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.

Kawéskar, (D) Huilliche, and (E) Pehuenche) modeled in (maximum |Z-score| = 3.3, 3.0, 3.0, and 2.8, respectively; with transversions only the |Z-scores| are 3.0, 2.9, 3.3, and 3.1, respectively). The maximum |Z-score| is 2.8 on this SNP set without the modern Patagonians added in, and 2.8 with only transversions. We could not model the modern Patagonian groups in the same graph due to attractions of the groups with each other, which could be due to artifactual modern vs. ancient DNA bias or recent gene flow between the different groups. Z-scores were determined from standard errors obtained from jackknife resampling. Selk'nam_500BP

Supplementary Note 1. Additional Background on Southern Patagonia:
From a material culture point of view, the shared reliance on marine resources of the two westernmost groups and on terrestrial resources of the two most northeastern groups could potentially be correlated to shared ancestry. The affinities of the Haush, whose unique food procurement strategy relying both on terrestrial resources like the Selk'nam who flank them to the north along the coast, and on marine resources like the Yámana who flank them to the west, has been of particular interest 1 .
Ethnographers have documented shared symbolic systems between the northern Selk'nam and Haush-for example their joint celebration of male initiation into adulthood (the Hain) 2 -suggesting that the Haush could be viewed as an eastern subgroup of a broader entity that also includes the Selk'nam, with no similar cultural relationship to the western Yámana 3 . If the Haush are best seen as a subgroup of a larger entity also including the Selk'nam, then it would be plausible for them not to be admixed with Yámana-related ancestry.

Supplementary Note 2. Details about analyzed individuals.
We generated genome-wide data from skeletal remains of 20 ancient individuals:  13 . Before her death, Dr. Chapman asked RAG to guarantee the return of the skeletons to the province of Tierra del Fuego, a request he fulfilled. The other human remains that belong to the MFM were found by chance and/or amateur excavations during the 70s and 80s. As part of the research program led by RAG, specialized work was done to improve the conservation and storage conditions of the MFM 14 , and the current digital documentary database of the MFM was also generated 15 . The individuals from the CADIC were excavated by MS and FS, who were called when human remains were found 16 . In these cases, they performed rescue archeology 17 , which aims to preserve heritage that would have been lost due to environmental disturbance 18

Description of Archaeological Sites:
A summary of all information obtained for genetic or radiocarbon dating, including genetic sex and carbon and nitrogen isotope data is presented in Supplementary Data File 1. One sample (I12358) analyzed in this study is from an adult male (18-23 years old) from this site.

Laguna Toro (Argentina
It is a simple burial that was found 30 m from the top of the cliff and 50 cm depth, the last 10 to 15 cm of which were formed by sterile earth and the rest with an anthropic origin, almost entirely covered by a limestone slab. The skeleton was almost complete, in an extended dorsal decubitus position, with the head to the north and the face upwards. It is a primary burial and it was not accompanied by artifacts. Some faunal remains also came from this same site. A stable isotope value of δ 13 C(col)= −12.3‰ was obtained in association with the date 13

