Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

Pinotti, Thomaz; Bergström, Anders; Geppert, Martin; Bawn, Matt; Ohasi, Dominique; Shi, Wentao; Lacerda, Daniela R.; Solli, Arne; Norstedt, Jakob; Reed, Kate; Dawtry, Kim; González-Andrade, Fabricio; Paz‐y‐Miño, César; Revollo, Susana; Cuellar, Cinthia; Jota, Marilza S.; Santos, José Eduardo dos; Ayub, Qasim; Kivisild, Toomas; Sandoval, José R.; Fujita, Ricardo; Xue, Yali; Roewer, Lutz; Santos, Fabrício R.; Tyler‐Smith, Chris

doi:10.1016/j.cub.2018.11.029

Cited by 100 publications

(190 citation statements)

References 62 publications

(100 reference statements)

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“…, mirroring observations of rapid diversification of mitochondrial and Y-chromosome lineages at this time(24,25) but 215 not previously observed using autosomal data. While this inference is sensitive to SMC++ parameter settings and likely counteracted by very recent bottlenecks in the Native American groups, other populations do not display similar histories under these parameter settings.…”

supporting

confidence: 85%

Insights into human genetic variation and population history from 929 diverse genomes

Bergström

McCarthy

Hui

et al. 2019

Preprint

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169

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30Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in 35 southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple 40Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

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supporting

confidence: 85%

Insights into human genetic variation and population history from 929 diverse genomes

Bergström

McCarthy

Hui

et al. 2019

Preprint

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169

290

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“…For example, the basic haplogroup C defined by the SNP M130 is widespread in Central and East Asia, Australia and the Americas. Mutations further down the C branch arose later and are, therefore, restricted to lately occupied parts of the New World, for example, the derived American founder mutation C3 defined by SNP MPB373 occurs only in native groups living in the Northwest of South America (Pinotti et al, ). In Europe, collaborative exercises with blind samples are annually organized since 2017 in order to validate ancestry prediction methods for forensic use.…”

Section: Ancestry Inference Using the Y Chromosomementioning

confidence: 99%

“…The red line depicts concordance between observed and estimated haplotype frequencies; the green line marks the threshold of the DL frequency estimation for very rare haplotypes in this MP which is based on the distribution of singletons frequency estimates. To the left, the density distribution of the singleton estimates is plotted (modified from native groups living in the Northwest of South America (Pinotti et al, 2018). In Europe, collaborative exercises with blind samples are annually organized since 2017 in order to validate ancestry prediction methods for forensic use.…”

Section: Ancestry Inference Using the Y Chromosomementioning

confidence: 99%

Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA

Roewer

2019

WIREs Forensic Science

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The analysis of short tandem repeat (STR) markers located on the Y chromosome is an established method in forensic casework analysis. Usually this method is applied in cases of male‐on‐female sexual assault, in which the victim's DNA is in great excess and masked the male contribution. Y‐STR analysis is able to detect the presence of minuscule amounts of male DNA of one or multiple donors and resulting genetic profiles can be compared to known reference samples. The expert has to determine whether the Y‐STR result of a trace is suitable for a biostatistical calculation in case of a match. The Discrete Laplace method which is implemented in the Y chromosome haplotype reference database (YHRD) can be used to estimate haplotype frequencies with a better approximation than other methods namely the counting method. Moreover, Y‐SNPs in combination with Y‐STRs can infer the biogeographical origin of an unknown male person with comparably high precision due to the availability of a robust phylogenetic tree and large reference data collections. Y‐based ancestry prediction and familial searching can, therefore, provide important investigative leads in crime cases without suspect. This article is categorized under: Forensic Biology > Haploid Markers Forensic Biology > Ancestry Determination using DNA Methods Forensic Biology > DNA Databases and Biometrics Forensic Biology > Forensic DNA Technologies

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“…Within M3, two major lineages have been established as founding of Native Americans, Q‐Y4308 and Q‐M848 (Pinotti et al, ). Q‐Y4308 has been found in low frequencies, but with a wide range of distribution, observed from Siberia to South America (Grugni et al, ).…”

Section: Introductionmentioning

confidence: 99%

“…Q‐Y4308 has been found in low frequencies, but with a wide range of distribution, observed from Siberia to South America (Grugni et al, ). On the other hand, Q‐M848 is widely distributed, representing the most representative founding lineage Q‐M3 (Pinotti et al, ). Within M848, the International Society of Genetic Genealogy (ISOGG) has recognized several sublineages, among which are Q1b1a1a1a (M19), Q1b1a1a1b (M194), Q1b1a1a1c (M199), Q1b1a1a1d (SA01), Q1b1a1a1e (CTS11357), Q1b1a1a1f (Z35840) and Q1b1a1a1g–Q1b1a1a1w (ISOGG, ).…”

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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Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

Cited by 100 publications

References 62 publications

Insights into human genetic variation and population history from 929 diverse genomes

Insights into human genetic variation and population history from 929 diverse genomes

Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA

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

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