Discrepancy between Cranial and DNA Data of Early Americans: Implications for American Peopling

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Discrepancy between Cranial and DNA Data of Early Americans: Implications for American Peopling
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  Discrepancy between Cranial and DNA Data of EarlyAmericans: Implications for American Peopling S. Ivan Perez 1 * , Valeria Bernal 1 , Paula N. Gonzalez 1 , Marina Sardi 1 , Gustavo G. Politis 2 1 CONICET, Divisio´n Antropologı´a, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina,  2 CONICET, Divisio´nArqueologı´a, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina Abstract Currently, one of the major debates about the American peopling focuses on the number of populations that srcinated thebiological diversity found in the continent during the Holocene. The studies of craniometric variation in American humanremains dating from that period have shown morphological differences between the earliest settlers of the continent andsome of the later Amerindian populations. This led some investigators to suggest that these groups—known asPaleomericans and Amerindians respectively—may have arisen from two biologically different populations. On the otherhand, most DNA studies performed over extant and ancient populations suggest a single migration of a population fromNortheast Asia. Comparing craniometric and mtDNA data of diachronic samples from East Central Argentina dated from8,000 to 400 years BP, we show here that even when the oldest individuals display traits attributable to Paleoamericancrania, they present the same mtDNA haplogroups as later populations with Amerindian morphology. A possibleexplanation for these results could be that the craniofacial differentiation was a local phenomenon resulting from random(i.e. genetic drift) and non-random factors (e.g. selection and plasticity). Local processes of morphological differentiation inAmerica are a probable scenario if we take into consideration the rapid peopling and the great ecological diversity of thiscontinent; nevertheless we will discuss alternative explanations as well. Citation:  Perez SI, Bernal V, Gonzalez PN, Sardi M, Politis GG (2009) Discrepancy between Cranial and DNA Data of Early Americans: Implications for AmericanPeopling. PLoS ONE 4(5): e5746. doi:10.1371/journal.pone.0005746 Editor:  Dennis O’Rourke, University of Utah, United States of America Received  February 14, 2009;  Accepted  May 4, 2009;  Published  May 29, 2009 Copyright:    2009 Perez et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided the srcinal author and source are credited. Funding:  The authors have no support or funding to report. Competing Interests:  The authors have declared that no competing interests exist.* E-mail: iperez@fcnym.unlp.edu.ar Introduction The biological diversity of South American human populationshas been the focus of extensive research for more than a hundred years (see review in [1] ). These investigations have been associatedwith intense interdisciplinary studies regarding the peopling of the Americas. The great interest in this subject is partially due to thefact that America was the latest continent colonized by modernhumans (ca. 11,000–13,000 years B.P.; [2] ) and also due to thehigh levels of morphological variation found in Native Americanpopulations. In this context, two main hypotheses have beenproposed to account for this biological variation: a) the migratoryhypothesis, which suggests that the biological variation among South American groups was the result of a variable number of migratory waves [3,4]; and b) the local diversification hypothesis,i.e. that all South American groups descend from the sameancestral population or from populations related to each other,with local random (i.e. genetic drift) and non-random factors (i.e.selection and phenotypic plasticity) as the main causes of thediversification [5 – 7]. In recent years, the migratory hypothesis that postulatesdifferent biological srcins for South American populations hasreceived increased attention by researchers working with cranio-metric evidence [8 – 10]. This hypothesis, known as  two mainbiological components  , asserts that the morphological diversity of  American human populations results from two successivemigratory events. The first component, named Palaeoamericans,derived from Pleistocene Southeast Asian populations whichexpanded into America around 14,000 years BP. Morphologicallythey were characterized by long and narrow cranial vault (i.e.dolichocephalic morphology) and a narrow face. The secondcomponent, named Amerindians, from which most of modern American groups derive, corresponds to a migration of popula-tions from Northeast Asia which occurred during the EarlyHolocene (ca. 8,000 years BP; [8 – 11 ]). These populations exhibited short and wide cranial vault, along with wide faces (i.e.brachycephalic morphology). In addition, it was pointed out thatthis Amerindian morphology corresponds with a mongoloidpattern of craniofacial shape. The presence of this cranial shapein America has been explained as the result of a ‘‘fixation’’ of