Archaeogenetics, Ancient Genomics, Ancient DNA, Palaeontology, Zooarchaeology

Canids Evolution_Genomics_Palaeontology

Ancestral remains should be regarded not as “artifacts” but as human relatives who deserve respect

A genomic view of the peopling of the Americas

Pontus Skoglund and David Reich

Peopling of the Americas as inferred from ancient genomics

Abstract excerpt: In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas.

Genomes Reveal Humanity’s Journey into the Americas

DNA has upended neat and tidy accounts of the peopling of the American continents
By Jennifer Raff - An anthropological geneticist at the University of Kansas. She studies genomes of contemporary humans and their ancestors for insights into prehistory, with a focus on the initial peopling of North America.

Phylogenetics

Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation

Jennifer Raff, Deborah Bolnick 2015

The paper critically evaluates the hypothesis that mitochondrial haplogroup X indicates ancient trans-Atlantic migration to the Americas. It examines genetic, archaeological, and paleoclimate evidence to argue against this model, maintaining that a Beringian migration model remains the most robust explanation for the ancestry of Native Americans. Through a detailed analysis of mitochondrial genetic data, the authors conclude that there is no credible support for pre-Columbian trans-Atlantic gene flow.

Baby teeth found at the Yana Rhinoceros Horn Site in Russia

These Ice Age Humans Somehow Survived North of the Arctic Circle Archaeologists uncover ancient human tools, mammoth bones and crafting supplies that show Yana society was king of the north.
The teeth came from two boys who belonged to a previously unknown population, now called the Ancient North Siberians.

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia

Jennifer Raff, Ben A. Potter, Dennis H. O’Rourke 2015

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka). Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans. As such, USR1 represents a distinct Ancient Beringian population.

The population history of northeastern Siberia since the Pleistocene

Sikora, Pitulko et al_2019 published in Nature
Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-yearold (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found.
...The Yana RHS human remains represent the earliest direct evidence of human presence in northeastern Siberia, a population we refer to as
“Ancient North Siberians” (ANS). Both Yana RHS individuals were unrelated males, and belong to mitochondrial haplogroup U, predominant among ancient West Eurasian hunter-gatherers, and to Y chromosome haplogroup P1, ancestral to haplogroups Q and R, which are widespread among present-day Eurasians and Native Americans.

...We next investigated how Yana relates to another enigmatic ancient Siberian population, the “Ancestral North Eurasians” (ANE) represented by the 24 kya Mal’ta individual from the Lake Baikal region, from which Native Americans were shown to derive ~40% of their ancestry.

Ancient Paleosiberians and the origins of Native Americans
Following the occupation at Yana RHS, there is an absence of archaeological sites in northeastern Siberia that lasts until the end of the LGM, when groups bearing a very distinctive stone tool technology appear in the region (~18 kya). It was within that intervening period that the ancestral Native American population emerged15,41, but prior to this study no genomes from individuals dating from this time period had been recovered in northeastern Siberia. We resolve this absence with the 9.8 kya Kolyma1 individual, representing a group we term “Ancient Paleosiberians” (AP). Our results indicate that AP are derived from a first major genetic shift observed in the region..

We then estimated the demographic parameters of population history models including Kolyma1 as well as the recently identified Ancient Beringians41 (Upward Sun River 1 [USR1]) and present-day Native Americans (Karitiana). We find that the ancestors of Kolyma1, Ancient Beringians and Native Americans diverged ~30 kya (26.8-36.4) from present-day East Asians (Han), in agreement with previous results41, with a subsequent divergence of Kolyma1 from the Ancient Beringian / Native American ancestral population at ~24 kya (20.9-27.9)

..results from the admixture analyses suggest differences in the ANS ancestry proportions between Kolyma1 and USR1, thereby favouring the two-independent pulses model. Kolyma1 thus represents the closest relative to the ancestral Native American population in northeastern Siberia known to date.

We find that the first inhabitants of northeastern Siberia were not the ancestors of either Native Americans or modern Siberians. Instead, they were the earliest descendants of a deeply diverged early Eurasian lineage that apart from Yana is currently only represented by two ancient individuals from central Siberia (Mal’ta and Afontova Gora), widely separated from northeastern Siberia. The finding that these early groups were so highly distinct, and diverged so soon after 38 kya, suggests that the combined ANS/ANE lineages are much more complex than previously supposed. Although represented by just a few individuals, and lacking direct descendants, traces of their presence are recorded in ancient and modern genomes across northern Eurasia and the Americas. One of these groups, the “Ancient Paleosiberians”, likely also once had a wide geographic distribution across northern Eurasia Its genetic legacy among present-day Siberians is more limited, restricted to groups in northeastern Siberia but also the Americas. Nonetheless, this distribution implies that the majority of Native American genetic ancestry likely originated in northeastern Siberia, rather than south-central Siberia, as inferred from modern mitochondrial and Y chromosome DNA54. The Neosiberians occupying much of the range previously inhabited by ANS and AP, represent a more recent arrival that originated further south. The replacement processes we have revealed for the northeastern portion of Siberia are mirrored in far western Eurasia by the regional replacement of the Saami people in the Late Holocene, suggesting similar processes likely took place in many other parts of the northern hemisphere.

