Virgin Soil, Widowed Land: Overview and Scope Update

Clinic, Pilot Point, Alaska

Well, it’s certainly been a while since I introduced this series! The coronavirus hasn’t gone anywhere, though, and neither have I. I’ve been reading lots of fascinating stuff on New World (de)population and disease history, and I have a pretty good idea of the way the series is going to look overall. I’m still not sure how long it’s going to take (at least several months) or how many posts it will ultimately include. I have enough of a sense now, though, to give a tentative outline of the topics I intend to cover, and that’s what I’ll do in this post. I’ve also decided to make a couple changes to the scope of the series, which I’ll also discuss here.

To take the latter issue first, I initially said I would limit the scope of the history I’m looking at to exclude the Black Death of the fourteenth century and the 1918 “Spanish Flu” pandemic, with the idea that the epidemics of interest for Native American population mostly occurred between the two, each of which has been the subject of such an immense scholarly literature that it would be easy to get bogged down. After digging a bit further into the overall topic, though, I realized there were good reasons to look at both these pandemics, and indeed others both earlier and later. The issue of getting bogged down is a real one, which I’ve managed to mostly avoid with the Spanish Flu but less so with the Black Death. Still, so much of the scholarly literature on disease history and the general impacts of epidemics involves or relies on study of these most prominent examples that it doesn’t really make sense to arbitrarily exclude them.

Furthermore, looking both earlier and later than the core period between these two pandemics turns out to be pretty important. Earlier, there were some important epidemics worthy of study for many reasons, including the light they may shed on the history and evolution of certain diseases (especially now that ancient DNA analysis techniques have reached the point that specific pathogens can be unambiguously identified in ancient remains). Later, there were some specific epidemics postdating 1918 that turn out to be very important for the scholarly history of “virgin soil” epidemics and depopulation, in part because they were directly witnessed by doctors trained in modern scientific medicine. Of these, the most important are a series of epidemics in the Yukon Territory associated with the building of the Alaska Highway in the 1940s and another series in the Amazon in the 1960s. So I’ve essentially abandoned any hard temporal bounds on the scope of the series, although the main focus will of course be on the period from roughly 1500 to 1900.

Okay, on to the outline. To anticipate the overall conclusions a bit, despite a long history of research on the topic of Native American depopulation and the role of epidemic disease, I’ve found that there’s never really been a solid consensus about anything related to these topics and such a consensus is, if anything, further away now than it’s ever been. There have been general trends in the popularity of certain interpretations and methodological approaches, which can be (and have been) conveniently categorized into periods of one approach or another being dominant, but a closer look shows that there has always been a diversity of views that really cluster most clearly by academic discipline. I’ll get into this in more detail later, but the general idea is that rather than “high counters” and “low counters” exchanging periods of hegemony, there have always been both, concentrated in their own disciplinary zones, though their influence as measured by the spread of their ideas into other disciplines does show a certain back-and-forth pattern over time.

With that overall idea in mind, and despite my skepticism about a general chronological patter being most important, I do intend to structure the first part of the series chronologically. I’ll have posts for each major “era” in the modern study of these topics, which will hopefully give a sense of the major players and their ideas through time. After that overview, I’ll do multiple subseries of posts looking at the question from our current perspective, taking account of the various contributions from different disciplines.

These subseries will include one organized nosologically, or by the modern categorization of diseases and the pathogens that we now know to cause them. Another subseries will be geographic, looking at the different regions of the New World and what we know (and don’t know) about their population and disease histories. I may also do a third subseries looking chronologically at the big picture of population and disease throughout the different periods of contact and colonization in the Western Hemisphere, but I’m not as sure about that one yet.

So that’s the general idea. As I mentioned above, the series will definitely take a minimum of several months (it’s already taken more than three months to get to this second post!), but I don’t know how long it will ultimately take or how many posts it will involve. It’s a big but fascinating and important topic.

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Chaco Is Closed

“Area Closed” Sign at Fajada Butte View

This is just a quick post to share some information likely to be of interest to my readers. There has been a lot of confusion about exactly how the National Park Service is responding to the government shutdown, which park units are accessible and not, and so forth. I’ve been pretty confused myself, and unfortunately this led me to give incorrect advice to a reader who asked if Chaco Canyon is accessible during the shutdown. I said my understanding, based on media reports, was that the parks are open but no visitor services are being provided. Since Chaco is mostly a self-guided experience, I took that to mean that the park would be accessible but the visitor center would be closed and no tours would be provided.