themongoloid morphology in North Asia, previous to the Amerindianmigration.In contrast, the molecular evidence available to date (i.e.mtDNA and nuclear DNA information) supports a single srcin inNortheast Asia ca. 15,000 years BP for almost all Americanpopulations, followed by local diversification—probably with theexception of the Esquimo and Na-Dene groups [12– 14].Particularly, mtDNA studies have detected four major pan- American founding haplotypes (A2, B2, C1, D1), which are alsofrequent in Asia. In addition, other founding mtDNA haplotypesoccur in the Americas, such as X2a, D2, and D3, which are foundnearly exclusively in North America [12,13]. The haplogroupdistribution, together with the similar coalescence time for thesehaplotypes, has been used to support a single srcin for extant PLoS ONE | www.plosone.org 1 May 2009 | Volume 4 | Issue 5 | e5746   American populations, as well as a swift pioneering process of theinitial north to south migration [12]. In addition, coalescentanalyses suggest an initial differentiation of the Northeast Asiapopulations, a bottleneck in Beringia ca. 20,000 years BP, endedwith a population expansion in America ca. 15,000 years BP[12,13].The discrepancies between craniometric and molecular data, aswell as the hypotheses supported by each kind of evidence, couldbe related either to the properties of both types of data, whichprovide different types of genealogical information, or todifferences between the samples studied in each case. Particularly,quantitative traits and mtDNA differ in their respective mecha-nisms of inheritance (uniparental in mtDNA and biparental inquantitative traits), rate of change and degree of environmentalinfluence [15 – 17]. On the other hand, the molecular data havebeen mainly obtained from extant or recent populations, whereascraniofacial variation has been assessed using skeletal samples fromEarly and Late Holocene populations. Hence, researchers whoproposed the hypothesis of two main biological components assertthat if the Paleoamericans did not survive or if their contributionto the biological variation of modern American populations was very small [7 – 9], the variation found among Later Late Holocene groups would not be relevant to discuss the early peopling One way to approach this problem is by analyzing the cranialmorphology of diachronic samples, ranging from Early to LateHolocene, for which ancient mtDNA data are also available. Thefew areas able to provide human remains dated as Early Holoceneon the basis of   14 C dates of human bones are [18]: East CentralBrazil (Lagoa Santa, ca. 9,000–5,000 yr  14 C BP; [10,19 ]), the Bogota´ savannah, Colombia (Tequendama, ca. 7,300–5,800 yr 14 C BP; [20] ) and the East Central Argentina (Arroyo Seco 2, ca.7,800–6,300 yr  14 C BP; [21]). However, East Central Argentina isthe only region with a diachronic sequence ranging from 8,000 to200 years BP [21,22] for which both mtDNA and craniometricdata are available. Even though this region holds importantevidences, it has not yet been included in the discussion about thebiological diversity of South American populations from adiachronic perspective. In this study we present the first analysisof a skeletal sample from East Central Argentina including bothcraniometric and molecular data. The goal of this work is tocompare the pattern of temporal and spatial variation in bothtypes of data and to discuss them in light of the current hypothesesabout the peopling of America. The analysis of these data allowsfor a renewed approach to the problem of the biological diversityand peopling of this continent. Materials and Methods Samples We studied the early site from East Central Argentina (i.e.Southeast of Pampa and Northeast of Patagonia, Fig. 1, Table 1)known as Arroyo Seco 2, dated between Late Pleistocene andEarly/Middle Holocene—the human remains that were used hereare dated on ca. 7,800–6,300 yr 14C BP [21,23]—plus foursamples of human remains corresponding to Middle and EarlierLate Holocene and four samples corresponding to Later LateHolocene from the same region. In addition, seven Late Holocenesamples from neighbour regions were also analyzed (Table 1). Allthese samples include adult individuals of both sexes from hunter-gatherer groups, with presence of pottery in the Later LateHolocene.The Arroyo Seco 2 archaeological site presents exceptionalevidence to study the early peopling of America [23]. This multi-component open-air site is dated from 12,500  14 C yr BP to theXIX Century [24] and nowadays is located at about 50 km northfrom the Atlantic Coast in the Buenos Aires Province of Argentina(38 u 21 9  lat S. and 60 u 14 9  lon W). Arroyo Seco 2 has an earlycomponent containing a lithic assemblage of unifacial, marginallyretouched tools associated with bone remains of guanaco(camelid), Pampean deer, and nine extinct megafauna:  Paleolama  , Equus  ,  Hippidion ,  Toxodon ,  Megatherium ,  Eutatus  ,  Glossotherium ,  Ma-crauchenia  , and  Glyptodon  [23]. Apart from this early component, thesite contains one of the best records of human remains for theEarly/Middle Holocene transition in South America. To date, 45human skeletons have been uncovered and there are 21 dates fromca. 