Pleistocene peopling of the Americas

Our species colonized North and South America last of all the major land masses, thereby ending the spread that began a million years earlier when ancestral members of the genus Homo first ventured out of Africa. But who were the first Americans? When did they arrive? Did they come in one migration or many? How quickly and by what adaptive strategies did they move across the environmentally diverse and trackless New World? How do they relate to contemporary native Americans? We have plenty of answers to these questions. Unfortunately, we can't agree which ones are right. This much is certain: the first Americans were Homo sapiens who came from northeast Asia via the Bering Straits (Fig. 1). They may have walked from Siberia to Alaska across Beringia, the land bridge formed when vast Pleistocene glaciers froze 5% of the world's water,¹ lowering global sea levels and exposing the shallow continental shelf between Asia and America. These hunter-gatherers were present throughout the Americas by 11,500 years ago, in time to witness the climatic and ecological changes, including the extinction of thirty-five genera of megafauna, that signalled the end of the Pleistocene. Beyond those bare facts there is controversy. Here, then, is a brief summary of the state of the argument over the peopling of the Americas.     

The peopling of the Americas and the origin of the Beringian occupation model

The current model for peopling of the Americas involves divergence from an ancestral Asian population followed by a period of population isolation and genetic diversification in Beringia, and finally, a rapid expansion into and throughout the Americas. Studies in the 1970s sought to characterize the biological relationships between different indigenous populations and first proposed an occupation of Beringia. More recent studies using molecular genetic markers often neglect to reference early works that laid the groundwork for current colonization models. We address this matter, and briefly summarize the literature and technological advances that contributed to our current understanding of the peopling of the Americas. Furthermore, we argue that describing the process of peopling of the Americas as “migrations from Asia” minimizes the significant genetic diversification that occurred outside of Asia, and offends indigenous Americans by discounting their origin narratives and land rights. Rather than referring to the indigenous peoples of the Americas as “migrants” or “immigrants,” we recommend consistency in the language used to describe all post‐glacial expansions of people into Asia, Europe and the Americas.     

Disease,climate and the peopling of the Americas

Archaeological discussions surrounding the reasons for pre-Columbian Native American disease susceptibility have encompassed a wide range of issues particularly that the cold of Beringia acted as a barrier to the entry of infectious disease during initial human migrations: ‘the cold-screen hypothesis’. This paper aims to critically review this hypothesis, particularly in relation to (1) the paleopathological evidence; (2) effects of temperature, effective population size/density and animal reservoir diversity on pathogen survival/maintenance and (3) disease patterns in the past and present circumpolar region. Results demonstrate that a number of conditions, such as tuberculosis, treponemal infection and parasitic infections, were present in the pre-Columbian Americas. Epidemiological evidence also demonstrates that while temperature (cold) can affect the survival of some pathogens, other factors were more likely influential in the emergence and maintenance of disease in the pre-Columbian Americas.

http://zoobank.org/714351F3-8F4C-4134-955F-D28C1B07617C     

Clovis in context: New light on the peopling of the Americas

Until recently, the first Americans were thought to be fluted-point spear-hunters from the Siberian steppes. Near the end of the Ice Age, they followed big-game herds over the Bering land bridge into the open, upland habitats of the interior of North America about 12,000 years ago. Rapidly extinguishing the big game herds with their deadly hunting methods, they pressed southward in search of new herds and reached the tip of South America about a thousand years later. Today, nearly 70 years after the first excavations at Clovis, New Mexico, the type site for this culture, new sites and new dates from both North and South America are forcing a revision of the earlier picture of the migrations and adaptations of the first Americans. But despite recurring claims that human colonization of the Western Hemisphere began as early as 20,000 or more years ago with the arrival of generalized foragers lacking a projectile-point tradition, no definitive data gives empirical support for a human presence before c. 12,000 before the present (B.P.). All supposed pre-Clovis cultures except one in Alaska have failed to withstand careful scrutiny of their data. In addition, despite recent claims for cultural and biological links of the migrants to Europe or the Pacific Islands, the skeletons and cultural assemblages of Paleoindians throughout the hemisphere point consistently to a northeast Asian origin. According to new data, Paleoindian ancestors in Beringia c. 12,000 years ago were not specialized, fluted-point hunters of large game, but broad-spectrum hunter-gatherers using triangular or bipointed, lanceolates. Diverse cultures descended from these ancestors, not only the big-game hunting Clovis culture of the North American high plains. And just as Clovis did not set the cultural pattern for the hemisphere, it was not the earliest culture. Fully contemporary with the earliest possible Clovis dates of c. 11,200, in South America there already were maritime foragers on the Pacific coast, small-game hunters in the southern pampas, and tropical forest riverine foragers in the eastern tropical lowlands. The Clovis culture thus was just one of several regional cultures developed in the millennium after the initial migration. It could not have been the ancestor of the other early Paleoindian cultures. This new picture of Paleoindian cultures changes understanding of initial human adaptive radiation in the Americas and has implications for general theories of human evolution and behavioral ecology.     

