Reconstructing the Deep Population History of Central and South America

Posth, Cosimo; Nakatsuka, Nathan; Lazaridis, Iosif; Skoglund, Pontus; Mallick, Swapan; Lamnidis, Thiseas Christos; Rohland, Nadin; Nägele, Kathrin; Adamski, Nicole; Bertolini, Emilie; Broomandkhoshbacht, Nasreen; Cooper, Alan; Culleton, Brendan J.; Ferraz, Tiago; Ferry, Matthew; Furtwängler, Anja; Haak, Wolfgang; Harkins, Kelly M.; Harper, Thomas K.; Hünemeier, Tábita; Lawson, Ann Marie; Llamas, Bastien; Michel, Megan; Nelson, Elizabeth A.; Oppenheimer, Jonas; Patterson, Nick; Schiffels, Stephan; Sedig, Jakob; Stewardson, Kristin; Talamo, Sahra; Wang, Chuan‐Chao; Hublin, Jean Jacques; Hübbe, Mark; Harvati, Katerina; Delaunay, A; Beier, Judith; Francken, Michael; Kaulicke, Peter; Reyes-Centeno, Hugo; Rademaker, Kurt; Trask, Willa R.; Robinson, Mark; Gutierrez, Said M.; Prufer, Keith M.; Salazar‐García, Domingo C.; Chim, Eliane Nunes; Gomes, Lisiane Müller Plumm; Alves, Marcony Lopes; Líryo, Andersen; Inglez, Mariana; Oliveira, Rodrigo Elias; Bernardo, Danilo Vicensotto; Barioni, Alberto; Wesolowski, Verônica; Scheifler, Nahuel A.; Rivera, Mario A.; Plens, Cláudia Regina; Messineo, Pablo G.; Figuti, Levy; Corach, Daniel; Scabuzzo, Clara; Eggers, Sabine; DeBlasis, Paulo; Reindel, Markus; Méndez, César; Politis, Gustavo G.; Tomasto-Cagigao, Elsa; Kennett, Douglas J.; Strauss, André; Fehren‐Schmitz, Lars; Krause, Johannes; Reich, David

doi:10.1016/j.cell.2018.10.027

Cited by 269 publications

(338 citation statements)

References 76 publications

(161 reference statements)

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“…To evaluate whether the improvements seen in the previous section mitigate reference bias in real ancient DNA data, we selected 34 previously published ancient DNA samples (Table 1), including Iron Age, Roman, and Anglo-Saxon period samples shotgun sequenced to low-medium coverage [20,21], high-coverage Yamnaya and Botai culture individuals [22], and target captured samples from South America [23]. These are representative of the different types of data produced in the field of aDNA, as they are of variable genomic coverage, they were generated as part of SNP array target capture or whole-genome shotgun sequencing experiments, and were subject to different enzymatic treatments.…”

Section: Aligning Ancient Samples To the 1000gp Variation Graphmentioning

confidence: 99%

“…Adapter trimming was done with AdapterRemoval [29] for [22] and [30] for [20]. Unaligned fastq data from the other two datasets [21,23] were already provided with trimmed adapters. We aligned trimmed reads to the human linear reference genome (hs37d5) using bwa aln [25] with parameters -l1024 -n 0.02 [31], keeping bases with quality above or equal to 15.…”

Section: Datasets and Sequence Data Processingmentioning

confidence: 99%

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Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

Martiniano

Garrison

Jones

et al. 2019

Preprint

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Background: During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA sequencing reads are short, single-ended and frequently mutated by post-mortem chemical modifications. All these features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Recently, alternative approaches for read mapping and genetic variation analysis have been developed that replace the linear reference by a variation graph which includes all the alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for ancient DNA. Results: We used vg to align multiple previously published aDNA samples to a variation graph containing 1000 Genome Project variants, and compared these with the same data aligned with bwa to the human linear reference genome. We show that use of vg leads to a much more balanced allelic representation at polymorphic sites and better variant detection in comparison with bwa, especially in the presence of post-mortem changes, effectively removing reference bias. A recently published approach that filters bwa alignments using modified reads also removes bias, but has lower sensitivity than vg. Conclusions: Our findings demonstrate that aligning aDNA sequences to variation graphs allows recovering a higher fraction of non-reference variation and effectively mitigates the impact of reference bias in population genetics analyses using aDNA, while retaining mapping sensitivity.