Well, the reader took my advice and headed out to Chaco, only to find that the gate was closed and the park was definitely neither open nor accessible. He let me know, and was nice about it, but I felt bad about leading him astray so I figured I would pass that information on here. Chaco is closed for the shutdown. Anyone planning to visit in the next few weeks should keep that in mind and monitor the news for information on when the government and the park will reopen.

If you do end up having to redirect a trip to Chaco as a result of the shutdown, Salmon Ruins in Bloomfield, New Mexico is one of the largest and most accessible Chacoan outlier sites, and since it’s managed by San Juan County rather than the federal government it is unaffected by the shutdown. Another option a little further afield is Edge of the Cedars in Blanding, Utah, which is a Utah state park and similarly unaffected. Most other Chacoan outlier sites that are open to the public are managed by federal agencies and will likely be inaccessible.

Edge of the Cedars Great House, Utah

In previous shutdowns parks have been closed entirely, which is the simplest and, from a resource-protection standpoint, most reasonable approach. This time it seems the NPS is taking a different and more complicated approach for reasons that are unclear. To try to get a better understanding of what exactly the NPS is doing with parks in this shutdown, particularly as it relates to Chaco, I took a look at the official NPS contingency plan. Two sections seem to explain what’s going on there:

As a general rule, if a facility or area is locked or secured during non-business hours (buildings, gated parking lots, etc.) it should be locked or secured for the duration of the shutdown.

This seems to explain what’s going on on the ground at Chaco, as reported by my reader who went there. The park loop road is ordinarily gated at night, so it appears that they’ve closed the gate for the duration of the shutdown. There are a few things to see on the way in to the park before the gate, but the vast majority of the sites and trails are beyond it.

At the superintendent’s discretion, parks may close grounds/areas with sensitive natural, cultural, historic, or archaeological resources vulnerable to destruction, looting, or other damage that cannot be adequately protected by the excepted law enforcement staff that remain on duty to conduct essential activities.

It’s possible that this section is also relevant, though it’s less clear. Certainly it would be best for resource protection to close all the major sites and trails; it’s hard enough for the law enforcement rangers to monitor visitor activity when the park is operating under normal circumstances. The test for this would be whether the attractions on the way into the park, particularly the Gallo Cliff Dwelling and the trail to Wijiji, are closed, which is not clear to me from the information I have. The park website currently says it’s closed entirely but without explanation of what that entails, so it may well be the case that this section has been invoked.

Hopefully the shutdown will be resolved soon and things will go back to normal, but for now it’s best to steer clear of Chaco. If I hear of any changes or get more information I’ll do another post.

Central Roomblock at Salmon Ruin

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Changes

Winter Solstice Sunset, Chaco Canyon

Today is the winter solstice, which means it’s the tenth anniversary of this blog.

Ten years is a long time for this sort of thing, and the online landscape has changed a lot in the time I’ve been doing this. When I started, blogging was still a relatively hip new thing, and there were blogs starting up all over the place on all sorts of topics. Social media as we know it today was in its infancy, and while most of the major platforms did exist they didn’t have nearly the reach or the cultural position that they do now.

Over those ten years, blogging has waned as a medium, and a lot of the discursive energy that made it so interesting migrated to various social media platforms. It never totally went away, as it’s a very good medium for the sort of long-form, infrequent content that does not fit easily into social media, and my own blogging has increasingly moved into that mode as well. I get few comments and fewer active discussions in comment threads these days, although that is partly due to the fact that I rarely engage in the comment threads myself anymore. Blogging has just become a different beast than it once was.

I also haven’t had as much time for it in recent years as I used to. My posting frequency has declined over time, and in recent years it’s generally been once a month. I’ve made a point of never missing a calendar month, although it’s been a close call a few times. Some of the posts I’ve done to meet those deadlines have been pretty insubstantial, though, and I’m not very proud of them. I’ve continued to do occasional longer, more in-depth posts, but I just don’t have as much time in my life for blogging as I used to.

