Peopling of the New World & Molecular Biology - New papers

[Jacques Cinq-Mars]

All,

The following Abstracts should be of interest to people who consider (as all people should) the so-called “initial Peopling of the New World, as part and parcel of a Late Pleistocene and Upper Palaeolithic  lengthy and complex human dispersal continuum/process whose biogeographical roots and chronological antecedents lie in Western Beringia and beyond.

While I realize that it is not fair nor cautious to review or criticize papers on the basis of abstracts alone, I feel, nonetheless (not having access to the full papers), that there is a need to come up with a few comments. This, I think, is warranted by the fact that both abstract mention or suggest that the conclusions reached by the authors on the basis of their “molecular” evidence are somehow supported or reinforced by “additional evidence” that, presumably, is, wholly or in part, of an archaeological nature.

In this regard, it appears that the authors of the two papers may have been rather selective (self serving ?) in their choice of archaeologically derived hypotheses or models that deal with the initial or early “peopling” issue. It seems to be evident, for example, that their interpretations both rely on, to a certain extent, and serve to validate, in some circular ways, recent variations on the “short chronology” theme. Nor do they appear to spend much time, if any at all, confronting their views with those of others who, also working with the tools provided by molecular biology, have managed, in recent years to come up with very different conclusions regarding “timing” and number of dispersal events (not to mention evidence coming out of linguistic and biological anthropology studies). While I realize that one can just go so far on the basis of abstracts, I can nevertheless conclude, I think, by saying: So much for integrated, interdisciplinary studies. I hope I am wrong in my assessment, but …

Jacques Cinq-Mars


Am. J. Hum. Genet., 71:187-192, 2002

Report

Mitochondrial Genome Diversity of Native Americans Supports a Single Early Entry of Founder Populations  into America

Wilson A. Silva Jr.,1,5  Sandro L. Bonatto, 6 Adriano J. Holanda, 1 Andrea K. Ribeiro-dos-Santos, 7 Beatriz M. Paixão, 1 Gustavo H. Goldman, 2 Kiyoko Abe-Sandes, 1,10 Luis Rodriguez-Delfin, 8 Marcela Barbosa, 2 Maria Luiza Paçó-Larson, 3 Maria Luiza Petzl-Erler, 9 Valeria Valente, 3 Sidney E. B. Santos, 7 and Marco A. Zago1,4

1Center for Cell Therapy and Regional Blood Center, 2 Faculdade  de Ciencias Farmaceuticas  de Ribeirão Preto, and Departments of 3 Cell and Molecular Biology  and Pathogenic  Agents and 4 Clinical Medicine, Faculty  of Medicine, University  of São Paulo, Ribeirão  Preto, Brazil; 5 Department of Genetics, Federal University  of Para, Santarem, Brazil; 6Centro de Biologia Genomica  e Molecular, Pontificia Universidade  Catolica do Rio Grande do Sul, Porto Alegre, Brazil; 7 Laboratory  of Human and Medical Genetics, University  of Para, Belem, Brazil; 8 Unidad de Biologia  Molecular, Facultad de Medicina, Universidad Nacional  de Trujillo, Trujillo, Peru;  9 Laboratory  of Human Molecular Genetics,  Department  of Genetics, Federal University  of Parana, Curitiba, Brazil;  and 10 Universidade Estadual  do Sudoeste  da Bahia, Jequié, Brazil

There is general agreement that the Native American founder populations migrated from Asia into America through Beringia sometime during the Pleistocene, but  the hypotheses concerning the  ages and the number of these migrations  and the size of the ancestral populations  are surrounded by controversy. DNA sequence variations  of several regions of the genome of Native Americans, especially  in the mitochondrial DNA (mtDNA) control region, have been studied  as a tool to help  answer these questions. However, the small number of nucleotides studied and the nonclocklike rate of mtDNA control-region evolution impose several limitations  to these results. Here we provide the sequence analysis of a continuous  region of 8.8 kb of the  mtDNA outside the D-loop for 40 individuals, 30  of whom  are Native Americans  whose  mtDNA belongs  to the four founder  haplogroups. Haplogroups  A, B, and C form monophyletic  clades, but  the five haplogroup D sequences  have unstable  positions  and usually do not group together. The high degree of similarity  in the nucleotide  diversity  and time of differentiation  (i.e., ?21,000 years before present) of these four haplogroups  support  a common origin for these sequences  and suggest that the populations  who harbor them may  also have  a common history. Additional evidence supports the idea that this age of differentiation coincides with the process of colonization of the New World and supports the hypothesis of a single and early entry of the ancestral Asian population into the Americas.