7,800 to 4,500  14 C yr BP related to them [23]. The span of dates from the primary and secondary burials of Arroyo Seco 2,suggests the use of the site—not continuously but redundantly— for inhumations purposes, for more than 3,000 years during theEarly and Middle Holocene.Middle and Earlier Late Holocene samples from East Central Argentina contain individuals of different sites from Laguna del Juncal archaeological locality (Laguna del Juncal, Rı´o NegroValley 1 and 2; see Table 1), placed south from Viedma city in theRı´o Negro Province of Argentina (40 u 48 9  lat S. and 62 u 58 9  lon W),and one sample from Southeast Pampa (Table 1). The samplesfrom East Central Argentina dated on Later Late Holocene comefrom various archaeological sites from Rı´o Negro, placed nearLaguna del Juncal and Peninsula San Blas (40 u 33 9  lat S. and62 u 13 9  lon W), and the Buenos Aires Province (Table 1).Specimens are housed at Divisio´n Antropologı´a of the Museo deLa Plata, Museo Etnogra´fico ‘J. B. Ambrosetti’ in Buenos Airesand INCUAPA in Olavarria, Argentina. Preliminary analyses Because most samples are sex balanced, males and females werepooled in the analyses to obtain a greater sample size. In order tocontrol some sources of variation related to sex, we analyzed sizestandardized adult individuals of both sexes. The observationalerror was controlled using the experimental design introduced byPerez [1]. The results showed that photographing and digitaliza-tion of landmarks and semilandmarks procedures did not generatesignificant observational error [1]. Morphometric analyses The craniofacial variation was analyzed with geometric morpho-metrics techniques [25,26] employing an arrangement of two-dimensional coordinates of biologically definable landmarks andsemilandmarks (Fig. 2). Most comparisons were done on the facialskeleton, which is not affected by the cranial deformation present inthese samples. We also performed an analysis of vault morphology innon-deformed skulls. Specimens were photographed with anOlympus SP 350 digital camera with the skull positioned according to the Frankfurt plane. For facial images, the camera lens was locatedin the coronal plane [27] and digital images were obtained from thecrania in frontal view. Facial images were taken at 250 mm from theprosthion point. Eight landmarks and seventy-four semilandmarks(Fig. 2A) were obtained from the facial skeleton. For vault skeleton,digital images were obtained from the crania in lateral (left side) view.Lateral view images were taken at 300 mm from the Euryon.Coordinates for two landmarks and seventy-eight semilandmarkswere recorded on the lateral view of the crania (Fig. 2B). Thelandmarks were located following the definitions of Buikstra andUbelaker [27]. The application MakeFan6 [28], which placesalignment ‘fans’ at equal angular displacements along a curve, wasused to ensure consistent placement of the craniofacial semilandmark coordinates. Both landmarks and semilandmarks were afterwardsdigitized by one of us (SIP) using tpsDIG 1.40 software [29]. American Crania and DNA DataPLoS ONE | www.plosone.org 2 May 2009 | Volume 4 | Issue 5 | e5746  In geometric morphometrics, shape variation can be defined asthe information that remains in the coordinates of landmarks andsemilandmarks after the differences due to location, scale andorientation (i.e. non-shape differences) have been removed [25].To eliminate non-shape variation in such coordinates—byoverlaying them according to a least-square optimization criteri- Figure 1. Map showing geographic location of the crania samples analyzed. doi:10.1371/journal.pone.0005746.g001American Crania and DNA DataPLoS ONE | www.plosone.org 3 May 2009 | Volume 4 | Issue 5 | e5746  on—the superimposition method known as Generalized Procrus-tes Analysis was used [25,26]. At the start the coordinates of anysingle individual are centered at the srcin (0,0) by substracting thecentroid or mean location of all landmarks and semilandmarks. After that, the centroid size of the configuration (the square root of the summed square distance of all landmarks from the centroid) isset to 1 dividing the coordinates by the initial centroid size of theindividual. An iterative procedure is used to determine the meanform onto which all individuals are aligned. To do so, allindividuals are first aligned as a single individual, and their meanshape is calculated. All individuals are then rotated to minimizethe added squared differences of point coordinates between eachone of them and the estimated mean shape or reference form. Thisprocedure is repeated until the mean shape does not changesubstantially after iteration of the orientation procedure. At thispoint, the individuals are in partial Procrustes superimpositiononto the reference form [25,26]. When outlines are digitized asdiscrete points (i.e. semilandmarks), a step is added to theGeneralized Procrustes Analysis to minimize the variationtangential to the curve, since individual curve points are notclaimed to be homologous in all subjects. Consequently, the variation along tangent directions is not informative, and only thecoordinate