group immigrating into the Southwest from Mesoamerica, and theories have been proposed along these lines, but the DNA evidence doesn’t particularly support this, and it’s much more likely based on all lines of evidence that the rise of an elite at Chaco was a primarily indigenous development involving some indirect influence from Mexico but little to no permanent population movement over that distance.

This is the last substantive post in my series about “tracing the connections” between the ancient and modern Southwest, although I will probably do a follow-up post linking to all the others for the convenience of readers. Overall, I think these posts have shown that we have substantial evidence from various perspectives that the modern Pueblos are the descendants of the ancient Anasazi (and other prehistoric Southwestern groups), but the evidence we have so far is not sufficient to connect any specific ancient sites with any specific modern pueblos. I am hopeful, however, that that may change as more evidence comes in and we are able to tie together new data with the evidence we already have to make some more specific connections.
ResearchBlogging.org
Carlyle SW, Parr RL, Hayes MG, & O’Rourke DH (2000). Context of maternal lineages in the Greater Southwest. American journal of physical anthropology, 113 (1), 85-101 PMID: 10954622

Kaestle FA, & Smith DG (2001). Ancient mitochondrial DNA evidence for prehistoric population movement: the Numic expansion. American journal of physical anthropology, 115 (1), 1-12 PMID: 11309745

Lorenz JG, & Smith DG (1996). Distribution of four founding mtDNA haplogroups among Native North Americans. American journal of physical anthropology, 101 (3), 307-23 PMID: 8922178

Smith DG, Malhi RS, Eshleman J, Lorenz JG, & Kaestle FA (1999). Distribution of mtDNA haplogroup X among Native North Americans. American journal of physical anthropology, 110 (3), 271-84 PMID: 10516561

Snow, M., Durand, K., & Smith, D. (2010). Ancestral Puebloan mtDNA in context of the greater southwest Journal of Archaeological Science, 37 (7), 1635-1645 DOI: 10.1016/j.jas.2010.01.024

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Dorset Culture Exhibit, Carnegie Museum, Pittsburgh,  Pennsylvania

Dorset Culture Exhibit, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania

To wrap up my series on tracing the connections between ancient Pueblo sites like Chaco Canyon and the modern Pueblos, I’d like to discuss a type of evidence I haven’t discussed much but that people often ask about: DNA evidence. This is the most direct way to tie one population to another, at least in theory, but it’s actually quite difficult to draw any specific conclusions from the work that has been done so far, and that’s not necessarily going to improve as more research is done. Which is not to say that research along these lines has been worthless; it hasn’t revealed anything inconsistent with data from other sources so far, but that in itself is interesting and provides support for the other approaches that have been tried. Because this is such a huge and important topic, I’ve decided to break my discussion of it into two posts, one on the archaeological study of DNA in general, and another on the application of these techniques to the Southwest in particular.

There are many different types of DNA analyses that can in theory be done, but when it comes to archaeological questions, especially those involving connections between ancient sites and modern people, it is generally necessary to analyze remains excavated by archaeologists. This involves studying what is known as “ancient DNA” (or “aDNA” for short), in addition to the DNA of modern populations. As Connie Mulligan of the University of Florida noted in an article published in American Antiquity in 2006, aDNA studies have a lot of potential but also a lot of challenges. Some of the major issues involved in aDNA research are preservation of the DNA, without which any study has no chance of success, and interpretation of the results of a successful analysis of ancient material.

Because DNA, like any other organic material, decays over time, aDNA studies are more difficult and expensive than DNA studies of modern populations, and in some cases there is simply not enough DNA left in archaeological material to do any analysis at all. Preservation is a function, in part, of local environmental conditions, which in the arid Southwest tend to be favorable for preserving organic material, so this is less of a concern in this area than in many others.

Another major consideration in doing aDNA analysis is contamination. The technique that makes aDNA analysis possible is called Polymerase Chain Reaction (PCR), which involves taking a small amount of DNA and exposing it to a chemical reaction that creates billions of copies which can then be analyzed. This can be enormously useful, but the reaction is very sensitive and if any extraneous organic material is introduced it is likely to reproduce its DNA instead of the ancient DNA, which can totally destroy the validity of the analysis. The main concern with aDNA analyses of human remains is modern human DNA from the researchers themselves, and this has been an issue with many studies. These days the major laboratories that do aDNA analysis have elaborate procedures to ensure that modern human DNA doesn’t contaminate their samples, and these are typically spelled out in the papers resulting from this research.