I’m not quitting, though. I’ve considered it, and even considered using this anniversary post to announce it, but I still have more to say. Tim Burke had a post recently about the decline of blogging, and a lot of it resonated deeply with me although not all of it is relevant to the type of blogging I do here. Particularly resonant was his conclusion:

And yet, I remain hopeful about blogging. I am not sure why. I am not sure when. This remains open for business, nevertheless.

Likewise, this site remains open for business, but with some changes. I still have plenty to say about the ancient Southwest as well as other topics, but I’ll be restricting my writing here to the former. I may find a new outlet (or more than one) for writing about other topics, including some that I’ve written about here in the past, and if I do I’ll mention it here. But in view of the particular audience for this site and its history, I think it’s best to keep the focus here fairly narrow going forward. I haven’t been as able to keep up on recent research on Chaco Canyon as I used to, but there’s been a lot of it and I’m sure I will return to it at some point. When I do, I’ll discuss it here.

I’m also going to dispense with the artificial monthly schedule and just post whenever I have something to say. The sorts of posts I have in mind, some of which I’ve been thinking about for years, will be long and take a while to write, and I don’t want to either rush them or put them off even longer in an effort to post with a consistent rhythm. Stay tuned.

Finally, to give this post a little bit of substantive content in addition to my blathering on, here’s a nice post, written fifteen years ago by another old-school blogger, Kieran Healy, about the Irish megalithic site of Newgrange and its solstice alignment. Healy’s conclusion about it is thought-provoking and seasonally appropriate, now more than ever:

A society—a civilization, if you like—is a hard thing to hold together. If you live in an agrarian society, and you have only stone, wood, and bone for tools, and you are on the western edge of Europe, few times are harder than the dead of Winter. The days are at their shortest, the sun is far away, and the Malthusian edge is right in front of you. It’s no wonder so many religious festivals take place around the solstice. Here were a people, more than five millennia ago, able not only to pull through the Winter successfully, but able also to build something like a huge timepiece to remind themselves that they were going to make it.

Times change, but we’ll make it too. Happy solstice.

Chetro Ketl, the Talus Unit, and Pueblo Bonito from the Cliff Top

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A Wedding on Kodiak

Kodiak, Alaska

In 1805, while visiting the Russian settlement on Kodiak Island as part of the first Russian circumnavigation of the globe, the Russian naval commander Yuri Lisianski observed among the local Alutiiq Natives the presence of individuals known as “schoopans” who had male genitalia but were brought up from childhood as girls, performing women’s work and marrying men. This was a highly honored role in Alutiiq society, and an example of the widespread “berdache” or “Two Spirit” tradition of the Americas that I have discussed before. Lisianski noted that the schoopans “even assume the manners and dress of the [female] sex so nearly, that a stranger would naturally take them for what they are not,” and continues in a footnote:

As a proof of how easily this mistake may be made; it once happened, that a toyon [rich man or “chief”] brought one of these unnatural beings to church to be married to him, and the ceremony was nearly finished, when an interpreter, who came in by chance, put a stop to the proceedings, by making known to the priest, that the couple he was joining in wedlock were both males.

This anecdote caught my attention in part because it is strikingly relevant to modern political debates over the rights of trans people, especially the so-called “bathroom bills” that have cropped up in various places over the past few years. Here in Anchorage, we have one of these measures, Proposition 1, on the municipal ballot right now in our first vote-by-mail election. Election Day is on Tuesday, April 3, but ballots have already been mailed and voting is going on right now.

I’m strongly opposed to Prop 1, which is highly discriminatory against the trans community and serves no real public purpose. Beyond its discriminatory nature, the very premise of Prop 1 is fundamentally absurd in ways highlighted by Lisianski’s story that would render it totally unenforceable and perhaps even cause the sorts of “problems” it purports to solve.

Many of the arguments for Prop 1 and similar measures rely on the assumption that gender is not just an “immutable” biological characteristic on a deep level, but one that is impossible to affect even superficially. Prop 1 seems to take it as a given that a trans person using the “wrong” bathroom under the law will be easily identifiable because they will look to any bystander like their “biological” gender.

This is however not true at all. As with the population as a whole, there is a lot of physical variation among trans people, but many look well within the physical norms of their preferred gender and fit in much better in the bathrooms they prefer to use than in those they don’t. That is to say, trans women really are women, in many cases even physically, visually, to strangers who don’t know anything more about them than how they look. And similarly, trans men really are men.