normal to the outline bears information aboutdifferences between individuals or groups. We aligned semiland-marks by means of perpendicular projection or minimumProcrustes distance criteria [26,30]. In addition to optimallytranslating, scaling, and rotating landmarks, the semilandmarksare slid along the outline curve until they match as much aspossible the positions of corresponding points along the outline of the reference individual [25,30], minimizing the Procrustesdistance between the subject and the reference individual.Shape differences among samples and individuals were studiedusing the aligned coordinates. These coordinates were used toperform a Principal Component or Relative Warp Analysis (RW)to describe major trends in shape among samples [25,26]. Animportant aspect of this analysis is that variation along the relativewarp axes can be expressed as intuitive deformation grid diagramsshowing the difference from the mean form or reference. tpsRelw1.44 [29] was used to perform the geometric morphometricanalyses.Thepatternofordination producedbythe firsttworelativewarpsof the facial data was compared with temporal and geographicaldifferences among the samples using the PROTEST analysis [31].To describe such differences we created an ordination matrix withradiocarbon dating and geographic coordinates (i.e. latitude andlongitude) for each sample. PROTEST analysis compare thisordination by using the sum of the squared residuals betweenordinations in their optimal superimposition such as a measurementof association (  m 12 ; [31 ]). There are several strategies forsuperimposition, but the Generalized Procrustes Analysis used ingeometric morphometrics is the simplest approach (see above; [31 ]). A permutation procedure (10,000 permutations) was used after-wards to assess the statistical significance of the Procrustean fit.PROTEST analysis was performed using vegan 1.8–8 package forR 2.6.1 [32]. Molecular data mtDNA haplogroups for some of the East Central Argentinasamples have previously been obtained in different works [33 – 36]. aDNA analytical methods used by Lalueza et al. [33] and Figueiroand Sans [36; Figueiro personal communication] are similar.Teeth and well-preserved bone pieces were handled understringent precautionary measures to prevent extraneous contam-inations. Teeth were sequentially soaked in 15% or 20% HCl for10 min to remove dirt and carbonate deposits (in addition,Lalueza et al. [33] employed 70% ethanol for 10 min and rinsedin sterile double-distilled water for 30 min). Subsequently, teethand bones were irradiated with UV lamp for 15 min. Next, theexternal surface of the samples was removed using a sand-blasterto eliminate both soil and exogenous DNA contaminants. Samples Table 1.  Sample composition, abbreviations, age, gender distribution and sample sizes. Samples Abbrev. Region Age* F M Total Southeast Pampa SEP-emH #  Southeast Pampa Early/Middle Holocene (ca. 7,800–6,300 years BP) 3 3 6SEP-elH Southeast Pampa Earlier Late Holocene (ca. 2,500–1,500 years BP) 2 7 9SEP-llH Southeast Pampa Later Late Holocene (ca. 1,500–200 years BP) 4 7 11Isla Gama IG-llH Northeast Patagonia Later Late Holocene (ca. 1,500–200 years BP) 7 5 12San Blas SB-llH Northeast Patagonia Later Late Holocene (ca. 1,500–200 years BP) 15 18 33Laguna del Juncal LJ-elH #  Northeast Patagonia Earlier Late Holocene (ca. 3,500–2,500 years BP) 12 19 31Negro River Valley RN-elH1 Northeast Patagonia Earlier Late Holocene (ca. 3,500–2,500 years BP) 13 10 23RN-elH2 Northeast Patagonia Earlier Late Holocene (ca. 2,500–1,500 years BP) 2 8 10RN-llH Northeast Patagonia Later Late Holocene (ca. 1,500–200 years BP) 9 12 21San Antonio Este SAE-llH Centre Patagonia Later Late Holocene (ca. 1,500–200 years BP) 3 5 8Chubut River Valley ChV-elH Centre Patagonia Earlier Late Holocene (ca. 2,500–1,500 years BP) 6 10 16ChV-llH Centre Patagonia Later Late Holocene (ca. 1,500–200 years BP) 18 20 38Southwest Chubut SWCh-llH Centre Patagonia Later Late Holocene (ca. 1,500–200 years BP) 7 7 14South Mendoza SM-elH Northwest Patagonia Earlier Late Holocene (ca. 2,500–1,500 years BP) 8 15 23SM-llH Northwest Patagonia Later Late Holocene (ca. 1,500–200 years BP) 6 9 15Delta of Parana Del-llH Northeast Pampa Later Late Holocene (ca. 1,500–200 years BP) 5 8 13Total 283 * Approximate sample ages according to radiocarbon dating obtained from human bones and contextual information. # Samples characterized molecularly.doi:10.1371/journal.pone.0005746.t001 American Crania and DNA DataPLoS ONE | www.plosone.org 4 May 2009 | Volume 4 | Issue 5 | e5746  Figure 2. Allocated geometric coordinates are displayed with different symbols.  Landmarks are represented as squares ( & ), whereassemilandmarks are represented as circles ( $ ) on face (A) and vault (B) views. The numbers correspond to the following landmarks: nasion (1);nasospinale (2); prosthion (3); alare (4); ectoconchion (5); frontotemporale (6); frontomalare temporale (7); ectomolare (8); post-mastoid (9).doi:10.1371/journal.pone.0005746.g002American Crania and DNA DataPLoS ONE | www.plosone.org 5 May 2009 | Volume 4 | Issue 5 | e5746
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