Furthermore, as Mulligan discusses, it’s important that researchers have a clear sense of what questions they are asking and how successful aDNA analyses are likely to be in answering them. For example, DNA analysis is unlikely to be able to unambiguously identify a given set of ancient remains as belonging (or ancestral) to a specific tribal group, since genetic affiliation doesn’t correlate with cultural identity at anything close to that level of specificity. In other words, aDNA analysis can potentially identify remains as being of Native American rather than European origin, but it can’t unambiguously identify remains with any particular modern tribe. On the other hand, it is potentially possible to use aDNA studies to identify migrations and population replacement in the past, if the groups in question are sufficiently distinct genetically. Mulligan actually uses an example from the prehistoric Southwest, which I’ll discuss further in the next post, to illustrate how it can be tricky to interpret differences in genetic characteristics between populations, especially at the level of detail at which these analyses are often conducted.

These concerns aside, DNA analysis can certainly be a  powerful tool for understanding the past, especially when aDNA studies can be integrated with studies of modern DNA. A great example of this is a study that was recently published in Science about the prehistory of the North American Arctic. In this paper, which is available free on the Science website, the researchers report on a combination of aDNA and modern DNA analyses that demonstrate clearly that the people of the mysterious Dorset culture that inhabited Arctic Canada and Greenland from about 800 BC to AD 1300 are not ancestral to the modern Inuit inhabiting the same area, who are instead descended from the people of the Thule culture who immigrated into Canada from northern Alaska around AD 1200. This is solid, careful research that shows what DNA studies can reveal about the human past.

Much of the aDNA research in the Americas has focused on mitochondrial DNA (mtDNA), which is contained in the mitochondria of each cell, as opposed to nuclear DNA, which is contained in the cell nucleus. There are two main reasons for this.

One is that mitochondrial DNA is passed on (generally) unchanged through the maternal line, as opposed to nuclear DNA which undergoes meiosis, the process by which DNA from the mother and father is recombined in the course of creating a new embryo, meaning that any part of the genome that has gone through it cannot be easily traced from generation to generation. Mitochondrial DNA, in contrast, is passed on directly from mother to child, and the only changes are whatever mutations develop over time, which can be used to define specific haplogroups, or genetic groupings sharing certain distinctive mutations that are interpreted as indicating shared descent. Within each haplogroup, further mutations can be used to define various sub-haplogroups, which indicate closer relationship among the haplotypes (individual genetic profiles) that comprise them. The Y chromosome, which is passed on directly from father to son, isn’t affected by recombination during meiosis and can be used to trace descent in a similar fashion. However, mtDNA is more widely used for aDNA studies than Y-chromosome DNA, due to an additional difference between mtDNA and nuclear DNA.  Due to the structure of mitochondria, each cell contains many more copies of its mtDNA than of its nuclear DNA, so mtDNA is much more likely to survive in ancient samples than nuclear DNA. This means there is much greater probability that studies of mtDNA using PCR will identify DNA to be replicated, and the result is that the existing database of mtDNA available for statistical analysis is much larger than that for nuclear DNA, including  Y-chromosome DNA. Most aDNA studies in North America, at least, have therefore used mtDNA as a primary focus for research.

Early research on both ancient and modern DNA identified four main mitochondrial haplogroups among Native American populations. These were labeled A, B, C, and D. (Haplogroups are conventionally identified by capital letters, with more specific sub-haplogroups indicated by sequences of numbers and lowercase letters following the haplogroup letter.) These haplogroups all arose from earlier East Asian haplogroups, which agrees with the traditional interpretation that Native Americans descend from Asian groups that migrated across the Bering Strait. Some modern populations in these early studies showed low levels of an additional haplogroup, X, which had previously only been documented in Europeans. There was some question at first about whether this indicated post-Contact admixture with Europeans or an additional “founding” haplogroup, but it was later found in aDNA, showing clearly that it was indeed ancient in the Americas. The implications of this finding are hard to understand, but the general consensus at this point seems to be that the American examples descend from a very ancient and otherwise unknown Central Asian offshoot of the European X haplogroup. Wherever it came from, however, it is now quite clear that X is one of the founding haplogroups in the Americas.

