No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks
Abstract
STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch, which makes it possible to find haplotypes that differ from the target haplotype by 0, 1, 2, 3, or more mutational steps. The program may operate in two modes: comparison of individuals and comparison of populations. Flexibility of the program (the possibility of using any external database), its usability (MS Excel spreadsheets are used), and the capability of being applied to other chromosomes and other species could make this software a new useful tool in population genetics and forensic and genealogical studies. The Haplomatch software is freely available on our website www.genofond.ru. The program is applied to studying the gene pool of Cossacks. Experimental analysis of Y-chromosomal diversity in a representative set (N = 131) of Upper Don Cossacks is performed. Analysis of the STR haplotypes detects genetic proximity of Cossacks to East Slavic populations (in particular, to Southern and Central Russians, as well as to Ukrainians), which confirms the hypothesis of the origin of the Cossacks mainly due to immigration from Russia and Ukraine. Also, a small genetic influence of Turkicspeaking Nogais is found, probably caused by their occurrence in the Don Voisko as part of the Tatar layer. No similarities between haplotype spectra of Cossacks and Caucasus populations are found. This case study demonstrates the effectiveness of the Haplomatch software in analyzing large sets of STR haplotypes.
... (Fluxus Technology Ltd., http://www.fluxus-engineering.com) and Network Publisher (Fluxus Engineering, Clare, United Kingdom) on the basis of the reduced median algorithm. Networks were constructed using the data from [44,45]. Search for matching haplotypes was carried out in the program Haplomatch [44]. ...
... Networks were constructed using the data from [44,45]. Search for matching haplotypes was carried out in the program Haplomatch [44]. ...
... Another feature of the gene pool of Sitskari, which is the presence of haplogroup J-P58 (6.7%) atypical of the Russian population, is a relatively recent inclusion of Sitskari migrants from the south in the gene pool: two haplotypes J-P58 found among all of the studied samples of Yaroslavl oblast are the same (Sitskari and Russian), while the third (Sitskari) differs from them by only one mutational step. Search for similar haplotypes using the program Haplomatch [44] for all the data set available in the literature revealed matching with distinction of three mutational steps with representatives of Azeri, Iranians, and Italians. ...
The Upper Volga region was an area of contacts of Finno-Ugric, Slavic, and Scandinavian speaking populations in the 8th–10th centuries AD. However, their role in the formation of the contemporary gene pool of the Russian population of the region is largely unknown. To answer this question, we studied four populations of Yaroslavl oblast (N = 132) by a wide panel of STR and SNP markers of the Y-chromosome. Two of the studied populations appear to be genetically similar: the indigenous Russian population of Yaroslavl oblast and population of Katskari are characterized by the same major haplogroup, R-M198 (xM458). Haplogroup R-M458 composes more than half of Sitskari’s gene pool. The major haplogroup in the gene pool of the population of the ancient town of Mologa is N-M178. Subtyping N-M178 by newest “genomeera” Y-SNP markers showed different pathways of entering this haplogroup into the gene pools of Yaroslavl Volga region populations. The majority of Russian populations have subvariant N3a3-CTS10760; the regular sample of Yaroslavl oblast is equally represented by subvariants N3a3-CTS10760 and N3a4-Z1936, while subvariant N3a4-Z1936 predominates in the gene pool of population of Mologa. This N3a4-Z1936 haplogroup is common among the population of the north of Eastern Europe and the Volga-Ural region. The obtained results indicate preservation of the Finno-Ugric component in the gene pool of population of Mologa and a contribution of Slavic colonization in the formation of the gene pool of the Yaroslavl Volga region populations and make it possible to hypothesize the genetic contribution of the “downstream” (Rostov- Suzdal) rather than “upstream” (Novgorod) Slavic migration wave.
... Five mutations -considering 15 Y-STRs and mutation rate 0.0021 per locus per generation -might occur within roughly two thousand years, which covers the time interval important for our analysis. The search for related haplotypes was performed in a database of 4495 Y-STR Asian haplotypes using the Haplomatch software 38 . This methodology is similar to that applied by Balaresque and colleagues 30 in their search for Asian primary descent clusters. ...
