Disentangling signatures of selection before and after European colonization in Latin Americans

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. While classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ~4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico and Peru. Our approach replicates previous reports of selection in the HLA region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly-used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

The Genomic Prehistory of the Indigenous People of Uruguay

The prehistory of the people of Uruguay is greatly complicated by the dramatic and severe effects of European contact, as with most of the Americas. After the series of military campaigns that exterminated the last remnants of nomadic peoples, Uruguayan official history masked and diluted the former indigenous ethnic diversity into the narrative of a singular people that all but died out. Here we present the first whole genome sequences of the Indigenous people of the region before the arrival of Europeans, from an archaeological site in eastern Uruguay that dates from 2,000 years before present. We find a surprising connection to ancient individuals from Panama and eastern Brazil, but not to modern Amazonians. This result may be indicative of a distinct migration route into South America that may have occurred along the Atlantic coast. We also find a distinct ancestry previously undetected in South America. Though this work begins to piece together some of the demographic nuance of the region, the sequencing of ancient individuals from across Uruguay is needed to better understand the ancient prehistory and genetic diversity that existed before European contact, thereby helping to rebuild the history of the indigenous population of what is now Uruguay.

The Ancient Civilizations

This chapter provides an interpretive synthesis of the current state of knowledge of the pre-Columbian civilizations of Central America from the time of earliest human habitation until European contact. In terms of cultural affinities, the northern portion of the area formed the southeastern periphery of the culture area of Mesoamerica, and the southern regions pertained to the Isthmo-Colombian area (or Intermediate Area). With its relatively high population density, the area is highly susceptible to volcanic, seismic, and climatic natural disasters such as droughts, tropical storms, flooding, and landslides, and the same was true in the past. A recurrent theme in the study of ancient Central American civilizations is the impact of natural disasters and societal responses to cataclysmic events.

The Kadazans and Sabah Politics

<p>The Kadazans - the indigenous non-Muslim tribal people of what was North Borneo under Chartered Company rule and is now Sabah, a state of Malaysia - have for the most part throughout their history been governed by others than themselves. Before European contact Muslim overlords from Brunei or the Sulu archipelago exercised a tenuous sovereignty; the London-based Chartered Company was concerned to extract wealth for shareholders and to keep the indigenes quiescent; and since the formation of Malaysia, with the covert or overt support of the federal government in Kuala Lumpur, for the greater part of the time Muslim rule has prevailed. This thesis is a detailed examination of the last quarter-of-a-century's political life in Sabah, with particular reference to the role of the Kadazan community therein. The growth of Kadazan consciousness or "nationalism" is traced, and the evolution of their political parties and fortunes. Political and socio-economic developments within the state are linked always to the federal framework within which they take place and must be understood. The author has been and is a participant-observer in the history with which he deals having been both newspaper editor and Radio Sabah commentator; back-bench M.P. in opposition and front-bench Cabinet Minister in Government; grass roots activist in villages and legal advisor to the present Government of Sabah headed by a Kadazan, Datuk Joseph Pairin Kitingan.</p>

The Kadazans and Sabah Politics

<p>The Kadazans - the indigenous non-Muslim tribal people of what was North Borneo under Chartered Company rule and is now Sabah, a state of Malaysia - have for the most part throughout their history been governed by others than themselves. Before European contact Muslim overlords from Brunei or the Sulu archipelago exercised a tenuous sovereignty; the London-based Chartered Company was concerned to extract wealth for shareholders and to keep the indigenes quiescent; and since the formation of Malaysia, with the covert or overt support of the federal government in Kuala Lumpur, for the greater part of the time Muslim rule has prevailed. This thesis is a detailed examination of the last quarter-of-a-century's political life in Sabah, with particular reference to the role of the Kadazan community therein. The growth of Kadazan consciousness or "nationalism" is traced, and the evolution of their political parties and fortunes. Political and socio-economic developments within the state are linked always to the federal framework within which they take place and must be understood. The author has been and is a participant-observer in the history with which he deals having been both newspaper editor and Radio Sabah commentator; back-bench M.P. in opposition and front-bench Cabinet Minister in Government; grass roots activist in villages and legal advisor to the present Government of Sabah headed by a Kadazan, Datuk Joseph Pairin Kitingan.</p>

Indigenous Australian laws of war: Makarrata, milwerangel and junkarti

Studies in Australian history have lamentably neglected the military traditions of First Australians prior to European contact. This is due largely to a combination of academic and social bigotry, and loss of Indigenous knowledge after settlement. Thankfully, the situation is beginning to change, in no small part due to the growing literature surrounding the Frontier Wars of Australia. All aspects of Indigenous customs and norms are now beginning to receive a balanced analysis. Yet, very little has ever been written on the laws, customs and norms that regulated Indigenous Australian collective armed conflicts. This paper, co-written by a military legal practitioner and an ethno-historian, uses early accounts to reconstruct ten laws of war evidently recognized across much of pre-settlement Australia. The study is a preliminary one, aiming to stimulate further research and debate in this neglected field, which has only recently been explored in international relations.

