New native South American Y chromosome lineages

Ms, Jota; Dr, Lacerda; Sandoval, José R.; Pp, Vieira; Ohasi, Dominique; Je, Santos-Júnior; Acosta, Oscar; Cuellar, Cinthia; Revollo, Susana; Paz‐y‐Miño, César; Fujita, Ricardo; Vallejo, Gustavo Adolfo; Tg, Schurr; Tarazona‐Santos, Eduardo; SDj, Pena; Ayub, Qasim; Tyler‐Smith, Chris; Fr, Santos

doi:10.1038/jhg.2016.26

Cited by 30 publications

(72 citation statements)

References 52 publications

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“…Haplogroup Q has two ancient sub-clades, Q1a-M3 and Q1b-M971, which were likely born somewhere in Siberia before the first dispersal into Americas, and which together capture the overwhelming majority of extant Native American Y chromosomes today (Jota et al 2016; Zegura et al 2004). Besides these two major clades a number of rare sub-clades of Q that are geographically restricted to Europe, Central and South Asia, or Siberia have been identified (Jota et al 2016; Karmin et al 2015; Mallick et al 2016; Poznik et al 2016).…”

Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

“…Besides these two major clades a number of rare sub-clades of Q that are geographically restricted to Europe, Central and South Asia, or Siberia have been identified (Jota et al 2016; Karmin et al 2015; Mallick et al 2016; Poznik et al 2016). Targeted PCR-based sequencing of a region surrounding the Q-M242 and Q1a-M3 markers confirmed the affiliation of the 10.3 KYA On Your Knees Cave Man (OYKCM) to haplogroup Q3-L275 (Kemp et al 2007).…”

Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

“…8). The Saqqaq’s Q2b-B143 lineage was not found to be present in a survey of 1863 haplogroup Q lineages from South America making it unlikely to have been among the initial founding pool of Beringian Y chromosomes (Jota et al 2016). From further ancient DNA analyses, we know that the Palaeo-Eskimos had extremely low genetic diversity, with only a single characteristic mtDNA lineage of haplogroup D2a1 being found in a wide range of sites from Northeast Canada and Greenland dated between 5000 to 700 years before present (Raghavan et al 2014a).…”

Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

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The study of human Y chromosome variation through ancient DNA

Kivisild

2017

Hum Genet

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High throughput sequencing methods have completely transformed the study of human Y chromosome variation by offering a genome-scale view on genetic variation retrieved from ancient human remains in context of a growing number of high coverage whole Y chromosome sequence data from living populations from across the world. The ancient Y chromosome sequences are providing us the first exciting glimpses into the past variation of male-specific compartment of the genome and the opportunity to evaluate models based on previously made inferences from patterns of genetic variation in living populations. Analyses of the ancient Y chromosome sequences are challenging not only because of issues generally related to ancient DNA work, such as DNA damage-induced mutations and low content of endogenous DNA in most human remains, but also because of specific properties of the Y chromosome, such as its highly repetitive nature and high homology with the X chromosome. Shotgun sequencing of uniquely mapping regions of the Y chromosomes to sufficiently high coverage is still challenging and costly in poorly preserved samples. To increase the coverage of specific target SNPs capture-based methods have been developed and used in recent years to generate Y chromosome sequence data from hundreds of prehistoric skeletal remains. Besides the prospects of testing directly as how much genetic change in a given time period has accompanied changes in material culture the sequencing of ancient Y chromosomes allows us also to better understand the rate at which mutations accumulate and get fixed over time. This review considers genome-scale evidence on ancient Y chromosome diversity that has recently started to accumulate in geographic areas favourable to DNA preservation. More specifically the review focuses on examples of regional continuity and change of the Y chromosome haplogroups in North Eurasia and in the New World.

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Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

Section: Ancient Y Chromosomes Of the Native Americansmentioning

confidence: 99%

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The study of human Y chromosome variation through ancient DNA

Kivisild

2017

Hum Genet

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“…Subsequently, additional analysis of 64 Y- SNPs was used to refine several paternal lineages (Jota et al 2016). PCRs for Y-STRs were performed as described (Sandoval et al 2013b).…”

Section: Methodsmentioning

confidence: 99%

Genetic ancestry of families of putative Inka descent

et al. 2018

Self Cite

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This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries. We used single-nucleotide polymorphisms and short tandem repeat (STR) markers of the Y chromosome (Y-STRs), as well as mitochondrial DNA D-loop sequences, to investigate the paternal and maternal descent of the 18 alleged Inka descendants. Two Q-M3* Y-STR clusters descending from different male founders were identified. The first cluster, named AWKI-1, was associated with five families (eight individuals). By contrast, the second cluster, named AWKI-2, was represented by a single individual; AWKI-2 was part of the Q-Z19483 sub-lineage that was likely associated with a recent male expansion in the Andes, which probably occurred during the Late Intermediate Period (1000–1450 AD), overlapping the Inka period. Concerning the maternal descent, different mtDNA lineages associated with each family were identified, suggesting a high maternal gene flow among Andean populations, probably due to changes in the last 1000 years.Electronic supplementary materialThe online version of this article (10.1007/s00438-018-1427-4) contains supplementary material, which is available to authorised users.

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“…The major derived haplogroup Q clade in Western and Central Europe, the North and East of Asia, and America (excluding Eskimoes) is Q‐L54. In America, most individuals who belong to haplogroup Q but are not M3, are identified as the paragroup Q‐L54(xQ‐M3) (Jota et al, ). Recently, it has been established that the majority of individuals within this paragroup are monophyletic to clade Q‐Z780, which reunites most, if not all, the haplogroup Q(xM3) lineages of pre‐Columbian origin (Grugni et al, ).…”

Section: Introductionmentioning

confidence: 99%

Identifying new lineages in the Y chromosome of Colombian Amazon indigenous populations

Rivera-Franco

Braga

Fajardo

et al. 2020

American J Phys Anthropol

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Objectives: The Y chromosome has highly informative markers, such as singlenucleotide polymorphisms (SNPs), that are useful for making historical inferences about the settlement of the Americas. However, the scarcity of these markers has limited their use. This study aims to identify new SNPs and increase the phylogenetic resolution of haplogroup Q for the Americas, mainly focusing on the lineages of the Amazon region. Materials and Methods: Next-generation sequencing was performed on two Y chromosomes belonging to haplogroup Q-M3 using samples with divergent short tandem repeat haplotypes from the Colombian Amazon, and 14 of the new variants identified were selected for characterization in 207 samples of indigenous Colombians belonging to haplogroup Q-M3. Results: This methodology allowed us to establish nine new lineages within Q-M3, including its paragroups. The most basal lineages were predominant in communities of Andean origin, such as the Embera-Katio, the Nasas, and the Pastos. In contrast, the most distal lineages were restricted to inhabitants of the Amazon region of Vaupés. Discussion: The SNPs reported here advance the development of subhaplogroups of Q-M3 with a higher level of phylogenetic resolution than has been previously reported, which allowed the differentiation between populations that inhabit two regions of Vaupes area: the Pirá-Paraná region and the upper and middle sections of the Vaupés River, and the region encompassing the Papurí River and the lower Vaupés. They are very useful for the microevolutionary analysis of the Amerindian populations of Colombia and of the Americas.

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New native South American Y chromosome lineages

Cited by 30 publications

References 52 publications

The study of human Y chromosome variation through ancient DNA

The study of human Y chromosome variation through ancient DNA

Genetic ancestry of families of putative Inka descent

Identifying new lineages in the Y chromosome of Colombian Amazon indigenous populations

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