Background
Within the southern end of South America, Western Patagonia arises as an intricate region of channels, fjords, and islands. This region holds evidence of human occupation since ca. 14,500 ...cal years BP, with distinctive maritime adaptations developing around 7300 cal years BP. Historically, three major populations were characterized as part of these maritime traditions: Yámana, Kawésqar, and Chono. The arrival of European population had a profound impact in these communities, affecting their lifestyles, territory and population size and health. The northernmost populations, living within the Chonos Archipelago, were the most affected and the least known communities from Western Patagonia.
Objectives
This research aims to characterize the mitochondrial DNA diversity of ancient individuals from the Chonos Archipelago, evaluating their genetic affinities with other ancient and present‐day populations from Patagonia.
Materials and Methods
A total of 46 individuals from the region were sampled for ancient DNA analysis. Mitochondrial DNA haplogroups were characterized and compared with ancient and present‐day populations from Southern South America.
Results
All individuals from the Chonos Archipelago belong to C and D haplogroups, particularly to C1b, C1b13, D1, D1g, and D4h3a5. As a group, the individuals from Chonos Archipelago lay closer to ancient individuals from Kawésqar territory, immediately south of them. Using mitogenomes, we characterized two new D4h3a5 lineages almost exclusively associated with populations from Western Patagonia.
Discussion
Our results contribute to the understanding of the peopling and human interactions in Western Patagonia, suggesting these unique maritime traditions developed within local populations, genetically associated with earlier terrestrial populations.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Objectives
To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population movement to Santiago (capital of Chile). The ...intensity of migration was quantified using three mitochondrial lineages restricted to South‐Central native groups.
Methods
D‐loop sequences were genotyped in 550 unrelated individuals from San Felipe‐Los Andes (n = 108), Santiago (n = 217), and Concepción (n = 225). Sequence processing, alignment, and haplogroup inference were carried out, and different genetic structure analyses were performed for haplogroup frequencies and D‐loop sequences.
Results
The Native lineages B2i2, C1b13, and D1g were the most frequent haplogroups, especially in Santiago (71.8%). Despite the distance, this city showed a high‐genetic affinity with southern populations, including Concepción (~500 km distant) and native groups, rather than with those from San Felipe‐Los Andes (<100 km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr = −0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepción, and other southern populations. Finally, we found lineages from Concepción acting as ancestral nodes in the northern clade.
Conclusions
Considering the geographic distances from these cities, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north‐to‐south migration during admixture onset in Concepción and in addition, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post‐European contact.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Background: An early recovery of Achilles Tendon Rupture Score (ATRS) and single-leg heel raises after Achilles rupture is a desirable aim to favor the sport return, but is unknown if the patient' ...outcomes could be defined only by the kind of treatment. Objectives: To determine the number of clusters obtained based on ATRS and number of repetitions of single-leg heel rises after 12-weeks of Achilles tenorrhaphy in patients treated with either immediate or traditional rehabilitation treatment, compare the identified clusters of short-term recovery of single-leg by heel rise repetitions and ATRS, compare the proportion of treatment and heel rise ability contained into the clusters, and compare the dimension of the ATRS between clusters. Methods: Twenty-four patients (43.1 + or - 8.2 years-old, BMI 29.2 + or - 3.9 kg/m.sup.2) treated with immediate or traditional rehabilitation were included. The single-leg heel rise repetitions, the single-leg heel rise ability/disability and ATRS patient-reported outcomes were evaluated 12 weeks after Achilles tenorrhaphy. Results: The first cluster had high repetitions in heel rise and ATRS, principally treated by immediate rehabilitation. The second cluster had low repetitions in heel rise and ATRS, principally treated by traditional rehabilitation. The third cluster had the highest repetitions in heel rise but lower ATRS, treated only by immediate rehabilitation. Conclusions: An early recovery of the heel rise capacity could be achieved after Achilles tenorrhaphy and it is more probable to achieve an faster treatment. Keywords: Achilles Tendon, Surgery, Physiotherapy, Calf Muscle Strength
Abstract Ancient DNA analysis has greatly contributed to understanding the population history of several species. In the last 20 years, the field has undergone an important transformation: ...particularly in our species, thousands of ancient genomes have been analyzed worldwide, providing evidence of population movements and interactions through time. However, several researchers have raised concerns about the way the field is developing and how collaborations are being established. In this work, we describe and evaluate the situation in Latin America, considering both what we have learned about population history through paleogenetics and how it has developed in the region.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Over the past decade, genomic data have contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by ...populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 156 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great’s army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Ancient Ancestral South Indians. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.
