Traditional knowledge, along with archaeological and linguistic evidence, documents that California supports cultural and linguistically diverse Indigenous populations. Studies that have included ancient genomes in this region, however, have focused primarily on broad-scale migration history of the North American continent, with relatively little attention to local population dynamics. Here, in a partnership involving researchers and the Muwekma Ohlone tribe, we analyze genomic data from ancient and present-day individuals from the San Francisco Bay Area in California: 12 ancient individuals dated to 1905 to 1826 and 601 to 184 calibrated years before the present (cal BP) from two archaeological sites and eight present-day members of the Muwekma Ohlone tribe, whose ancestral lands include these two sites. We find that when compared to other ancient and modern individuals throughout the Americas, the 12 ancient individuals from the San Francisco Bay Area cluster with ancient individuals from Southern California. At a finer scale of analysis, we find that the 12 ancient individuals from the San Francisco Bay Area have distinct ancestry from the other groups and that this ancestry has a component of continuity over time with the eight present-day Muwekma Ohlone individuals. These results add to our understanding of Indigenous population history in the San Francisco Bay Area, in California, and in western North America more broadly.
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South-to-north migration preceded the advent of intensive farming in the Maya region
Abstract 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.
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- Award ID(s):
- 1632061
- NSF-PAR ID:
- 10319573
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 13
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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ABSTRACT The Lofoten and Vesterålen archipelagos are located off the outer coast of northern Norway far from the center of the former Fennoscandian Ice Sheet and near the continental shelf edge. Existing relative sea‐level (RSL) data indicate a pronounced mid‐Holocene transgression and interesting connections with the region's prehistoric human settlement history. Here we present seven new sea‐level index points from isolation basins and five terrestrial limiting points from a coastal sedimentary sequence to refine the region's RSL history. Ingression and isolation contacts in isolation basin sediment cores are identified using sedimentary geochemical data, scanning X‐ray fluorescence profiles and phytoplankton analysis. The ages of these contacts are determined using radiocarbon‐based age models. Our index points range from 11.2 to 1.5k cal a
bp and are combined with previously published data to predict the spatiotemporal evolution of sea level in this region using an ensemble of spatiotemporal empirical hierarchical models (STEHME). The new RSL curve constrains the timing of the mid‐Holocene transgression, which occurred from c. 9 to 6k cal abp when sea level increased from −4 to 7 m above present day. From c. 6 to 5k cal abp , RSL rapidly fell to c. 4 m above present values, and more gradually declined at an average rate of c. 0.8 m ka−1over the last 5k cal abp. Isobase maps derived using the STEHME show a decrease in the regional shoreline gradients since the transgression maximum from 0.25 to 0.07 m km−1. Our data also better define how RSL variations influenced the location and preservation of coastal settlement locations and harbors from the early Stone Age through historic intervals, improving understanding of regional human–environment interactions. -
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Abstract Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the “Criollo”) horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the “gait-keeper”
DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the “gait-keeper”DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant “gait-keeper” allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing theDMRT3 locus to this day. The lack of the detectable signature of selection associated with theDMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (includingCHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else. -
Calibrating human population dispersals across Earth’s surface is fundamental to assessing rates and timing of anthropogenic impacts and distinguishing ecological phenomena influenced by humans from those that were not. Here, we describe the Hartley mammoth locality, which dates to 38,900–36,250 cal BP by AMS 14 C analysis of hydroxyproline from bone collagen. We accept the standard view that elaborate stone technology of the Eurasian Upper Paleolithic was introduced into the Americas by arrival of the Native American clade ∼16,000 cal BP. It follows that if older cultural sites exist in the Americas, they might only be diagnosed using nuanced taphonomic approaches. We employed computed tomography (CT and μCT) and other state-of-the-art methods that had not previously been applied to investigating ancient American sites. This revealed multiple lines of taphonomic evidence suggesting that two mammoths were butchered using expedient lithic and bone technology, along with evidence diagnostic of controlled (domestic) fire. That this may be an ancient cultural site is corroborated by independent genetic evidence of two founding populations for humans in the Americas, which has already raised the possibility of a dispersal into the Americas by people of East Asian ancestry that preceded the Native American clade by millennia. The Hartley mammoth locality thus provides a new deep point of chronologic reference for occupation of the Americas and the attainment by humans of a near-global distribution.more » « less
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Abstract Objectives This study aims to characterize the genetic histories of ancient hunter‐gatherer groups in Fuego‐Patagonia (Chile) with distinct Marine, Terrestrial, and Mixed Economy subsistence strategies. Mitochondrial (mtDNA) and Y‐chromosome data were generated to test three hypotheses. H0: All individuals were drawn from the same panmictic population; H1: Terrestrial groups first populated the region and gave rise to highly specialized Marine groups by ~7,500 cal BP; or H2: Marine and Terrestrial groups represent distinct ancestral lineages who migrated independently into the region.
Methods Ancient DNA was extracted from the teeth of 50 Fuegian‐Patagonian individuals dating from 6,895 cal BP to after European arrival, and analyzed alongside other individuals from previous studies. Individuals were assigned to Marine, Terrestrial, and Mixed Economy groups based on archeological context and stable isotope diet inferences, and mtDNA (HVR1/2) and Y‐chromosome variation was analyzed.
Results Endogenous aDNA was obtained from 49/50 (98%) individuals. Haplotype diversities, FSTcomparisons, and exact tests of population differentiation showed that Marine groups were significantly different from Terrestrial groups based on mtDNA (
p < 0.05). No statistically significant differences were found between Terrestrial and Mixed Economy groups. Demographic simulations support models in which Marine groups diverged from the others by ~14,000 cal BP. Y‐chromosome results showed similar patterns but were not statistically significant due to small sample sizes and allelic dropout.Discussion These results support the hypothesis that Marine and Terrestrial economic groups represent distinct ancestral lineages who diverged during the time populations were expanding in the Americas, and may represent independent migrations into Fuego‐Patagonia.
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41467-022-29158-y