Blood group O alleles in Native Americans: Implications in the peopling of the Americas

All major ABO blood alleles are found in most populations worldwide, whereas the majority of Native Americans are nearly exclusively in the O group. O allele molecular characterization could aid in elucidating the possible causes of group O predominance in Native American populations. In this work, we studied exon 6 and 7 sequence diversity in 180 O blood group individuals from four different Mesoamerican populations. Additionally, a comparative analysis of genetic diversity and population structure including South American populations was performed. Results revealed no significant differences among Mesoamerican and South American groups, but showed significant differences within population groups attributable to previously detected differences in genetic drift and founder effects throughout the American continent. Interestingly, in all American populations, the same set of haplotypes O¹, O^1v, and O^1v(G542A) was present, suggesting the following: (1) that they constitute the main genetic pool of the founding population of the Americas and (2) that they derive from the same ancestral source, partially supporting the single founding population hypothesis. In addition, the consistent and restricted presence of the G542A mutation in Native Americans compared to worldwide populations allows it to be employed as an Ancestry informative marker (AIM). Present knowledge of the peopling of the Americas allows the prediction of the way in which the G542A mutation could have emerged in Beringia, probably during the differentiation process of Asian lineages that gave rise to the founding population of the continent. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas

It is well accepted that the Americas were the last continents reached by modern humans, most likely through Beringia. However, the precise time and mode of the colonization of the New World remain hotly disputed issues. Native American populations exhibit almost exclusively five mitochondrial DNA (mtDNA) haplogroups (A-D and X). Haplogroups A-D are also frequent in Asia, suggesting a northeastern Asian origin of these lineages. However, the differential pattern of distribution and frequency of haplogroup X led some to suggest that it may represent an independent migration to the Americas. Here we show, by using 86 complete mitochondrial genomes, that all Native American haplogroups, including haplogroup X, were part of a single founding population, thereby refuting multiple-migration models. A detailed demographic history of the mtDNA sequences estimated with a Bayesian coalescent method indicates a complex model for the peopling of the Americas, in which the initial differentiation from Asian populations ended with a moderate bottleneck in Beringia during the last glacial maximum (LGM), around approximately 23,000 to approximately 19,000 years ago. Toward the end of the LGM, a strong population expansion started approximately 18,000 and finished approximately 15,000 years ago. These results support a pre-Clovis occupation of the New World, suggesting a rapid settlement of the continent along a Pacific coastal route.     

Control region variability of haplogroup C1d and the tempo of the peopling of the Americas

Background

Among the founding mitochondrial haplogroups involved in the peopling of the Americas, haplogroup C1d has been viewed as problematic because of its phylogeny and because of the estimates of its antiquity, apparently being much younger than other founding haplogroups. Several recent analyses, based on data from the entire mitochondrial genome, have contributed to an advance in the resolution of these problems. The aim of our analysis is to compare the conclusions drawn from the available HVR-I and HVR-II data for haplogroup C1d with the ones based on whole mitochondrial genomes.

Methodology/Principal Findings

HVR-I and HVR-II sequences defined as belonging to haplogroup C1d by standard criteria were gathered from the literature as well as from population studies carried out in Uruguay. Sequence phylogeny was reconstructed using median-joining networks, geographic distribution of lineages was analyzed and the age of the most recent common ancestor estimated using the ρ-statistic and two different mutation rates. The putative ancestral forms of the haplogroup were found to be more widespread than the derived lineages, and the lineages defined by np 194 were found to be widely distributed and of equivalent age.

