Human Y‐chromosome SNP characterization by multiplex amplified product‐length polymorphism analysis

Medina, Laura Smeldy Jurado; Schwab, Marisol; Costantino, M. Leticia Bravi; Barreto, Guillermo; Bailliet, Graciela

doi:10.1002/elps.201400020

Cited by 9 publications

(6 citation statements)

References 19 publications

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“…In a preliminary screening, the Y-chromosome haplogroups were estimated by means of a Bayesian method executed by the Haplogroup Predictor (Athey, 2006). To confirm the geographical origin assignment, the male samples were screened for 15 single Y-SNPs diagnostic for each haplogroup described by Jurado Medina et al (2014) including Y-SNPs M242, M346, and M3, which defined the Native American haplogroup Q1b1a1a (Q-M3) according to ISOGG terminology (https://isogg.org/tree/index.html).…”

Section: Y-chromosome Dnamentioning

confidence: 99%

Uniparental origins of the admixed Argentine Patagonia

Tamburrini

Pierre

Bravi

et al. 2021

American J Hum Biol

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Objectives: We aimed to contribute to the understanding of the ancient geographic origins of the uniparentally inherited markers in modern admixed Argentinian populations from central Patagonia with new information provided for the city of Trelew. We attempted to highlight the importance of combining different genetic markers when studying population history. Methods: The mtDNA control region sequence was typified in 89 individuals and 12 Y-STR and 15 Y-SNP loci were analyzed in 66 males. With these data, analysis of molecular variance and Network analyses were carried out. We exhaustively compared the modern data with ancient mtDNA information.Finally, we tested the differences in continental origins estimated by uniparental and previously published biparental markers.Results: Native American mtDNAs (53.9%) increased when maternal ancestors were born in the northern (81.8%) and southern (58.5%) regions of Argentina or in Chile (77.8%). Population substructure was only observed for Y-chromosome haplotypes. Some mtDNA haplogroups have been present in the area for at least ca. 2762-2430 and ca. 500 (D1g and D1g4 haplogroups) and ca. 6736 and ca. 6620 (C1b and C1c haplogroups) years, respectively. In contrast, haplogroups B2i2 and C1b13, frequent in modern Patagonia populations, had not been found in previous ancient DNA studies of the region. Conclusions:The results suggest that Native American ancestry is well preserved in the region. Trelew samples had characteristic native mtDNA haplogroups previously described in Chilean and Argentine Patagonian populations, but not observed in ancient samples until now. These findings support the idea that these lineages have a recent regional origin. Finally, the estimated proportions of continental ancestry depend on the genetic marker analyzed.

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Section: Y-chromosome Dnamentioning

confidence: 99%

Uniparental origins of the admixed Argentine Patagonia

Tamburrini

Pierre

Bravi

et al. 2021

American J Hum Biol

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“…The DNA samples were extracted from 15 ml of blood through the “salting out” method [ 139 ]. Haplogroup determination was made by Polymerase Chain Reaction-Product Length Polymorphism (PCR-APLP) designed by Umetsu et al [ 140 , 141 ] and adapted according to Jurado-Medina et al [ 142 ]. Q Haplogroup was identified in individuals using specific primers for Q-M242, Q-M3, and Q-M346 markers following the multiplex PCR-APLP technique [ 142 ], and Q-Z780 and Q-Z19231 through sequencing markers [ 38 , 142 ].…”

Section: Methodsmentioning

confidence: 99%

“…Haplogroup determination was made by Polymerase Chain Reaction-Product Length Polymorphism (PCR-APLP) designed by Umetsu et al [ 140 , 141 ] and adapted according to Jurado-Medina et al [ 142 ]. Q Haplogroup was identified in individuals using specific primers for Q-M242, Q-M3, and Q-M346 markers following the multiplex PCR-APLP technique [ 142 ], and Q-Z780 and Q-Z19231 through sequencing markers [ 38 , 142 ]. We selected the samples belonging to the Q-M3 and Q-Z780 haplogroups according to their haplotypes in a network built with 17 STR (YFiler) previously reported [ 25 ].…”

Section: Methodsmentioning

confidence: 99%

Human Y chromosome sequences from Q Haplogroup reveal a South American settlement pre-18,000 years ago and a profound genomic impact during the Younger Dryas

et al. 2022

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The settlement of the Americas has been the focus of incessant debate for more than 100 years, and open questions regarding the timing and spatial patterns of colonization still remain today. Phylogenetic studies with complete human Y chromosome sequences are used as a highly informative tool to investigate the history of human populations in a given time frame. To study the phylogenetic relationships of Native American lineages and infer the settlement history of the Americas, we analyzed Y chromosome Q Haplogroup, which is a Pan-American haplogroup and represents practically all Native American lineages in Mesoamerica and South America. We built a phylogenetic tree for Q Haplogroup based on 102 whole Y chromosome sequences, of which 13 new Argentine sequences were provided by our group. Moreover, 1,072 new single nucleotide polymorphisms (SNPs) that contribute to its resolution and diversity were identified. Q-M848 is known to be the most frequent autochthonous sub-haplogroup of the Americas. The present is the first genomic study of Q Haplogroup in which current knowledge on Q-M848 sub-lineages is contrasted with the historical, archaeological and linguistic data available. The divergence times, spatial structure and the SNPs found here as novel for Q-Z780, a less frequent sub-haplogroup autochthonous of the Americas, provide genetic support for a South American settlement before 18,000 years ago. We analyzed how environmental events that occurred during the Younger Dryas period may have affected Native American lineages, and found that this event may have caused a substantial loss of lineages. This could explain the current low frequency of Q-Z780 (also perhaps of Q-F4674, a third possible sub-haplogroup autochthonous of the Americas). These environmental events could have acted as a driving force for expansion and diversification of the Q-M848 sub-lineages, which show a spatial structure that developed during the Younger Dryas period.

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“…, APLP(Jurado Medina et al 2014) , and Sanger sequencing Pre-print version. Visit http://digitalcommons.wayne.edu/humbiol/ after publication to acquire the final version.…”

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confidence: 99%