... software. The search for related haplotypes was conducted using the Haplomatch software 38 . Phylogenetic analysis was conducted using the Reduced-Median method 61 in Network 5 software 62 (http://www. ...
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
... [31] was utilized for these calculations. The Y-chromosome STR haplotypes were subjected to comparison using the Haplomatch tool [32]. To conduct a comparative analysis, we compiled a comprehensive dataset consisting of previously published information (N = 3856 haplotypes for 17 Y-STRs) derived from population samples of Kazakhs [30,[33][34][35][36] and various Kazakh tribes [9,23,27,28,[37][38][39]. ...
The Kerey is one of the prominent Kazakh tribes and has long been a subject of ethnographic scrutiny, with a lack of consensus on its origin and traditional genealogy. Their historical significance, intertwined with the emergence of the empire established by Genghis Khan, necessitates a comprehensive understanding of their genetic history. This study focuses on unraveling the genetic heritage of the Kerey tribe. We conducted a comprehensive analysis of Y-chromosome data from genetic genealogy as citizen science and genetic screening of 23 Y-STRs and 37 Y-SNPs on 207 males from the Kerey tribe within academic science. Our results reveal two prevalent phylogenetic lineages within the C2a1a3a-F3796 haplogroup, also known as the C2*-Star Cluster (C2*-ST), which is one of the founding paternal lineages of the ancient Niru’un clan of the Mongols: C2-FT411734 and C2-FT224144, corresponding to the Abak and Ashamaily clans. While indicating a common male ancestry for them, our findings challenge the notion that they are full siblings. Additionally, genetic diversity analysis of the Y-chromosomes in the Kerey tribe and Kazakhs confirms their kinship with the Uissun tribe but refutes the claim of the Abak clan’s progenitor originating from this tribe. Furthermore, genetic evidence fails to support popular historical and ethnographic hypotheses regarding the Kerey tribe’s kinship with the Uak, Sirgeli, Adai, Törtkara, Karakerey, and Kereyit Kazakh tribes. The absence of a genetic paternal connection with the Kereyt tribe raises doubts about the genealogical link between the Kerey tribe and the stepfather of Genghis Khan.
... Potential matrilineal and patrilineal genetic continuity of the Pazyryk culture population was investigated based on already available archaeogenetic data for two individuals exhumed from the Ak-Alakha-1 Pazyryk burial site (Pilipenko et al. 2015). Y-STR haplotypes matching with or having only a few allelic variations from that observed in the two Scythians from Ak-Alakha-1 were compiled through searches at the Y-Chromosome STR Haplotype Reference Database (YHRD), Y-Search Utility of the Laboratory of Human Population Genetics, Research Centre of Medical Genetics, Moscow, and literature (Willuweit and Roewer 2015;Chukhryaeva et al. 2016). In cases where the Y-chromosomal SNP based haplogroup assignments were not available, the online 21-haplogroup version of the Whit Athey haplogroup assignment algorithm was used instead (Athey 2006). ...
In this study, geographic and linguistic distributions of contemporary and ancient matches with the paternal and maternal lineages of two individuals exhumed from the exemplary Pazyryk culture burial site of Ak-Alakha-1 mound 1 were investigated. Using the shared paternal and maternal haplotypes observed in both ancient individuals, extensive database and literature searches were conducted revealing numerous full matches among contemporary Eurasians, majority of whom speak Altaic Languages. Despite the current focus on the two Pazyryk individuals, a rare glimpse into the ancient migrations was gained through the discovery of paternal and maternal haplotype matches across an immense geography that spans from Yakutia to Turkey. In addition to a vast array of archaeological findings in such Scythian “frozen graves” across Central Asia, accumulating archaeogenetic data are expected to shed light on the anthropology of these otherwise mysterious people.
... Genogeographical atlases of Y chromosome and mtDNA [33] help to identify the likely region of origin for the paternal (Fig. 4) and maternal lines. This is complemented by analysis of the STR haplotype using the Russian program Haplomatch [83]: the program specifies in which populations the identical and similar haplotypes were found. This information is retrieved from the database, most of the haplotypes of which refer to the samples of the Biobank of Northern Eurasia. ...