Indeed, if we are judging gender the way most of us do in practice, by how people look rather than by careful inspection of their genitals or birth certificates, Prop 1 would likely lead to, if anything, a massive increase in the number of “men” in women’s restrooms, because trans men who look like and lead their lives as men would be forced by the terms of the law to use women’s restrooms. In other communities that have adopted laws like this trans men have posted pictures to social media showing what this looks like; it looks like a man in a women’s restroom. If seeing that is what people who support Prop 1 are concerned about, voting for it is certainly not going to help.

The greater visibility of trans issues in recent years may make the idea of gender diversity seem new and strange, but there is actually a long history of different concepts of gender in many societies around the world. The berdache or Two Spirit tradition, present in many indigenous societies of the Americas, including some in Alaska, is one of the most striking examples of a socially accepted, often high-status role for individuals who do not conform to a strict gender binary typical of European societies.

I’ve been digging into the ethnographic and ethnohistoric data on berdaches in Alaska Native societies specifically, which don’t seem to have gotten a whole lot of attention in the anthropological research on gender diversity. The data are spotty and difficult to interpret to an even greater degree than for many other societies, but there are a lot of fascinating nuggets in there like Lisianski’s anecdote about the wedding. I’m thinking of doing a research project to synthesize the existing data, maybe in blog posts here but maybe in a more formal venue. It’s a fascinating topic with a lot of relevance to issues today, which makes it of particular interest to me. Stay tuned.

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Can Trump Actually Abolish Those Monuments?

Bears Ears from Natural Bridges National Monument

Last week, President Donald Trump signed an Executive Order requiring the Secretary of the Interior to review all presidential designations of national monuments under the Antiquities Act since 1996 where the size of the designated monument exceeds 100,000 acres or where “the Secretary determines that the designation or expansion was made without adequate public outreach and coordination with relevant stakeholders,” and to provide a report within 120 days evaluating the extent to which any monument designations did not conform to the requirements of the Act and recommending actions the president or Congress might take to remedy these problems. This order has widely been interpreted and reported as an attempt by Trump to abolish controversial national monuments designated by his predecessors, especially Barack Obama, who designated more monuments than any other president. This certainly seems like a fair reading of Trump’s intent in signing the order, or at least of the impression he sought to make with it.

It’s not clear that he can actually do this, though. It’s noteworthy that the Executive Order itself only orders a review and report on whether there are problems with the designations and what might be done about them if so. It doesn’t directly have any substantive impact on anything. While this is a common pattern with Trump’s executive actions so far, in this case there is a very clear reason for it, which is that it’s not at all clear that a president actually has the authority to abolish a national monument or to revoke a designation made by one of his predecessors.

Much of the discussion of this order has centered on Bears Ears National Monument in southeastern Utah, which President Obama designated on December 28, 2016. Local officials in Utah were furious about this particular designation and have been trying to overturn it since it was made. Bears Ears is the only specific monument designation mentioned by name in the Executive Order, in a section that requires an interim report within 45 days on it and any other designations the Secretary sees fit to include. Bears Ears is also potentially of interest to readers of this blog as the location of numerous ancient Pueblo (and other) archaeological sites, including the Mule Canyon and Butler Wash Ruins, which are easily accessible Utah Highway 95 and developed for visitation. It surrounds Natural Bridges National Monument, which also contains many archaeological sites in addition to the geological structures for which it is named.

Butler Wash Cliff Dwelling near Blanding, Utah

To understand why it is unclear whether the president has the authority to abolish a national monument designated under the Antiquities Act, it is necessary to go back and look at the Act itself. Passed in 1906 under president Theodore Roosevelt, who went on to use it to establish many monuments including Chaco Canyon in 1907, the Antiquities Act is noteworthy these days for being both remarkably short and remarkably ambiguous. It states:

That the President of the United States is hereby authorized, in his discretion, to declare by public proclamation historic landmarks, historic and prehistoric structures, and other objects of historic or scientific interest that are situated upon the lands owned or controlled by the Government of the United States to be national monuments, and may reserve as a part thereof parcels of land, the limits of which in all cases shall be confined to the smallest area compatible with the proper care and management of the objects to be protected