Peopling the Americas: Not “Out of Japan”

PaleoAmerica A journal of early human migration and dispersal
Abstract excerpt:
A widely accepted model for the peopling of the Americas postulates a source population in the Northeast Asian maritime region, which includes northern Japan. The model is based on similarities in stone artifacts (stemmed points) found in North American sites dating as early as 15,000 years ago and those of comparable age in Japan and neighboring regions of Northeast Asia. Here we show, on the basis of data and analyses in biological anthropology, that the people who made stemmed points in northern Japan (labeled “Incipient Jomon” in the archaeological literature) represent an unlikely source population for the indigenous peoples of the Western Hemisphere.

Anthropologists debunk popular theory that Native Americans originated from Japan

Researchers analyzed over 1,500 dentitions and found no evidence that Native Americans came from Japan

Late Pleistocene exploration and settlement of the Americas by modern humans

image: Page-Ladson site, Florida, ~14,550 years ago
The ancestral history of the earliest peoples in the Americas will be realized as genetic knowledge from living populations and ancient individuals is combined with archaeological, geological, ethnographic, and oral records. This will require scientists and Indigenous peoples working as partners to uncover the past.

Shuká Káa (Tlingit: Man Ahead Of Us) is given a final resting place after 10,300 years

(Observations During the Ceremony: Sept. 25-27, 2008) - Mim Dixon -
January 2009 A young man who had experienced periods of hunger and probably died hunting a bear was finally laid to rest by the Tlingit people of Prince of Wales Island in Southeast Alaska on Thursday, September 25, 2008. He died 10,300 years ago.

On Your Knees Cave (49-PET-408) is an archaeological site located in southeastern Alaska

Shuká Káa (Tlingit: Man Ahead Of Us)

The Discovery of Ancient Human Remains in Southeast Alaska

Inclusive Archaeology at "On Your Knees Cave" in the Tongass National Forest - Leads to Lasting Partnerships

Anzick-1

Anzick-1 was a young (1–2 years old) Paleoindian child whose remains were found in south central Montana, United States, in 1968. He has been dated to 12,990–12,840 years Before Present.[1] The child was found with more than 115 tools made of stone and antlers and dusted with red ocher, suggesting a deliberate burial.[2] Anzick-1 is the only human whose remains are associated with the Clovis culture, and is the first ancient Native American genome to be fully sequenced.[3]

Reassessing the chronology of the archaeological site of Anzick

Abstract excerpt:
Paleogenomic data obtained for Anzick-1 suggest that this individual is (i) genetically closer to modern Native Americans than any other group, (ii) shares genetic information with the Upper Paleolithic Siberian Mal’ta population, and (iii) shows a closer affinity to Central and South American indigenous groups than northern counterparts—likely indicating a divergence in Native American populations that predates Anzick-1 (11). Considering the geographic location and antiquity of the burial, these findings hold important spatiotemporal implications that further add to the complexity of the peopling process and render Anzick one of the most important archaeological sites in First Americans research.

Kennewick Man

Kennewick Man or Ancient One was a Native American man who lived during the early Holocene, whose skeletal remains were found washed out on a bank of the Columbia River in Kennewick, Washington, on July 28, 1996. Radiocarbon tests show the man lived about 8,400 to 8,690 years BP [Before Present].

The ancestry and affiliations of Kennewick Man

Abstract excerpt: We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man.

Genome of the Ancient One (a.k.a. Kennewick Man)

Media Response, by Jennifer Raff

A Brief History and Perspective on Spirit Cave, Nevada

2018

DNA of world's oldest natural mummy unlocks secrets of Ice Age tribes in the Americas

Canids

Subjects: Evolution_Genomics_Palaeontology
Keywords: Canis Lupis Familiaris_Palaeodiet_Palaeogenetics_Pre-European Contact Dog (PCD)

Early holocene dog bones from the Zhokhov Site (East Siberian Arctic) and the question of the reliability of identification of early canis familiaris from archaeological excavations

Highlights
• Early Holocene-aged faunal remains of domestic dogs are analyzed. • Two craniomorphology indices serve as reliable dog domestication criteria. • Sled dog breed existed in the Arctic as early as 9000 years ago. • Sled dogs could have been used in Siberia starting around 15,000 years ago.

Karst caves in Haida Gwaii: Archaeology and paleontology at the Pleistocene-Holocene transition

Karst cave investigations in the south of Haida Gwaii have opened a small window on human and paleontological components of the early post-glacial landscape. At three cave locations (K1, Gaadu Din 1 and Gaadu Din 2) our investigations recovered a paleontological record extending from ca. 13,400 to 11,000 years ago

Domestic dog remains with a direct radiocarbon age of 13,100 years ago are the earliest indicator of human presence from the cave assemblages, and are also the earliest known domestic dog remains reported on in the Americas.