Am. J. Hum. Genet., 71:415-421, 2002

Report

Analysis of Mitochondrial DNA Diversity in the Aleuts of the Commander Islands and Its Implications for the Genetic History of Beringia

Olga A. Derbeneva, 1 Rem I. Sukernik,1 Natalia V. Volodko,1 Seyed H. Hosseini, 2 Marie T. Lott, 2 and Douglas C. Wallace 2

1Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and 2 Center for Molecular Medicine, Emory University, Atlanta

The Aleuts are aboriginal inhabitants of the Aleutian archipelago, including Bering and Copper (Medny) Islands of the Commanders, and seem to be the survivors of the inhabitants of the southern belt of the Bering Land Bridge that connected Chukotka/Kamchatka and Alaska during the end of the Ice Age. Thirty mtDNA samples collected in the Commanders, as well as seven mtDNA samples from Sireniki Eskimos in Chukotka who belong to the Beringian-specific subhaplogroup D2, were studied through complete sequencing. This analysis has provided evidence that all 37 of these mtDNAs are closely related, since they share the founding haplotype for subhaplogroup D2. We also demonstrated that, unlike the Eskimos and Na-Dene, the Aleuts of the Commanders were founded by a single lineage of haplogroup D2, which had acquired the novel transversion mutation 8910A. The phylogeny of haplogroup D complete sequences showed that (1) the D2 root sequence type originated among the latest inhabitants of Beringia and (2) the Aleut 8910A sublineage of D2 is a part of larger radiation of rooted D2, which gave rise to D2a (Na-Dene), D2b (Aleut), and D2c (Eskimo) sublineages. The geographic specificity and remarkable intrinsic diversity of D2 lineages support the refugial hypothesis, which assumes that the founding population of Eskimo-Aleut originated in Beringan/southwestern Alaskan refugia during the early postglacial period, rather than having reached the shores of Alaska as the result of recent wave of migration from interior Siberia.

[Alec Christensen]

I just read the Silva et al. paper, and I have a couple of observations. First and foremost, it is a comparison of 40 Brazilians with 53 previously published sequences and the reference sequence. Of those 40, 30 are Native American and the others Euro-, Afro-, or Asian-Brazilian. This is not exactly a huge sample size.

They constructed several phylogenetic trees, although they only illustrate the neighbor-joining one. In this, haplogroups A, B, and C are each monophyletic, while D is not--although they say that D was monophyletic in some of the other analyses.

I can't pretend to fully understand the methodology behind the date estimates or the calculations of nucleotide diversity. Looking at the phylogenetic tree raises some questions in my mind, however. For instance, within haplogroup C, individual Khirgiz, Evenki, and Buriat samples cluster together at the end of the tree. No more than three of the nine South American samples can form a monophyletic group without including the Siberians as well. This suggests to me that either diversification within C occurred in Siberia, or there was extensive back migration. Or, of course, the tree is flawed.

As for interdisciplinary studies, Silva et al. simply cite earlier mtDNA analyses that also argued for "a single and early wave of migration for the peopling of the Americas." It makes me wonder how long geneticists have been citing each other for archaeological conclusions, rather than reading the archaeology (or linguistics for that matter) themselves.

Alec Christensen

[Jacques Cinq-Mars]

[quote author=Alec Christensen

As for interdisciplinary studies, Silva et al. simply cite earlier mtDNA analyses that also argued for "a single and early wave of migration for the peopling of the Americas." It makes me wonder how long geneticists have been citing each other for archaeological conclusions, rather than reading the archaeology (or linguistics for that matter) themselves.

Alec Christensen

Thanks for these comments based on the actual paper.

Regarding the last part of your post, I would say that there is no need to wonder. As shown by a survey of the literature dealing specifically with “molecular” investigations on the nature, origin, and dating of early human dispersals in the New World, it is clear that quite a number of researchers (fortunately, not all of them) have systematically ignored (or been ignorant of) evidence emanating from other field of research or, at the very best (!) have made a curiously selective, over simplistic, uncritical, and self serving use of the kind of evidence (?) that supports their explanatory expectations. Not to mention that they frequently give little attention to contradictory statements coming from their own discipline. To be fair, I should add that this rather amazing “scientific” way of doing things is also rather commonly used by a number of workers investigating the same kinds of problems from different disciplinary angles. I am referring, here, to various archaeologists, geoarchaeologist, geologists, geomorphologist and palaeoecologist who also use in pretty much in the same fashion, the molecular anthropology statements that fit or validate their pet paradigms. Essentially, one could say that they all feed on one another. Hence, the sterile “circularity” I was talking about earlier.

Jacques Cinq-Mars

[Alec Christensen]

Here's an abstract from another AJHG paper that takes a slightly different view:

The Structure of Diversity within New World Mitochondrial DNA Haplogroups: Implications for the Prehistory of North America

Ripan S. Malhi,1 Jason A. Eshleman,2 Jonathan A. Greenberg,3 Deborah A. Weiss,2 Beth A. Schultz Shook,2 Frederika A. Kaestle,5 Joseph G. Lorenz,6 Brian M. Kemp,2 John R. Johnson,7 and David Glenn Smith2,4

1Department of Human Genetics, University of Michigan, Ann Arbor; 2Department of Anthropology, 3Center for Spatial Technologies and Remote Sensing, and 4California Regional Primate Research Center (CRPRC), University of California, Davis; 5Department of Anthropology, Indiana University, Bloomington; 6Coriell Institute for Medical Research, Camden, NJ; and 7Santa Barbara Museum of Natural History, Santa Barbara, CA

Received September 5, 2001; accepted for publication January 10, 2002; electronically published February 13, 2002.