Presidents since Roosevelt have interpreted this authority broadly, and have used it to designate monuments of up to millions of acres to protect the “objects of historic and scientific interest” therein. (Bears Ears alone is about 1.35 million acres.) This seems inconsistent with the colloquial meaning of the term “monument,” which to many people implies something much smaller than, say, a national park, but in fact the broad interpretation goes back to the very beginning and even Roosevelt himself designated 800,000 acres as Grand Canyon National Monument (which, like many monuments, was later changed by Congress into a national park). Furthermore, the courts have generally agreed with this broad interpretation of the president’s power under the Act, including in an important Supreme Court case in 1920 regarding Grand Canyon. Thus, opponents of particular monuments, such as the Utah politicians upset about Bears Ears, have sometimes been inclined to try to get a subsequent president to revoke a monument designation.

Tower at Mule Canyon, Utah

However, as a recent Congressional Research Service report explains, no president has ever tried to do this, and while this means there has been no test in court of a president’s authority in this area, there are other indications that it is unlikely to hold up. In 1938 President Franklin Roosevelt wanted to abolish a monument and consulted with his Attorney General to determine if this was possible. The AG determined that the text of the Act did not explicitly give the president the power to abolish a monument, and that there was no precedent for that power being given implicitly either. Roosevelt elected not to put this to the test.

It may seem odd that the president would have authority to take an action but not to revoke it, especially since Executive Orders are often described in exactly these terms (i.e., that they are weaker than Acts of Congress because a future president can unilaterally revoke them). A designation under the Antiquities Act isn’t quite a regular Executive Order, however. This is not an inherent power of the executive, but a Congressional power delegated explicitly to the president through the Act. Congress can also designate national monuments, and only it can establish national parks. The power to establish parks is an authority that Congress has not delegated to the president. The authority to abolish national monuments, including those designated by a president under the Antiquities Act, appears to be another such undelegated authority retained by Congress alone, and Congress has in fact abolished a few presidentially designated monuments by statute.

Sun Marker at Edge of the Cedars with Bears Ears in Background

So it seems that if Trump were to unilaterally try to revoke Obama’s proclamation and abolish Bears Ears or another monument covered by this Executive Order, the move would probably (but not necessarily) be overturned by the courts. This doesn’t mean these monuments are totally safe, however. There has been precedent for a president to add or subtract land from an existing national monument, and while the addition of land appears to be legally valid under the same theory underlying the power to create new monuments, the authority to remove land is more questionable. While this is also untested by the courts, presidents who have removed land from monuments have claimed to  have authority to do so under the provision of the Antiquities Act requiring that monuments be confined to the “smallest area compatible with the proper care and management of the objects to be protected.” In theory this means Trump could reduce the size of a monument like Bears Ears to a tiny area, perhaps the immediate surroundings of the eponymous buttes, and claim to be within the law. Obama’s proclamation, however, in this case referred to “numerous objects of historic and of scientific interest” within the monument boundaries, without being very specific about what those objects are, which might make it difficult for a reduction in size to pass muster with the courts. As with so much else on this topic, however, this theory remains untested in an actual court case.

Finally, setting aside all of these questions about the president’s authority, there’s Congress. Note that Trump’s order asks the Secretary for recommendations on congressional as well as presidential action to address any problems he identifies with the monument designations. Here, there is no legal ambiguity: Congress has the authority to modify or abolish a national monument in any way it wants. With Republican majorities in both houses of Congress, and Trump in the White House, it might seem like the obvious approach for the anti-monument forces would be for Congress to pass a law abolishing Bears Ears and whichever other monuments the Secretary recommends getting rid of. In theory this would indeed be possible, but in practice the current Congress and president have had a lot of trouble passing even their highest-profile priorities, so it’s by no means a sure thing that they would be able to get a bill like this through. Public lands are quite popular with the country as a whole, if not with Utah politicians, and it’s likely that any attempt to roll back monuments would stoke extensive public opposition that would make it a hard lift for a Congress with plenty of problems already. Similarly, while Congress could effectively neuter the management of new monuments by withholding funding for them from spending bills, the current state of budget negotiations suggests that they would have trouble doing that as well.

Does all this mean Bears Ears and the other monuments are definitely safe from the machinations of Trump and his congressional allies? By no means; if they’re committed enough there are definitely things they can do to harm them, such as through budgeting decisions within the executive branch departments tasked with managing them. But like so much else in our system of government, once a monument is in place it’s no easy feat to get rid of it.