Supplementary Note 4. Description of main findings in Spanish
Una mirada genética sobre la historia de las poblaciones de Patagonia Austral En este estudio encontramos que dos de los individuos más antiguos de la región estudiados hasta el momento (que tienen una antigüedad de entre 5800 y 6600 años) son muy similares genéticamente a pesar de estar asociados a distintas estrategias de aprovechamiento de los recursos. Uno fue hallado en la costa del Estrecho de Magallanes en la península de Brunswick (Chile) y está asociado al consumo de recursos marítimos y el otro fue hallado en el norte de la Isla Grande de Tierra del Fuego (Argentina) y está asociado al consumo de recursos terrestres. Este hallazgo nos hace pensar que las distintas estrategias de adaptación no están asociadas a poblaciones diferentes, sino que fue una misma población que llegó a la región y que luego implementó distintas maneras de aprovechar los recursos, según la zona donde se ubicó.
Según los datos analizados, en los individuos de los últimos dos milenios, se detectan dos migraciones independientes. Una que habría llegado por la vertiente pacífica hace entre 4700 y 2000 años, asociada a los grupos canoeros y que se encuentra representada en los grupos de los Archipiélagos Occidentales y del Canal de Beagle. Y la otra que habría llegado alrededor de 2000 años antes del presente por la vertiente atlántica desde el centro de Chile y que se encuentra representada en todas las poblaciones de la región. Estas migraciones pueden asociarse, respectivamente, a ciertos cambios tecnológicos, tales como el abandono del uso de la obsidiana verde en los archipiélagos occidentales y la aparición de un nuevo tipo de punta de proyectil en el sur del continente y el norte de Tierra del Fuego.
En cuanto a las poblaciones de la península Mitre de los últimos 400 años, se encontró que las mismas son descendientes de poblaciones del norte de la Isla Grande de Tierra del Fuego y del Canal de Beagle. Este proceso de mestizaje habría ocurrido hace unos 1500 años aproximadamente. Y la combinación genética se corresponde con las características tecnológicas de las poblaciones de esta región, que incluyen similitudes con sus vecinos tanto del norte como del sur de la isla.
Se encontró también que entre los 2200 y 1200 años antes del presente, todos los grupos del sur de Patagonia experimentaron un proceso de mestizaje con sus vecinos más cercanos, lo cual generó similitudes genéticas entre los individuos que se correlacionan con la distancia a lo largo de la línea de costa.
Por último, en los casos en los que se cuenta con información genómica de representantes actuales de las comunidades originarias (Kaweskar y Yaghanes de Chile), se pudo determinar que existe una continuidad genética entre los individuos antiguos de los últimos dos milenios y los individuos que viven actualmente en el mismo territorio. When collagen samples were too poorly preserved, they were pre-treated using a modified XAD process 37 . These samples were cleaned using hand tools and sectioned with disposable Dremel cut-off wheels and then demineralized in 0.5 N HCl for 2-3 days at 5°C. The demineralized collagen pseudomorph was then gelatinized at 60°C in 1-2 mL 0.01 N HCl for eight to ten hours. Sample gelatin was pipetted into a pre-cleaned 10 mL disposable syringe with an attached 0.45 mm Millex Durapore PVDF filter (pre-cleaned with methanol and Nanopure H2O) and put into a thick-walled culture tube. The filtered solution was lyophilized and the percent gelatinization and yield were determined by weight. The sample gelatin was then hydrolyzed in 2 mL 6 N HCl for 22 h at 110°C. Supelco ENVI-Chrom® SPE (Solid Phase Extraction; Sigma-Aldrich) columns were prepped with 2 washes of HCl (2 mL) and rinsed with 10 mL DI H2O. The SPE Column was equilibrated with 50 mL 6 N HCl with a 0.45 mm Millex Durapore filter attached, and the washings were discarded. 2 mL collagen hydrolyzate as HCl was pipetted onto the SPE column and driven with an additional 10 mL 6 N HCl dropwise with the syringe into a 20 mm culture tube. The hydrolyzate was finally dried into a viscous syrup by passing UHP N2 gas over the sample heated at 50°C for ~12 h.

Supplementary Note 5. Description of Radiocarbon Dating Methodology
Carbon and nitrogen concentrations and stable isotope ratios of the XAD amino acid samples were measured with a Costech elemental analyzer (ECS 4010) and Thermo DeltaPlus analyzer 38 .
Sample quality was evaluated by % crude gelatin yield, %C, %N and C/N ratios before AMS 14 C dating.
Samples (~2.1 mg) were then combusted for 3 h at 900°C in vacuum-sealed quartz tubes with CuO and Ag wires. Sample CO2 was reduced to graphite at 550°C using H2 and a Fe catalyst, with reaction water drawn off with Mg(ClO4)2. Graphite samples were pressed into targets in Al boats and loaded on a target wheel with OX-1 (oxalic acid) standards, known-age bone secondaries, and a 14 C-free Pleistocene whale blank. Samples were cleaned to remove adhering residues, and then acid-etched to remove secondary carbonate prior to hydrolysis. After rinsing in Nanopure H2O and drying at 50°C, samples were evaluated for the integrity of their enamel using Fourier Transform Infared Spectroscopy. Samples and standards were placed then in BD Vacutainer septum-stopper vials, and digested with 85% orthophosphoric acid.
The evolved CO2 was graphitized as above and the 14 C measurements were made on a modified National Electronics Corporation compact spectrometer with a 0.5 MV accelerator (NEC 1.5SDH-1).