Population biobanks are collections of thoroughly annotated biological material stored for many years. Population biobanks are a valuable resource for both basic science and applied research and are essential for extensive analysis of gene pools. Population biobanks make it possible to carry out fundamental studies of the genetic structure of populations, explore their genetic processes, and reconstruct their genetic history. The importance of biobanks for applied research is no less significant: they are essential for development of personalized medicine and genetic ecological monitoring of populations and are in high demand in forensic science. Establishment of an efficient and representative biobank requires strict observance of the principles of sample selection in populations, protocols of DNA extraction, quality control, and storage and documentation of biological materials. We reviewed regional biobanks and presented the organizational model of population biobank establishment based on the Biobank of Indigenous Population of Northern Eurasia created under supervision of E.V. Balanovska and O.P. Balanovsky. The results obtained using the biobanks in transdisciplinary research and prospective applications for the purposes of genogeography, genomic medicine, and forensic science are presented.
In this study, geographic and linguistic distributions of contemporary and ancient matches with the paternal and maternal lineages of two individuals exhumed from the exemplary Pazyryk culture burial site of Ak-Alakha-1 mound 1 were investigated. Using the shared paternal and maternal haplotypes observed in both ancient individuals, extensive database and literature searches were conducted revealing numerous full matches among contemporary Eurasians, majority of whom speak Altaic Languages. Despite the current focus on the two Pazyryk individuals, a rare glimpse into the ancient migrations was gained through the discovery of paternal and maternal haplotype matches across an immense geography that spans from Yakutia to Turkey. In addition to a vast array of archaeological findings in such Scythian “frozen graves” across Central Asia, accumulating archaeogenetic data are expected to shed light on the anthropology of these otherwise mysterious people.
This study presents a comprehensive analysis of 23 Y-STR data for the Merkit clan, a subgroup within the Kerey tribe of the Kazakh people. A total of 64 complete haplotypes were generated using the PowerPlex Y23 System. The data obtained using 23 Y-STR markers has been submitted to the Y Chromosome Haplotype Reference Database (YHRD) at yhrd.org, which will significantly enhance the forensic database for the Kazakh population in Kazakhstan. The research focuses on the distribution of haplotypes within the clan and their genealogical lines, which were visualized using a Median-joining network and Multidimensional scaling plot. The study identifies four distinct haplogroup clusters, revealing important insights into the genetic makeup and historical lineage of the Merkits. This dataset not only enriches our understanding of Kazakh genetic structure but also holds significant value for anthropological and population genetic research, as well as for forensic genetics. This work bridges a notable gap in genetic research on the Merkit clan, contributing to a deeper understanding of Central Asian nomadic tribes.
The review surveys the development and the current state of genetic genealogy, a branch of science dealing with the history of individuals, families, and kins using molecular genetic methods. The main milestones in the development of genetic genealogy are established: the appearance of essential prerequisites (development of DNA genotyping and forensic techniques of evaluating biological kinship); the first publications on the topic in the late 1990s; the establishment of commercial companies, periodicals, and noncommercial organizations dealing with this subject. The theory and practical applications of dating individuals back to the most recent common ancestors on the basis of Y-chromosomal amd mitochondrial DNA data are briefly considered.
We analyzed 40 single nucleotide polymorphism and 19 short tandem repeat Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation, and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language coevolution occurred within geographically isolated populations, probably due to its mountainous terrain.
The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.
The Phoenicians were the dominant traders in the Mediterranean Sea two thousand to three thousand years ago and expanded from their homeland in the Levant to establish colonies and trading posts throughout the Mediterranean, but then they disappeared from history. We wished to identify their male genetic traces in modern populations. Therefore, we chose Phoenician-influenced sites on the basis of well-documented historical records and collected new Y-chromosomal data from 1330 men from six such sites, as well as comparative data from the literature. We then developed an analytical strategy to distinguish between lineages specifically associated with the Phoenicians and those spread by geographically similar but historically distinct events, such as the Neolithic, Greek, and Jewish expansions. This involved comparing historically documented Phoenician sites with neighboring non-Phoenician sites for the identification of weak but systematic signatures shared by the Phoenician sites that could not readily be explained by chance or by other expansions. From these comparisons, we found that haplogroup J2, in general, and six Y-STR haplotypes, in particular, exhibited a Phoenician signature that contributed > 6% to the modern Phoenician-influenced populations examined. Our methodology can be applied to any historically documented expansion in which contact and noncontact sites can be identified.
Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< approximately 50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.
We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.
A total of 17 Y-specific STR loci were studied in 12 districts of the European part of Russia aiming to ascertain the amount of substructure required for the construction of a representative regional database. All groups exhibited high haplotype diversities but low inter-population variance as measured by an analysis of molecular variance. However, when Western Russia is taken as a whole, the genetic distances to the neighbouring populations were significant. Whereas gradual change in the Y chromosome pool exists between Russia and the Slavic-speaking populations to the West, remarkable discontinuities were observed with neighbouring populations in the East, North and South.
Electronic supplementary material
The online version of this article (doi:10.1007/s00414-007-0222-2) contains supplementary material, which is available to authorized users.
Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, and Druze. In the present study, 926 Lebanese men were typed with Y-chromosomal SNP and STR markers, and unusually, male genetic variation within Lebanon was found to be more strongly structured by religious affiliation than by geography. We therefore tested the hypothesis that migrations within historical times could have contributed to this situation. Y-haplogroup J*(xJ2) was more frequent in the putative Muslim source region (the Arabian Peninsula) than in Lebanon, and it was also more frequent in Lebanese Muslims than in Lebanese non-Muslims. Conversely, haplogroup R1b was more frequent in the putative Christian source region (western Europe) than in Lebanon and was also more frequent in Lebanese Christians than in Lebanese non-Christians. The most common R1b STR-haplotype in Lebanese Christians was otherwise highly specific for western Europe and was unlikely to have reached its current frequency in Lebanese Christians without admixture. We therefore suggest that the Islamic expansion from the Arabian Peninsula beginning in the seventh century CE introduced lineages typical of this area into those who subsequently became Lebanese Muslims, whereas the Crusader activity in the 11(th)-13(th) centuries CE introduced western European lineages into Lebanese Christians.
A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion of variation between populations. It differs in taking explicit account of the mutation process at microsatellite loci, for which a generalized stepwise mutation model appears appropriate. Simulations of subdivided populations were carried out to test the performance of R(ST) and F(ST). It was found that, under the generalized stepwise mutation model, R(ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long [corrected].
Spectacular progress has been made recently in the study of evolution at the molecular level, primarily due to new biochemical techniques such as gene cloning and DNA sequencing. In this book, the author summarizes new developments and seeks to unify studies of evolutionary histories of organisms and the mechanisms of evolution into a single science - molecular evolutionary genetics.
A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25 x 10(-4) (95% CI 0.05 x 10(-3)-1.53 x 10(-3)) at DYS438 and 6.36 x 10(-3) (95% CI 2.75 x 10(-3)-12.49 x 10(-3)) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice.
Father-son pairs from three populations (African American, Caucasian, and Hispanic) of Texas were typed for the 17 Y STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR YfilerTM kit. With 49,578 allele transfers, 102 mutations were detected. One three-step and four two-step mutations were found, and all others (95.1%) were one-step mutations. The number of gains (48) and losses (54) of repeats were nearly similar. The average mutation rate in the total population is 2.1 x 10(-3) per locus (95% CI (1.7-2.5)x10(-3)). African Americans showed a higher mutation rate (3.0 x 10(-3); 95% CI (2.4-4.0)x10(-3)) than the Caucasians (1.7 x 10(-3); 95% CI (1.1-2.5)x10(-3)) and Hispanics (1.5 x 10(-3); 95% CI (1.0-2.2)x10(-3)), but grouped by repeat-lengths, such differences were not significant. Mutation is correlated with relative length of alleles, i.e., longer alleles are more likely to mutate compared with the shorter ones at the same locus. Mutation rates are also correlated with the absolute number of repeats, namely, alleles with higher number of repeats are more likely to mutate than the shorter ones (p-value=0.030). Finally, occurrences of none, one, and two mutations over the father-son transmission of alleles were consistent with the assumption of independence of mutation rates across loci.