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Section: Aligning Ancient Samples To the 1000gp Variation Graphmentioning

confidence: 99%

Section: Datasets and Sequence Data Processingmentioning

confidence: 99%

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

Martiniano

Garrison

Jones

et al. 2019

Preprint

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“…On the other hand, the D1 haplotypes network (Figure ) shows that D1 and D1g are the most shared, frequent, and well‐distributed haplogroups in southern South America, mainly among extant and pre‐Hispanic individuals in Central‐Northern Patagonia. Interestingly, a D1g lineage with nodal mutations was described at the Arroyo Seco 2 archaeological site (Posth et al, ), which suggests a certain continuity of this subhaplogroup in the region from about 7,700 YBP to the present. Particularly, the D1g4 lineage, characterized by transition 16290T and identified in one of the Paso Alsina 1 individuals, is shared with an extant individual from Central‐Southern Patagonia (de Saint Pierre, Bravi, et al, ; de Saint Pierre, Gandini, et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Genetic analysis of contemporary and past human groups has become increasingly important to improve understanding of the evolutionary history of human settlement in southern South America (Arencibia et al, ; Bobillo et al, ; Crespo, Favier Dubois, Russo, Lanata, & Dejean, ; de la Fuente et al, , ; de Saint Pierre et al, , ; García‐Bour et al, ; Llamas et al, ; Moraga et al, ; Motti et al, ; Parolin et al, ; Perez et al, ; Posth et al, ). The most widely used genetic marker is mitochondrial DNA (mtDNA), which indicates the maternal lineage of individuals.…”

Section: Introductionmentioning

confidence: 99%

“…YBP) (Borrero, 2016;Politis, 2014;Politis, Gutiérrez, Rafuse, & Blasi, 2016;Steele & Politis, 2009). Nevertheless, little is known about the molecular diversity and microevolutionary processes that took place in Pampa (e.g., Llamas et al, 2016;Posth et al, 2018) and Patagonia (e.g., Arencibia et al, 2019;Crespo, Favier Dubois, et al, 2017;Crespo, Russo, Hajduk, Lanata, & Dejean, 2017;Parolin et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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First analysis of mitochondrial lineages from the eastern Pampa–Patagonia transition during the final late Holocene

Postillone

Martínez

Flensborg

et al. 2020

American J Phys Anthropol

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Objective Studies on population genetics have become highly relevant for understanding the evolutionary history of human settlement in southern South America. The eastern Pampa–Patagonia transition is an area that stands out due to its complex population dynamics, especially during the last about 1,000 years BP. The aim of this work is to characterize the maternal lineages of individuals buried in the Paso Alsina 1 archaeological site (ca. 500 years BP) through the analysis of mitochondrial genetic variability, in order to discuss the population models previously proposed for the southern cone of South America. Methods Mitochondrial HyperVariable Region I sequences were analyzed on teeth belonging to 20 adult individuals. Statistical analyses were carried out to compare the interpopulation and intrapopulation molecular variability between the results obtained in this work and those previously published data from pre‐Hispanic human groups. D1 haplotype network was constructed drawing from data on ancient and extant population group samples. Results Thirteen sequences (65%) were obtained from the 20 analyzed samples. The maternal lineages or subhaplogroups identified were D1g (69.24%), C1 (15.38%), D1 (7.69%), and D1j (7.69%). There was low haplotype variability within the site; some individuals could be matrilineally related. Discussion The subhaplogroups registered in Paso Alsina 1 site are in accordance with those reported for ancient and contemporary Patagonian populations. The results suggest that an initial nucleus of individuals carrying mostly subhaplogroup D1g settled in northern Patagonia, from which local diversity of this matrilineage could have arisen. The existence of gene flow in the final late Holocene with groups from Northern Andean Patagonia, as well as from Central Argentina, is proposed. The D1j variant probably developed in the latter region.

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Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre‐Hispanic populations from Central Argentina

Nores

Tavella

Fabra

et al. 2022

American J Hum Biol

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Objectives The study of the ancient populations of Central Argentina has a crucial importance for our understanding of the evolutionary processes in the Southern Cone of South America, given its geographic position as a crossroads. Therefore, the aim of this study is to evaluate the temporal and geographical patterns of genetic variation among the groups that inhabited the current territory of Córdoba Province during the Middle and Late Holocene. Methods We analyzed the mitochondrial haplogroups of 74 individuals and 46 Hypervariable Region I (HVR‐I) sequences, both novel and previously reported, from archeological populations of the eastern Plains and western Sierras regions of the province of Córdoba. The HVR‐I sequences were also compared with other ancient groups from Argentina and with present‐day populations from Central Argentina by pairwise distance analysis and identification of shared haplotypes. Results Significant differences in haplogroup and haplotype distributions between the two geographical regions were found. Sierras showed genetic affinities with certain ancient populations of Northwestern Argentina, while Plains resembled its neighbors from Santiago del Estero Province and the Pampas region. We did not observe genetic differences among the pre 1200 and post 1200 yBP temporal subsets of individuals defined by the emergence of horticulture, considering both geographical samples jointly. Conclusions The observed patterns of geographical heterogeneity could indicate the existence of biologically distinct populations inhabiting the mountainous region and the eastern plains of Córdoba Province in pre‐Hispanic times. Maternal lineages analyses support a scenario of local evolution with great temporal depth in Central Argentina, with continuity until the present.

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Reconstructing the Deep Population History of Central and South America

Cited by 269 publications

References 76 publications

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

First analysis of mitochondrial lineages from the eastern Pampa–Patagonia transition during the final late Holocene

Ancient DNA analysis reveals temporal and geographical patterns of mitochondrial diversity in pre‐Hispanic populations from Central Argentina

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