Much aDNA research in North America, then, has focused on identifying the haplogroups of ancient remains and comparing them to those of other populations, both ancient and modern. Much of this research has involved treating assemblages of ancient remains (either from single sites or across a whole archaeological “culture”) as samples that can be compared statistically to samples from modern tribes. I find this dubious, since the ancient samples are typically small and there’s no way to tell how representative they are of the actual underlying population (however it’s defined). The statistical procedures often used to analyze haplogroup frequencies implicitly assume that these are random samples representative of the population, but there’s no real way to know if this is true and in most cases no particular reason to think it is. In theory it’s possible that the modern samples, at least, are representative of their populations, but I suspect it’s often not the case in practice here either. For both modern and ancient samples, it’s likely that other factors, such as level of preservation and willingness to provide samples, have strongly affected the composition of the samples. These factors may or may not have skewed the representativeness of the samples; the point is that there’s no real way to tell.

Given this sampling issue, I think the most conservative and defensible approach is to treat haplogroup distributions as nominal-level data: the most we can really say about a given haplogroup in a given sample is whether it is present or absent. That’s not very helpful, though, and it may be reasonable to take a further leap and treat the distributions as ordinal-level data: this allows us to make use of the fact that some haplogroups are much more common in a given sample than others to make some broad conclusions about haplogroup distributions on a larger scale. What isn’t justified, however, is treating the frequencies of haplogroups in a sample as interval/ratio-level data: using the actual numbers as if they are meaningfully representative of the underlying population, and plugging them into elaborate statistical formulas to compare them to other samples/populations. Not all aDNA studies do this sort of thing, but it’s common enough that I think it’s important to emphasize that it’s a problematic approach at best, and that any conclusions regarding probable relationships between populations based on this method shouldn’t be taken very seriously.

A better way to go beyond the crude data of haplogroup assignment is to sequence additional portions of the mitochondrial genome that are known to contain mutations that define sub-haplogroups within the assigned overall haplogroup. Enough research has been done at this point that quite a few sub-haplogroups are known, and when they show up in multiple samples, either ancient or modern, that provides a much firmer basis for hypothesizing meaningfully close relationships than statistical comparisons of haplogroup distributions among whole samples. Furthermore, since the mutations that define sub-haplogroups can be grouped hierarchically, it’s possible to construct trees showing how individuals in a given sample, or even across samples, that belong to the same haplogroup relate to each other. (Note that this isn’t quite the same as showing how the people were actually related, since we don’t know when the mutations that define these groups actually occurred or how the people whose remains were sampled were related to the people in whom the mutations originally occurred.) There’s a probabilistic aspect to this type of evidence, since there are multiple ways a particular set of mutations could have ended up together in the same haplotype, and determining the most likely sequence of events can require modeling and simulation. The more samples are analyzed, the larger the database of known mutations and sub-haplogroups becomes, and the more reliable the conclusions that can be drawn about relationships are.

So that’s the basic outline of how ancient DNA analysis works and the methodological concerns that need to be kept in mind when evaluating it. In the next post, we’ll look at some of the specific studies that have applied these methods to the Southwest, and what their results can and can’t tell us about Southwestern prehistory.
ResearchBlogging.org
Mulligan, C. (2006). Anthropological Applications of Ancient DNA: Problems and Prospects American Antiquity, 71 (2) DOI: 10.2307/40035909

Raghavan, M., DeGiorgio, M., Albrechtsen, A., Moltke, I., Skoglund, P., Korneliussen, T., Gronnow, B., Appelt, M., Gullov, H., Friesen, T., Fitzhugh, W., Malmstrom, H., Rasmussen, S., Olsen, J., Melchior, L., Fuller, B., Fahrni, S., Stafford, T., Grimes, V., Renouf, M., Cybulski, J., Lynnerup, N., Lahr, M., Britton, K., Knecht, R., Arneborg, J., Metspalu, M., Cornejo, O., Malaspinas, A., Wang, Y., Rasmussen, M., Raghavan, V., Hansen, T., Khusnutdinova, E., Pierre, T., Dneprovsky, K., Andreasen, C., Lange, H., Hayes, M., Coltrain, J., Spitsyn, V., Gotherstrom, A., Orlando, L., Kivisild, T., Villems, R., Crawford, M., Nielsen, F., Dissing, J., Heinemeier, J., Meldgaard, M., Bustamante, C., O’Rourke, D., Jakobsson, M., Gilbert, M., Nielsen, R., & Willerslev, E. (2014). The genetic prehistory of the New World Arctic Science, 345 (6200), 1255832-1255832 DOI: 10.1126/science.1255832

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