Conclusions/Significance

The analysis of control region sequences is found to still harbor great potential in tracing microevolutionary phenomena, especially those found to have occurred in more recent times. Based on the geographic distributions of the alleles of np 7697 and np 194, both discussed as possible basal mutations of the C1d phylogeny, we suggest that both alleles were part of the variability of the haplogroup at the time of its entrance. Moreover, based on the mutation rates of the different sites stated to be diagnostic, it is possible that the anomalies found when analyzing the haplogroup are due to paraphyly.     

On the number of New World founders: a population genetic portrait of the peopling of the Americas

The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size.     

Nonparametric estimation for the three-stage irreversible illness-death model

In this paper, we present new nonparametric estimators of the stage-occupation probabilities in the three-stage irreversible illness-death model. These estimators use a fractional risk set and a reweighting approach and are valid under stage-dependent censoring. Using a simulated data set, we compare the behavior of our estimators with previously proposed estimators. We also apply our estimators to data on time to Pneumocystis pneumonia and death obtained from an AIDS cohort study.     

The exploitation of megafauna during the earliest peopling of the Americas: An examination of nineteenth-century fossil collections

This paper describes human-modified bones originally from the Pampas region, and that form part of nineteenth-century fossil collections of native fauna. We describe the morphological and configurational features of the marks, relate them to the various stages in the butchering process, and discuss access type. An examination of various different American sites is used to interpret this evidence at a coarse-grained level. Although these collections are more biased than current archaeological materials with regard to their sedimentary origin and previous handling, the application of modern technology has allowed us to obtain new data. Therefore, despite their complex history, these artefacts can be incorporated into the broader body of modern archaeological research. This type of study adds new value to our historic heritage and underscores its usefulness in modern enquiries, in this case, related to the topic of how Homo sapiens interacted with the native fauna in the southern Cone of South America.     

Craniometric analysis in groups from tierra del Fuego/Patagonia and the peopling of the south extreme of the Americas

Five large craniometric samples from extinct tribes (Selk’nam, Kawéskar and Yámana) from Tierra del Fuego and from Patagonia have been analyzed through multivariate techniques. The purpose was to test the hypothesis of one or two different migration waves in the peopling of the south extreme of South America. A cluster analysis has been made, using the squared Euclidean distance as a measure of proximity, and the UPGMA and neighbor joining algorithms as a tree building method. The robustness of the branches has been assessed with bootstrap analysis through 100 random iterations of the original data set. Results show that, despite their cultural differences, the three hunter-gatherer groups. from Tierra del Fuego tend to cluster together, indicating a similar morphological pattern. This suggests that geographic distance (in latitudinal sense) is the main factor that influenced the differentiation of the human groups from Tierra del Fuego and Patagonia, from a single ancestral population.     

Mitochondrial genome diversity in arctic Siberians, with particular reference to the evolutionary history of Beringia and Pleistocenic peopling of the Americas

Through extended survey of mitochondrial DNA (mtDNA) diversity in the Nganasan, Yukaghir, Chuvantsi, Chukchi, Siberian Eskimos, and Commander Aleuts, we filled important gaps in previously unidentified internal sequence variation within haplogroups A, C, and D, three of five (A-D and X) canonical mtDNA lineages that defined Pleistocenic extension from the Old to the New World. Overall, 515 mtDNA samples were analyzed via high-resolution SNP analysis and then complete sequencing of the 84 mtDNAs. A comparison of the data thus obtained with published complete sequences has resulted in the most parsimonious phylogenetic structure of mtDNA evolution in Siberia-Beringia. Our data suggest that although the latest inhabitants of Beringia are well genetically reflected in the Chukchi-, Eskimo-Aleut-, and Na-Dene-speaking Indians, the direct ancestors of the Paleosiberian-speaking Yukaghir are primarily drawn from the southern belt of Siberia when environmental conditions changed, permitting recolonization the high arctic since early Postglacial. This study further confirms that (1) Alaska seems to be the ancestral homeland of haplogroup A2 originating in situ approximately 16.0 thousand years ago (kya), (2) an additional founding lineage for Native American D, termed here D10, arose approximately 17.0 kya in what is now the Russian Far East and eventually spread northward along the North Pacific Rim. The maintenance of two refugial sources, in the Altai-Sayan and mid-lower Amur, during the last glacial maximum appears to be at odds with the interpretation of limited founding mtDNA lineages populating the Americas as a single migration.     