Entrance Sign for Natural Bridges National Monument, Est. 1908

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The Rebel Rangers

National Park Service Alaska Regional Office, Anchorage, Alaska

It’s been interesting to me to see a lot of the early resistance to the Trump administration coming from National Park Service employees, starting with the famous tweets about climate change from the Badlands National Park Twitter account and continuing with the various “Alt-NPS” Twitter feeds (the authenticity of which is impossible to confirm, of course, but it’s quite possible at least some are legit). There are some very specific reasons having to do with the NPS’s structure and policies that make it a particularly likely source for this type of thing, and I think some of them are actually problems that really should be addressed in the long term, despite how useful they may be in the short term in pushing back against Trump’s agenda. (I haven’t been very political on this blog in a while, but it should be clear from the above where my sympathies lie, and I think most people who care about scientific inquiry and public lands are lining up similarly.)

First, the NPS relies very heavily on non-permanent staff who are hard to keep in line with threats to their job security because they don’t have any to start with. It’s been reported that the Badlands tweets were actually by a former employee who still had access to the account, which is the justification park management gave for deleting them. It’s possible this is just an excuse made up by management to save face in front of the new administration, but I doubt it. I think it’s most likely that Badlands hadn’t changed their Twitter password in a while, and a former seasonal or term interpretive ranger who still knew it was able to get in and make the tweets before anyone was the wiser.

So far so good, but it’s not actually good for an agency to rely so heavily on such a transient workforce. There are some good reasons for so much of the work being seasonal, to be sure. Many parks have very pronounced seasonal patterns in visitation that require big differences in staffing levels, especially for the jobs that require a lot of interaction with visitors (mostly interpretation and law enforcement). A lot of seasonal staff are young people at a transitional point in their lives, and a short seasonal gig fits well; this was the case for me at Chaco, and it was a great experience that I don’t regret at all. So I’m not saying the NPS should do away with seasonal work entirely. There are a lot of people, however, who decide to make park-rangering a career, which typically requires several seasonal jobs in different parks before a permanent opening opens up. These are not good jobs. The pay is low, and they come with very meager benefits, especially compared to permanent federal jobs. So people who decide to devote their lives to the serving their country through working in its parks have to go through several years of eking out a living with no job security before they get their first “real” job with some semblance of stability. (There are some interesting parallels here to academia.)

A better way to accommodate the seasonality of NPS work might be to expand the use of so-called “career-seasonal” jobs, which guarantee continued employment in subsequent seasons even though they only allow for a certain number of hours per year. This sort of arrangement isn’t for everyone, but it could help provide more stability to people who want to continue doing this work rather than moving on to something else. Whether or not this would be a viable option, some sort of shift away from such heavy reliance on short-term seasonal staff would have a lot of benefits, I think.

Similarly, I think the NPS overuses so-called “term” jobs, which are typically one to four years in duration, for work that is really a part of ongoing operations. Again, these jobs, which are more typically back-office administrative positions rather than visitor-facing ones, have fewer benefits than permanent ones and don’t pay particularly well, and they lead to the same pattern of career people moving from park to park for years before they can snag a permanent position. Unlike with seasonal jobs, I don’t see any valid justification for such extensive reliance on term employees for this sort of work. There is a role for this kind of job, but it should really be focused on short-term special projects rather than ongoing operations.

Secondly, the proliferation of renegade tweets on official accounts early on, and of renegade accounts once management began to crack down on those, is a symptom in part of the highly decentralized structure of the NPS compared to other land-management agencies. There are real problems with the considerable amounts of autonomy granted to park superintendents, which has contributed to recent scandals at parks like Grand Canyon, Yellowstone, and Yosemite. Tighter oversight of superintendents by regional management would be a good idea, I think.

But the decentralization goes well beyond them, and to some degree is a function of the nature of the work itself, as encapsulated in the term “ranger” itself. There’s just a limit to how much supervision even park management can exercise over individual employees when wandering around the park is a big part of the job. I can attest that when I was first starting to lead tours at Chaco I was told that a senior ranger would go on one of my own tours within the first couple weeks to check on me. It never happened, not just in the first two weeks but ever. Especially at smaller parks where staffing is always stretched pretty thin, there’s not a whole lot of effective supervision and management just has to trust that employees are doing things right. And again, many of these employees are seasonals without any real job security, which further limits the options management has for dealing with a rogue ranger. This has been another contributing factor to the scandals I mentioned above. Visitor feedback is one of the main mechanisms for supervision in this context, which is a good thing to keep in mind if you have a particularly bad (or good!) encounter with a ranger at a park as a visitor. They really do read those comment forms.