Human impacts on the environment and wildlife in California’s past: Lessons from California archaeology

The long history of human-animal interactions in California prior to European contact is frequently not considered when setting ecological baselines and, by consequence, when planning conservation and management expectations and strategies for native species. This article reviews archaeological perspectives that explore the relationship between human niche construction, plant and wildlife populations, and human health in pre-European contact Central California, with an emphasis on the Central Valley and Delta, the surrounding foothills, and the San Francisco Bay Area. A summary of the archaeological record for Central California is provided, along with how niche construction and related evolutionary based models have been used in prehistoric California. Examples of the influences of human niche construction on flora, fauna, and human health from the archaeological and ethnographic record are then discussed. This information is tied to modern wildlife research and management practices that would serve contemporary fish and wildlife management given that human influences on species “natural” habitats and ecological baselines extends much further into the past than current ecological baselines and wildlife management strategies traditionally recognize.

Jews and Jewish Communal Identity in Early America

Jewish communities in the Americas followed in the wake of European contact with the western hemisphere at the end of the 15th century, and were a byproduct of the process of European colonization. Early Jewish settlements relied on a combination of economic investment, political negotiation, social networking, and subterfuge to establish the means of communal survival. While the Jewish experience in the Americas continued to operate within the sphere of European attitudes and modalities of behavior brought over to the western hemisphere by the colonizers, the remoteness of these New World communities and the friction caused by competing inter-imperial goals eventually allowed Jews to take advantage of new economic opportunities and expand their social and political range beyond what was feasible for Jewish communities in Europe in the same period. New World colonization shifted the ways that Jews were seen within European cultures, as contact with Indigenous peoples of the Americas and the importation of Africans as slaves allowed Europeans to see Jews as comparatively less alien than they had previously been defined. While Jews, as individuals and as communities, continued to face discriminatory treatment (such as extraordinary taxation, prohibitions on voting and officeholding, scapegoating, and social exclusion), they were able to exercise many of the status privileges accorded to those with European Christian identities. These privileges included the capacity to freely pursue economic activities in trade and agriculture and to exploit enslaved peoples for their labor and for other purposes. With this elevated status came tension within the Jewish community over assimilation to European Christian norms, and an ongoing struggle to preserve Jewish identity and communal distinctiveness.

Cultural macroevolution of musical instruments in South America

Musical instruments provide material evidence to study the diversity and technical innovation of music in space and time. We employed a cultural evolutionary perspective to analyse organological data and their relation to language groups and population history in South America, a unique and complex geographic area for human evolution. The ethnological and archaeological native musical instrument record, documented in three newly assembled continental databases, reveals exceptionally high diversity of wind instruments. We explored similarities in the collection of instruments for each population, considering geographic patterns and focusing on groupings associated with language families. A network analysis of panpipe organological features illustrates four regional/cultural clusters: two in the Tropical Forest and two in the Andes. Twenty-five percent of the instruments in the standard organological classification are present in the archaeological, but not in the ethnographic record, suggesting extinction events. Most recent extinctions can be traced back to European contact, causing a reduction in indigenous cultural diversity.

Historic and bioarchaeological evidence supports late onset of post-Columbian epidemics in Native California

Catastrophic decline of Indigenous populations in the Americas following European contact is one of the most severe demographic events in the history of humanity, but uncertainty persists about the timing and scale of the collapse, which has implications for not only Indigenous history but also the understanding of historical ecology. A long-standing hypothesis that a continent-wide pandemic broke out immediately upon the arrival of Spanish seafarers has been challenged in recent years by a model of regional epidemics erupting asynchronously, causing different rates of population decline in different areas. Some researchers have suggested that, in California, significant depopulation occurred during the first two centuries of the post-Columbus era, which led to a “rebound” in native flora and fauna by the time of sustained European contact after 1769. Here, we combine a comprehensive prehistoric osteological dataset (n = 10,256 individuals) with historic mission mortuary records (n = 23,459 individuals) that together span from 3050 cal BC to AD 1870 to systematically evaluate changes in mortality over time by constructing life tables and conducting survival analysis of age-at-death records. Results show that a dramatic shift in the shape of mortality risk consistent with a plague-like population structure began only after sustained contact with European invaders, when permanent Spanish settlements and missions were established ca. AD 1770. These declines reflect the syndemic effects of newly introduced diseases and the severe cultural disruption of Indigenous lifeways by the Spanish colonial system.