This study uses community-engaged and multi-disciplinary methods to investigate the interplay between oral and genetic histories in four Southwest Indian populations: Bunt, Kodava, Nair, and Kapla. Combining whole-genome sequencing data with unique oral histories from these populations reveals that oral and genetic histories do not always provide consistent accounts.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Viking smallpox diversity
Humans have a notable capacity to withstand the ravages of infectious diseases. Smallpox killed millions of people but drove Jenner's invention of vaccination, which ...eventually led to the annihilation of this virus, declared in 1980. To investigate the history of smallpox, Mühlemann
et al.
obtained high-throughput shotgun sequencing data from 1867 human remains ranging from >31,000 to 150 years ago (see the Perspective by Alcamí). Thirteen positive samples emerged, 11 of which were northern European Viking Age people (6th to 7th century CE). Although the sequences were patchy and incomplete, four could be used to infer a phylogenetic tree. This showed distinct Viking Age lineages with multiple gene inactivations. The analysis pushes back the date of the earliest variola infection in humans by ∼1000 years and reveals the existence of a previously unknown virus clade.
Science
, this issue p.
eaaw8977
; see also p.
376
Variola virus DNA sequences isolated from ancient human remains reveal the presence of smallpox in 7th-century northern Europe.
INTRODUCTION
Variola virus (VARV), the causative agent of smallpox, is estimated to have killed between 300 million and 500 million people in the 20th century and was responsible for widespread mortality and suffering for at least several preceding centuries. Humans are the only known host of VARV, and smallpox was declared eradicated in 1980. The timeline of the emergence of smallpox in humans is unclear. Based on sequence data up to 360 years old, the most recent common ancestor of VARV has been dated to the 16th or 17th century. This contrasts with written records of possible smallpox infections dating back at least 3000 years and mummified remains suggestive of smallpox dating to 3570 years ago.
RATIONALE
Ancient virus sequences recovered from archaeological remains provide direct molecular evidence of past infections, give detail of genetic changes that have occurred during the evolution of the virus, and can reveal viable virus sequence diversity not currently present in modern viruses. In the case of VARV, ancient sequences may also reduce the gap between the written historical record of possible early smallpox infections and the dating of the oldest available VARV sequences. We therefore screened high-throughput shotgun sequencing data from skeletal and dental remains of 1867 humans living in Eurasia and the Americas between ~31,630 and ~150 years ago for the presence of sequences matching VARV.
RESULTS
VARV sequences were recovered from 13 northern European individuals, including 11 dated to ~600–1050 CE, overlapping the Viking Age, and we reconstructed near-complete VARV genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years. Eleven of the recovered sequences fall into a now-extinct sister clade of the modern VARVs in circulation prior to the eradication of smallpox, while two sequences from the 19th century group with modern VARV. The inferred date of the most recent common ancestor of VARV is ~1700 years ago.
The number of functional genes is generally reduced in orthopoxviruses with narrow host ranges. A comparison of the gene content of the Viking Age sequences shows great contrast with that of modern VARV. Three genes that are active in all modern VARV sequences were inactive over 1000 years ago in some or all ancient VARV. Among 10 genes inactive in modern and Viking Age VARV, the mutations causing the inactivations are different and the genes are predicted to be active in the ancestor of both clades, suggesting parallel evolution. Fourteen genes inactivated in modern VARV are active in some or all of the ancient sequences, eight of which encode known virulence factors or immunomodulators. The active gene counts of the four higher-coverage Viking Age viral genomes provide snapshots from an ~350-year period, showing the reduction of gene content during the evolution of VARV. These genomes support suggestions that orthopoxvirus species derive from a common ancestor containing all genes present in orthopoxviruses today, with the reduction in active gene count conjectured to be the result of long-term adaptation within host species.
CONCLUSION
The Viking Age sequences reported here push the definitive date of the earliest VARV infection in humans back by ~1000 years. These sequences, combined with early written records of VARV epidemics in southern and western Europe, suggest a pan-European presence of smallpox from the late 6th century. The ancient viruses are part of a previously unknown, now-extinct virus clade and were following a genotypic evolutionary path that differs from modern VARV. The reduction in gene content shows that multiple combinations of active genes have led to variola viruses capable of circulating widely within the human population.
Sample locations and genome evolution of Viking Age variola virus.
(Top left) Sample VK533 with dagger, in situ. (Bottom left) Positive sample locations. Higher- and lower-coverage samples have solid and open circles, respectively. (Right) Diverse gene inactivation patterns in the four higher-coverage 600–1000 CE Viking Age sequences, within clade and as compared to sequences from other human VARVs and the phylogenetically nearest animal poxviruses, camelpox and taterapox. Open circles show intact genes, circle colors (independent for each gene) indicate different inactivations. Gene names at the bottom.
Smallpox, one of the most devastating human diseases, killed between 300 million and 500 million people in the 20th century alone. We recovered viral sequences from 13 northern European individuals, including 11 dated to ~600–1050 CE, overlapping the Viking Age, and reconstructed near-complete variola virus genomes for four of them. The samples predate the earliest confirmed smallpox cases by ~1000 years, and the sequences reveal a now-extinct sister clade of the modern variola viruses that were in circulation before the eradication of smallpox. We date the most recent common ancestor of variola virus to ~1700 years ago. Distinct patterns of gene inactivation in the four near-complete sequences show that different evolutionary paths of genotypic host adaptation resulted in variola viruses that circulated widely among humans.
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