Software for Y-haplogroup predictions: a word of caution

Muzzio, Marina; Ramallo, Virgínia; Motti, Josefina María Brenda; Santos, Maria Rita de Morais Chaves; López-Camelo, Jorge S.; Bailliet, Graciela

doi:10.1007/s00414-009-0404-1

Cited by 28 publications

(14 citation statements)

References 16 publications

(18 reference statements)

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“…Both of the online calculators grouped our sample into haplogroups G2, J2, J1, R1b, R1a, L, I2, T, and E1b1b. It is shown that probability of wrong assignment of the haplogroups based on the online software could be high enough (Muzzio et al, 2011). For this reason, we tested the accuracy of the online calculators, using We repeated randomly selecting 10 individuals and the test procedure three times in order to increase the confidence of the results.…”

Section: Methodsmentioning

confidence: 99%

Human Paternal Lineages, Languages, and Environment in the Caucasus

et al. 2014

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Acknowledgments: Author contributions DT and AG analyzed the data and wrote the text. MM coordinated molecular genetic work and provided primary data analysis; MG did much of genetic analysis and identification of the haplogroups; GT initiated human genetic studies at Ilia State University, discussed the results from the standpoint of history and social sciences, and made much effort to provide the research with all necessary resources. Y-DNA haplogroup diversity is most commonly used for the analysis of the ancestry of individual ethnic groups or linguistic families (Kayser et al. 1997;Brisighelli, 2012). The reason is that Y-DNA haplogroups generally show more distinct ethno-geographic patterns than matrilineally inherited mt-DNA (Comas et al. 2000;Nasidze et al. 2003Nasidze et al. , 2004b. This is most likely due to higher dispersal rates of women (Seielstad et al. 1998;Oota et al. 2001;Nasidze et al. 2004a), the effects of selective pressures on the mitochondrial genome (Mishmar et al. 2003) and/or sex ratio in favor of women, causing more genetic drift in males (Dupanloup et al. 2003). Moreover, there is a popular nomenclature of the haplogroups linked to a well-established phylogenetic pattern (Underhill et al. 2001;Y Chromosome Consortium, 2002;Karafet et al. 2008;Chiaroni et al. 2009).The Caucasus is among the most linguistically and culturally diverse regions of Eurasia (Comrie, 2008;Nasidze et al. 2004b;Marchani et al. 2008;Balanovsky et al. 2011;Yunusbayev et al. 2012). Currently, the region hosts dozens of languages that are grouped into three language families (Comrie, 2008):Caucasian, Indo-European and Turkic. The Caucasian language family traditionally includes Adyghean, Vainakh, Daghestanian, and Kartvelian languages (Catford, 1977), although the common origin of these languages is disputed (Starostin, 1989). Recent study by Pagel et al. (2013) shows that the Kartvelian and Dravidic language families are the most basal in relation to the other Eurasian language families. Diakonoff and Starostin (1988) suggest that Vainakh and Daghestanian (i.e. Northeast Caucasian languages) are related to extinct Hurro-Urartian. Armenian and Ossetian languages belong to the IndoEuropean language family, and Oghuz and Kypchak subgroups of the Turkic language group are spoken in the Caucasus as well (Catford, 1977;Comrie, 2008). Linguistic differences, along with the differences in political history, influence (but do not determine) the ethnic identities of the people inhabiting the region. Some ethnic boundaries (e.g. that of Armenians or Ossetians) coincide with the linguistic boundaries but those of the other ethnic groups only partly do so. Some groups speaking several mutually unintelligible but related languages consider themselves to be part of a single ethnos -e.g. Georgians or Avarians.Simultaneously, language rather than religion accounts for ethnic identity in the Caucasus -e.g. Ossetians, Abkhazians and Georgians maintain ethnic integrity in spite of different religions practiced within each of these ...

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Section: Methodsmentioning

confidence: 99%

Human Paternal Lineages, Languages, and Environment in the Caucasus

et al. 2014

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“…We were aware of the issues present in estimating Y-chromosomal haplogroups from Y-STR frequencies (17), thus for the subsequent analyses (median networks) we used only the samples with Hg estimate probability higher than 90%.…”

Section: Methodsmentioning

confidence: 99%

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

Ehler

Vaněk²,

Stenzl³

et al. 2011

Croat Med J

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AimTo evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling.MethodsThe first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed.ResultsThe Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population.ConclusionThe Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics.

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“…There are several ways to analyze SNPs: RFLP , fluorescence techniques such as SNaPshot , and real‐time PCR ; however these methods are expensive and require specialized equipment. Software predictions from STRs combinations (haplotypes) are an alternative strategy to define haplogroups in the wet lab, though they have been questioned for their imprecision and high probability of wrong assignation .…”

Section: Sequence Of Oligonucleotide Primers Used For Multiplex Aflp mentioning

confidence: 99%

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

et al. 2014

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We designed an allele-specific amplification protocol to optimize Y-chromosome SNP typing, which is an unavoidable step for defining the phylogenetic status of paternal lineages. It allows the simultaneous highly specific definition of up to six mutations in a single reaction by amplification fragment length polymorphism (AFLP) without the need of specialized equipment, at a considerably lower cost than that based on single-base primer extension (SNaPshot™) technology or PCR-RFLP systems, requiring as little as 0.5 ng DNA and compatible with the small fragments characteristic of low-quality DNA. By designation of two primers recognizing the derived and ancestral state for each SNP, which can be differentiated by size by the addition of a noncomplementary nucleotide tail, we could define major Y clades E, F, K, R, Q, and subhaplogroups R1, R1a, R1b, R1b1b, R1b1c, J1, J2, G1, G2, I1, Q1a3, and Q1a3a1 through amplification fragments that ranged between 60 and 158bp.

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Software for Y-haplogroup predictions: a word of caution

Cited by 28 publications

References 16 publications

Human Paternal Lineages, Languages, and Environment in the Caucasus

Human Paternal Lineages, Languages, and Environment in the Caucasus

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

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

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