Luckily, in my experience the vast majority of NPS employees, regardless of their employment status, are conscientious and passionate about their jobs, so the lack of supervision and need to rely on trust aren’t as big a problem as they could be, although as the recent scandals have showed they can lead to big problems if management isn’t making a conscientious effort to exercise what supervision it can and to create a healthy working environment for all staff. The excessive autonomy of superintendents and especially the over-reliance on non-permanent staff are bigger problems, and the latter in particular is unconscionable even if it does enable some snarky tweets directed at Donald Trump.

Snow Ranger at Chaco Visitor Center

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The County of Lincoln

Fort Stanton State Historic Site

I’m in New Mexico this week visiting my mom, as I often do this time of year. As we also often do, we took a couple of days to go camping and hiking somewhere in the state. This time went to Lincoln County, where we also took in some of the sights in the area. I figured I would do a post just to discuss what we did, since I found in planning this trip that detailed information was hard to find about a lot of things.

Lincoln County is in the south-central part of the state. These days it’s relatively obscure, but it was important in the territorial period and there’s still a lot to see there that’s of historical interest. We focused primarily on Fort Stanton, which is a New Mexico State Historical Site that was an old frontier fort established in 1855. It’s still in remarkably good shape, partly because it was still in use for various purposes until quite recently, and is a bit of a hidden gem for those interested in historic architecture and frontier history. Very much worth visiting. We didn’t get to see the museum since we arrived right at 4:00 pm when it closes, but the grounds are open until 5:00 so we saw most of the other buildings.

Rio Bonito near Fort Stanton, New Mexico

Surrounding the State Historic Site is the Fort Stanton-Snowy River Cave National Conservation Area, managed by the Bureau of Land Management. We were intending to camp here, but it was quite hard to find detailed information about the two campgrounds. The main one, the Rob Jaggers Campground, turns out to be mainly oriented toward RVers and equestrians rather than tent campers like us, but the other one, the Cave Campground, was more our style. It’s a small but quite well-maintained campground that apparently gets very little visitation, probably because it’s right at Fort Stanton cave, which is now closed to public visitation because of White Nose Syndrome in bats. Highly recommended as a camping option in an area that has few. There are ramadas and picnic tables at three or four campsites, and a vault toilet that was very clean. There’s no water at the campground, so we had to fill up our jug in the nearby towns of Lincoln and Capitan.

There are a lot of trails on the NCA, and we did a small loop that went right by the Rio Bonito, which runs through this area and lives up to its name. There is also a petroglyph site at the southwestern end of the NCA which I wanted to see, but the road to it turns out to be extremely steep and rocky, and we decided it was not worth the risk to my mom’s small car to try to get there. Hiking to the site along the trails might be a better way to get there.

Old Courthouse (Murphy-Dolan Store), Lincoln, New Mexico

We also visited the town of Lincoln, which is famous for the Lincoln County War in the late 1870s which made Billy the Kid (in)famous. Many of the old buildings from that period are still very well preserved, and several of them are part of Lincoln State Historic Site. Some of them are set up as museums, although the exhibits in them get a bit repetitive at times since they all focus so much on the same short period of time. Still, it’s a very interesting place. The short video at the visitor center was quite helpful in summarizing the War and the background to it, which ultimately revolved around rival groups of ranchers and merchants trying to access government contracts to supply Fort Stanton and the nearby Mescalero Apache Indian Reservation. Having seen Fort Stanton first was helpful in contextualizing this, since it was a quite large and elaborate post for the time and place and supplying it would clearly have been quite lucrative.

On our way back to Albuquerque we stopped in Capitan and saw the Smokey Bear Historical Park. The “real” Smokey Bear was a cub discovered in the midst of a forest fire near Capitan in 1950 and brought to the National Zoo in DC to serve as a living embodiment of the fire-prevention mascot (who had already existed for a few years by then). The museum is mostly about forest fire safety, including a lot of discussion of how our understanding of the role of natural fire has changed over the years. There is also a garden showing various native plants of the Southwest, along with the burial place of Smokey, who died in 1976.