Updated model of the batch acetone-butanol fermentation

Summary The recent models of the Acetone-Butanol fermentation did not adequately describe the culture inhibition by the accumulating metabolites and were unable to simulate the acidogenic culture dynamics at elevated pH levels. The present updated modification of the model features a generalised inhibition term and a pH dependent terms for intracellular conversion of undissociated acids into solvent products. The culture dynamics predictions by the developed model compared well with experimental results from an unconventional acidogenic fermentation ofC. acetobutylicum.Nomenclature A acetone concentration in the fermentation broth, [g/L] - AA total concentration of dissociated and undissociated acetic acid, [g/L] - AA _undiss concentration of undissociated acetic acid, [g/L] - APS Absolute Parameter Sensitivity - AT acetoin concentration in the fermentation broth, [g/L] - B butanol concentration in the fermentation broth, [g/L] - BA total concentration of dissociated and undissociated butyric acid, [g/L] - BA _undiss concentration of undissociated butyric acid, [g/L] - E ethanol concentration in the fermentation broth, [g/L] - f(T) inhibition function as defined in Equation (2) - k ₁ constant in Equation (4), [g substrate/g biomass] - k ₂ constant in Equation (4), [g substrate/(g biomass.h)] - k ₁ constant in Equation (5), [g substrate/(g biomass] - k ₂ constant in Equation (5), [g substrate/(g biomass.h)] - k ₃ constant in Equation (6), [g butyric acid/g substrate] - k ₄ constant in Equation (6), [g butyric acid/(g biomass.h)] - k ₅ constant in Equation (7), [g butanol/g substrate] - k ₆ constant in Equation (8), [g acetic acid/g substrate] - k ₇ constant in Equation (8), [g acetic acid/(g biomass.h)] - k ₈ constant in Equation (9), [g acetone/g substrate] - k ₉ constant in Equation (10), [g ethanol/g substrate] - k ₁₀ constant in Equation (11), [g acetoin/g substrate] - k ₁₁ constant in Equation (12), [g lactic acid/g substrate] - K _I Inhibition constant, [g inhibitory products/L] - ke maintenance energy requirement for the cell, [g substrate/(g biomass.h)] - K _AA acetic acid saturation constant, [g acetic acid/L] - K _BA butyric acid saturation constant, [g butyric acid/L] - K _S Monod's saturation constant, [g substrate/L] - LA lactic acid concentration in the fermentation broth, [g/L] - m _i ,n _i constants in Equation (14) - n empirical constant, dependent on degree of inhibition. - P concentration of inhibitory products (B+BA+AA), [g/L] - P _max maximum value of product concentration to inhibit the fermentation, [g/L] - pK_a equilibrium constant - r _A rate of acetone production, [g acetone/L.h] - r _AA rate of acetic acid production, [g acetic acid/L.h] - r _AT rate of acetoin production, [g acetoin/L.h] - r _B rate of butanol production, [g butanol/L.h] - r _BA rate of butyric acid production, [g butyric acid/L.h] - r _E rate of ethanol production, [g ethanol/L.h] - RPS Relative Parameter Sensitivity - r _LA rate of lactic acid production, [g lactic acid/L.h] - r _S dS/dt=total substrate consumption rate, [g substrate/L.h] - r _S substrate utilization rate, [g substrate/L.h] - S substrate concentration in the fermentation broth, [g substrate/L] - S ₀ initial substrate concentration, [substrate/L] - t time, [h] - X biomass concentration, [g/L] - Y _X yield of biomass with respect to substrate, [g biomass/g substrate] - Y _{P i} yield of metabolic product with respect to substrate, [g product/g substrate] Derivatives dX/dt rate of biomass production, [g biomass/L.h] - dP _i /dt rate of product formation, [g product/L.h] Greek letters specific growth rate of the culture, [h^–1] - I specific growth rate of the culture in the presence of the inhibitory products, [h^–1] - µ_max maximum specific growth rate of the culture, [h^–1]