An early dog from southeast Alaska supports a coastal route for the first dog migration into the Americas

A recent genetic study demonstrated that these early pre-European contact dogs (PCDs) were not domesticated from North American wolves, having instead diverged from an ancestor shared with an approximately 9000-year-old dog population that inhabited Zhokhov Island in Eastern Siberia 3. Results (a) Radiocarbon calibration and stable isotope d13C The radiocarbon dating of PP-00128 returned a date of 9020 ± 85 14C years BP, with a calibrated date ranging from 10 412 to 9888 2-sigma cal years BP and a median date of 10 150 ± 262 years BP. Hence, this date is slightly older, by about 240 years, than the to-date earliest confirmed New World domestic dog remains, which are dated to 8840 ± 80 14C years BP with a calibrated median date of 9910 ± 280 years BP [13]. PP-00128 had a d13C value equal to -14.1‰. Compared to data from numerous terrestrial and marine mammals [13,52–60] and salmon (a common food resource in the region where PP-00128 was found), PP-00128 has a d13C at the higher end of the d13C spectrum, similar to marine mammals, particularly polar bears (electronic supplementary material, figure S1). This result indicates that the diet of this ancient dog was predominantly marine, with a value similar to ancient dogs from Nunalleq, a precontact Yup'ik archaeological site in coastal Southwestern Alaska [54].

Conclusion excerpt: ...Future nuclear genome analyses of precontact dogs, including PP-00128, will permit more complete insights of the fate of PCDs.

Evidence of the earliest domestic dogs in the Americas

Dog domestication and the dual dispersal of people and dogs into the Americas

Abstract excerpt:
by comparing population genetic results of humans and dogs from Siberia, Beringia, and North America, we show that there is a close correlation in the movement and divergences of their respective lineages. This evidence places constraints on when and where dog domestication took place. Most significantly, it suggests that dogs were domesticated in Siberia by ~23,000 y ago, possibly while both people and wolves were isolated during the harsh climate of the Last Glacial Maximum. Dogs then accompanied the first people into the Americas and traveled with them as humans rapidly dispersed into the continent beginning ~15,000 y ago.
Introduction excerpt: Canids were especially significant in southern British Columbia, where two sizes of dogs occur, and the smaller ‘wool’ dogs were particularly abundant.

Domestic dogs and wild canids on the Northwest Coast of North America: Animal husbandry in a region without agriculture?

Highlight excerpts: Canids frequently occur in archaeological assemblages across the Northwest Coast.
Canid abundance is highest in areas where small dogs were bred for wool production. • Domestic dogs occupy a large role in Northwest Coast social and economic practices.

The history of Coast Salish “woolly dogs” revealed by ancient genomics and Indigenous Knowledge

Abstract
Ancestral Coast Salish societies in the Pacific Northwest kept long-haired “woolly dogs” that were bred and cared for over millennia. However, the dog wool–weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from “Mutton,” collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Summary: A 19th century dog genome and Traditional Knowledge illuminate the life, history, and decline of Coast Salish woolly dogs

Mary Adams and her dog Jumbo_Port Madison Reservation 1920

Photograph

Dire wolves were the last of an ancient New World canid lineage

Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

Mummy of a juvenile sabre-toothed cat Homotherium latidens from the Upper Pleistocene of Siberia

Additional reading:

Who We Are and How We Got Here

2018 book on the contribution of genome-wide ancient DNA research to human population genetics by the geneticist David Reich. He describes discoveries made by his group and others, based on analysis and comparison of ancient and modern DNA from human populations around the world. Central to these is the finding that almost all human populations are mixtures resulting from multiple population migrations and gene flow.

Nicholas Wade and Race: Building a Scientific Façade

By Jennifer Raff, Contributor

...Nicholas Wade [author of "A Troublesome Inheritance: Genes, Race and Human History"] can't justify his first and primary point: his claim that the human racial groups we recognize today culturally are scientifically meaningful, discrete biological divisions of humans. This claim provides a direct basis for the whole second half of the book, in which he makes speculative arguments about national character.

See also: David Reich's book, "Who we are and how we got here" Ch.11 The Genomics of Race and Identity - sub section 4: The Genome Revolution’s Insight

Origin: A Genetic History of the Americas

by Jennifer Raff (Author)

Native American DNA: Tribal Belonging and the False Promise of Genetic Science

Because today’s DNA testing seems so compelling and powerful, increasing numbers of Native Americans have begun to believe their own metaphors: “in our blood” is giving way to “in our DNA.” In Native American DNA, Kim TallBear shows how Native American claims to land, resources, and sovereignty that have taken generations to ratify may be seriously—and permanently—undermined.

First Peoples in a New World: Populating Ice Age America

by David J. Meltzer (Author)

The ‘People of the British Isles’ project and Viking settlement in England

Introduction excerpt:
The recently concluded ‘People of the British Isles’ project combined large-scale, local DNA sampling with innovative data analysis to generate a survey of the genetic structure of Britain in unprecedented detail; the results were presented by Leslie and colleagues in 2015. Comparing clusters of genetic variation within Britain with DNA samples from Continental Europe, the study elucidated past immigration events via the identification and dating of historic admixture episodes

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