Sign at Smokey Bear Historical Park, Capitan, New Mexico

Since it was sort of on the way and my mom had not been there, although I had, we decided to stop at Gran Quivira on the way back as well. There is a relatively direct route to it, but we missed the (apparently quite subtle) turnoff and ended up going the long way around through Corona and Mountainair before getting to the site. It’s a really great site, I think.

So then we ended up back in Albuquerque, just as it was starting to rain yesterday evening. Yesterday was my birthday (I’m 32), and this trip was a nice way to celebrate it. I fly back to Alaska tomorrow.

“New” Church at Gran Quivira

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Centennial

Welcome Sign at North Entrance to Chaco Canyon

Today is the centennial of the establishment of the National Park Service on August 25, 1916. It’s getting more media attention than I had expected, although I had noticed that the NPS had mounted a noticeable publicity campaign in the lead up to the date itself, so I probably shouldn’t be surprised. Anyway, it’s a good milestone to mark. I have my issues with the way the NPS works and some of the things it does and has done, but it’s definitely a hugely important institution both to the country as a whole and to me personally.

I started this blog in December 2008 when I was working for the NPS at Chaco Canyon, and the early posts were mostly attempts to put the information from my tours and my background reading into a more permanent form so I could refer people to them long after I had left the park and moved on to other things. It’s worked quite well for that, although in the meantime the internet has moved on and blogs like this are much less of a focus for interaction than they were then. I’ve kept it up, though at a much less frequent pace of posting, because I like having a platform like this to talk about the things that interest me, and I now have a fairly small but consistent reader base that is interested as well. (Which is not easy to find for what is after all a pretty esoteric interest.)

But beyond being the starting point for this blog, the NPS is an important institution for setting me on the path my life has taken in more general ways too. That job at Chaco allowed me to really delve deep into the backstory of the area where I was born and where my family has a long history (at least by white-people standards). What I learned there has had a profound effect on my life since in all sorts of ways, and I expect that to continue indefinitely. This blog may have slowed in posting frequency in recent years, but it’s not from any decline in my interest in the subject matter, which I’m sure I will continue to write about for many years to come, not necessarily just here. I have some ideas for books I might want to write on related topics at some point, although I’ve been realizing recently that it’s awfully hard to find the time for a project of that magnitude while also working full time. But someday.

Welcome Sign at Alaska/Yukon Border

The influence of the Park Service on my life goes even further than the Chaco stuff, though. It was an internship with the NPS that brought me to Alaska a little less than five years ago, and my experience there, while frustrating in some ways, led me to discover the first place I had ever lived where I could seriously imagine living permanently. It’s not at all clear that I will actually end up settling down here, and the Alaska of 2016 is so different from the Alaska of 2011 that it’s hard to even explain the difference. But that feeling of finding a place I liked enough to stay, even if I didn’t necessarily have a lot in common with most of the people here, was important to me and it set a standard that anywhere else I might end up will have to meet or exceed for me to stay permanently. And I have the Park Service to thank for that too.

I may or may not ever work for the NPS again. My career path has never been along an established route, and I have no idea how much longer I’ll stay in my current job or what I’ll do next. Some of the most important factors in the future of my career are totally out of my control. But others are mine to control, and I’ll probably have to make some serious decisions in the next few years, if not sooner, about where I want my life to go next. I have to be honest that working for the Park Service again is not my top choice for a next step. It really was a frustrating place in some ways, for a variety of reasons, some of which are I think inherent to the structure and culture of the agency. But it’s a large organization, and I’m sure there are some positions within it that I would find congenial, so it’s definitely still on the list.

Anyway, despite my ambivalence about it, the Park Service has done a lot of good for me and I am very appreciative of that. I’m very happy to celebrate 100 years of this complex, occasionally infuriating but just as often inspiring, American institution. Happy birthday, NPS!

National Park Service Alaska Regional Office, Anchorage, Alaska

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The Evidence from DNA in the Southwest

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

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.

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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The Evidence from DNA

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.

Mulligan, C. (2006). Anthropological Applications of Ancient DNA: Problems and Prospects American Antiquity, 71 (2) DOI: 10.2307/40035909

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