The mitochondrial DNA haplogroups and hypervariable segment I (HVSI) sequences of 1,612 and 395 Native North Americans, respectively, were analyzed to identify major prehistoric population events in North America. Gene maps and spatial autocorrelation analyses suggest that populations with high frequencies of haplogroups A, B, and X experienced prehistoric population expansions in the North, Southwest, and Great Lakes region, respectively. Haplotype networks showing high levels of reticulation and high frequencies of nodal haplotypes support these results. The haplotype networks suggest the existence of additional founding lineages within haplogroups B and C; however, because of the hypervariability exhibited by the HVSI data set, similar haplotypes exhibited in Asia and America could be due to convergence rather than common ancestry. The hypervariability and reticulation preclude the use of estimates of genetic diversity within haplogroups to argue for the number of migrations to the Americas.

I find the final sentence the most interesting part. In the conclusions, they go on to write "Therefore, we are unable to distinguish whether shared mutations among geographically distinct individuals are due to prehistoric Native Americans existing as one population with little substructure for an extended period of time prior to intensification of resource utilization during Archaic times or, alternatively, due to convergence."

A rather different conclusion than Silva et al., no? For those interested, Malhi's former institution (he just finished at UC Davis and moved to U Michigan) has posted the text at http://www.cstars.ucdavis.edu/papers/pdf/malhietal2002a.pdf.

Alec Christensen

[John Hawks]

[quote author=Alec Christensen

As for interdisciplinary studies, Silva et al. simply cite earlier mtDNA analyses that also argued for "a single and early wave of migration for the peopling of the Americas." It makes me wonder how long geneticists have been citing each other for archaeological conclusions, rather than reading the archaeology (or linguistics for that matter) themselves.

Alec Christensen

Thanks for these comments based on the actual paper.

Regarding the last part of your post, I would say that there is no need to wonder. As shown by a survey of the literature dealing specifically with “molecular” investigations on the nature, origin, and dating of early human dispersals in the New World, it is clear that quite a number of researchers (fortunately, not all of them) have systematically ignored (or been ignorant of) evidence emanating from other field of research or, at the very best (!) have made a curiously selective, over simplistic, uncritical, and self serving use of the kind of evidence (?) that supports their explanatory expectations. Not to mention that they frequently give little attention to contradictory statements coming from their own discipline.

Jacques Cinq-Mars

I'd say in genetics at least this is a symptom of "data in search of a problem"--especially since the same labs have been producing the same data on the same uninformative genetic systems (i.e. mtDNA) for ten years now. Quantity rather than quality justifies the existence of these many redundant labs, and since all the PI's are reviewers for AJHG, it all gets published there. So no paper is complete without a fifteen word snippet about how this is a big problem in archaeology--and if they're all the same fifteen words anyway, why not just cite each other?

Is there a good relatively current review paper from an archaeological perspective? Or is this a topic in need of revisiting for archaeologists? It certainly is for geneticists--especially the epistemological problems of using genetic data for a problem like this--and I am thinking of writing something up.

John Hawks

[Jacques Cinq-Mars]

[quote author=John Hawks
I'd say in genetics at least this is a symptom of "data in search of a problem"--especially since the same labs have been producing the same data on the same uninformative genetic systems (i.e. mtDNA) for ten years now. Quantity rather than quality justifies the existence of these many redundant labs, and since all the PI's are reviewers for AJHG, it all gets published there. So no paper is complete without a fifteen word snippet about how this is a big problem in archaeology--and if they're all the same fifteen words anyway, why not just cite each other?

While I an not really in a position to argue very cogently. for or against the value of mtDNA studies relative to other avenues of investigation in the analysis of genetic systems, I can say as an archaeologist that -- but for a few interesting exceptions -- what I have read so far, is getting to be more and more confusing. The available literature is replete with contradictory and even cryptic statements, and the few  words or lines pertaining to archaeological interpretations (when they are included at all) appear too often as vaguely construed afterthoughts primarily designed, on the basis of a rather selective use of the archaological literature, to validate preordained conclusions and to provide these exercises with the appropriate interdisciplinary flavour. This is perhaps a bit too harsh but …

Is there a good relatively current review paper from an archaeological perspective? Or is this a topic in need of revisiting for archaeologists? It certainly is for geneticists--especially the epistemological problems of using genetic data for a problem like this--and I am thinking of writing something up.

John Hawks

Not to my knowledge, and yes, I do feel there is a definite and urgent need to initiate some form of useful and truly interdisciplinary “rapprochement” between the conceptual and epistemological approaches of both disciplines and, for that matter, of all disciplines interested in understanding human evolutionary history.

Jacques Cinq-Mars