Genetic continuity and change among the Indigenous peoples of California.

Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.

Trans-Holocene Bayesian chronology for tree and field crop use from El Gigante rockshelter, Honduras.

El Gigante rockshelter in western Honduras provides a deeply stratified archaeological record of human-environment interaction spanning the entirety of the Holocene. Botanical materials are remarkably well preserved and include important tree (e.g., ciruela (Spondias), avocado (Persea americana)) and field (maize (Zea mays), beans (Phaseolus), and squash (Cucurbita)) crops. Here we provide a major update to the chronology of tree and field crop use evident in the sequence. We report 375 radiocarbon dates, a majority of which are for short-lived botanical macrofossils (e.g., maize cobs, avocado seeds, or rinds). Radiocarbon dates were used in combination with stratigraphic details to establish a Bayesian chronology for ~9,800 identified botanical samples spanning the last 11,000 years. We estimate that at least 16 discrete intervals of use occurred during this time, separated by gaps of ~100-2,000 years. The longest hiatus in rockshelter occupation was between ~6,400 and 4,400 years ago and the deposition of botanical remains peaked at ~2,000 calendar years before present (cal BP). Tree fruits and squash appeared early in the occupational sequence (~11,000 cal BP) with most other field crops appearing later in time (e.g., maize at ~4,400 cal BP; beans at ~2,200 cal BP). The early focus on tree fruits and squash is consistent with early coevolutionary partnering with humans as seed dispersers in the wake of megafaunal extinction in Mesoamerica. Tree crops predominated through much of the Holocene, and there was an overall shift to field crops after 4,000 cal BP that was largely driven by increased reliance on maize farming.

South-to-north migration preceded the advent of intensive farming in the Maya region.

The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.

A genetic history of the pre-contact Caribbean.

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography.

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700-2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200-1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.

A Paleogenomic Reconstruction of the Deep Population History of the Andes.

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ∼9,000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today's genetic structure began to develop by 5,800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ∼2,000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. VIDEO ABSTRACT.

Reconstructing the Deep Population History of Central and South America.

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

High-precision chronology for Central American maize diversification from El Gigante rockshelter, Honduras.

The first steps toward maize (Zea mays subspecies mays) domestication occurred in the Balsas region of Mexico by ∼9,000 calendar years B.P. (cal B.P.), but it remains unclear when maize was productive enough to be a staple grain in the Americas. Molecular and microbotanical data provide a partial picture of the timing and nature of morphological change, with genetic data indicating that alleles for some domestication traits were not yet fixed by 5,300 cal B.P. in the highlands of Mexico. Here, we report 88 radiocarbon dates on the botanical remains from El Gigante rockshelter (Honduras) to establish a Bayesian chronology over the past ∼11,000 y spanning the transition to maize-based food production. Botanical remains are remarkably well preserved and include over 10,000 maize macrofossils. We directly dated 37 maize cobs to establish the appearance and local change of maize at the site. Cobs are common in deposits dating between 4,340 and 4,020 cal B.P., and again between 2,350 and 980 cal B.P. The earliest cobs appear robustly domesticated, having 10-14 rows, suggesting strong selection for increased yield. The later cobs are comparable to these earliest ones, but show clear emergence of diverse traits, including increased cob width, rachis segment length, and cupule width. Our results indicate that domesticated landraces of maize productive enough to be a staple grain existed in Central America by 4,300 cal B.P.

Characterization of Archaeological Sediments Using Fourier Transform Infrared (FT-IR) and Portable X-ray Fluorescence (pXRF): An Application to Formative Period Pyro-Industrial Sites in Pacific Coastal Southern Chiapas, Mexico.

Archaeological sediments from mounds within the mangrove zone of far-southern Pacific coastal Chiapas, Mexico, are characterized in order to test the hypothesis that specialized pyro-technological activities of the region's prehistoric inhabitants (salt and ceramic production) created the accumulations visible today. Fourier transform infrared spectroscopy (FT-IR) is used to characterize sediment mineralogy, while portable X-ray fluorescence (pXRF) is used to determine elemental concentrations. Elemental characterization of natural sediments by both instrumental neutron activation analysis (INAA) and pXRF also contribute to understanding of processes that created the archaeological deposits. Radiocarbon dates combined with typological analysis of ceramics indicate that pyro-industrial activity in the mangrove zone peaked during the Late Formative and Terminal Formative periods, when population and monumental activity on the coastal plain and piedmont were also at their peaks.

Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans.

Because of differences in craniofacial morphology and dentition between the earliest American skeletons and modern Native Americans, separate origins have been postulated for them, despite genetic evidence to the contrary. We describe a near-complete human skeleton with an intact cranium and preserved DNA found with extinct fauna in a submerged cave on Mexico's Yucatan Peninsula. This skeleton dates to between 13,000 and 12,000 calendar years ago and has Paleoamerican craniofacial characteristics and a Beringian-derived mitochondrial DNA (mtDNA) haplogroup (D1). Thus, the differences between Paleoamericans and Native Americans probably resulted from in situ evolution rather than separate ancestry.

Correlating the ancient Maya and modern European calendars with high-precision AMS 14C dating.

The reasons for the development and collapse of Maya civilization remain controversial and historical events carved on stone monuments throughout this region provide a remarkable source of data about the rise and fall of these complex polities. Use of these records depends on correlating the Maya and European calendars so that they can be compared with climate and environmental datasets. Correlation constants can vary up to 1000 years and remain controversial. We report a series of high-resolution AMS (14)C dates on a wooden lintel collected from the Classic Period city of Tikal bearing Maya calendar dates. The radiocarbon dates were calibrated using a Bayesian statistical model and indicate that the dates were carved on the lintel between AD 658-696. This strongly supports the Goodman-Martínez-Thompson (GMT) correlation and the hypothesis that climate change played an important role in the development and demise of this complex civilization.

Development and disintegration of Maya political systems in response to climate change.

The role of climate change in the development and demise of Classic Maya civilization (300 to 1000 C.E.) remains controversial because of the absence of well-dated climate and archaeological sequences. We present a precisely dated subannual climate record for the past 2000 years from Yok Balum Cave, Belize. From comparison of this record with historical events compiled from well-dated stone monuments, we propose that anomalously high rainfall favored unprecedented population expansion and the proliferation of political centers between 440 and 660 C.E. This was followed by a drying trend between 660 and 1000 C.E. that triggered the balkanization of polities, increased warfare, and the asynchronous disintegration of polities, followed by population collapse in the context of an extended drought between 1020 and 1100 C.E.