The freely accessible YHRD (Y Chromosome Haplotype Reference Database, www.yhrd.org) is designed to store Y chromosome haplotypes from global populations and had replaced three earlier database versions collecting European, Asian and US American Y chromosomes separately. The focus is to disseminate haplotype frequency data to forensic analysts, researchers, and to everyone who is interested in historical and family genetics. YHRD considers reduction of the available number of polymorphisms on the Y chromosome to a uniform data string of 11 highly variable Y-STR loci as an efficient way to rapidly screen many world populations and to make their Y chromosome profiles comparable. Typing of the YHRD 11-locus core set is facilitated by commercial products, namely diagnostic PCR kits, and endorsed by scientific and forensic analyst's societies as ISFG or SWGDAM. YHRD is structured by the assignment of each submitted population sample to a set of populations sharing a common linguistic, demographic, genetic or geographic background (metapopulations). This principle facilitates the statistical evaluation of haplotype matches due to a significant enlargement of sample sizes. With the rapid growth of the database the definition of homogeneous metapopulations is now also feasible solely on the basis of the genetic data as exemplified for the whole dataset of YHRD, release 19 (August 2006). Large sample numbers within genetically defined metapopulations also allows the development of biostatistical methods to estimate the frequency of unobserved or rare haplotypes ("haplotype frequency surveying method"). Essential for the YHRD project is its collaborative character relying on the engagement of individual laboratories to make their data accessible via YHRD and to share the YHRD standards regarding data quality.
A new measure of the extent of population subdivision as inferred from allele frequencies at microsatellite loci is proposed and tested with computer simulations. This measure, called R(ST), is analogous to Wright's F(ST) in representing the proportion of variation between populations. It differs in taking explicit account of the mutation process at microsatellite loci, for which a generalized stepwise mutation model appears appropriate. Simulations of subdivided populations were carried out to test the performance of R(ST) and F(ST). It was found that, under the generalized stepwise mutation model, R(ST) provides relatively unbiased estimates of migration rates and times of population divergence while F(ST) tends to show too much population similarity, particularly when migration rates are low or divergence times are long [corrected].
Mitochondrial DNA control region sequences were determined in 109 unrelated German Caucasoid individuals from north west Germany for both hypervariable regions 1 (HV1) and 2 (HV2) and 100 polymorphic nucleotide positions (nps) were found, 63 in HV1 and 37 in HV2. A total of 100 different mtDNA lineages was revealed, of which 7 were shared by 2 individuals and 1 by 3 individuals. The probability of drawing a HV1 sequence match within the north west Germans or within published sets of south Germans and west Austrians is similar (within a factor of 2) to drawing a sequence match between any two of these three population samples. Furthermore, HV1 sequences of 700 male inhabitants of one village in Lower Saxony were generated and these showed a nearly linear increase of the number of different haplotypes with increasing number of individuals, demonstrating that the commonly used haplotype diversity measure (Nei 1987) for population samples tends to underestimate mtDNA diversity in the actual population.
A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) to estimate Y-STR mutation rates. Seventeen Y chromosome STR loci (DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635 [GATA C4], GATA H4, and GATA A10) were analyzed in a sample of 3,026 father/son pairs. Among 27,029 allele transfers, 54 mutations were observed, with an overall mutation rate across the 17 loci of 1.998 x 10(-3) (95% CI, 1.501 x 10(-3) to 2.606 x 10(-3)). With just one exception, all of the mutations were single-step, and they were observed only once per gametogenesis. Repeat gains were more frequent than losses, longer alleles were found to be more mutable, and the mutation rate seemed to increase with the father's age. Hum Mutat 26(6), 520-528, 2005. (c) 2005 Wiley-Liss, Inc.
Donskie kazaki v proshlom i nastoyashchem (Don Cossacks in the Past and Present), Rostovon-Don GinGo
- Yu G Volkov
- Yu.G. Volkov
Opposition “us-them” and the mentality of the Don Cossacks, in Istoriya i kul’tura narodov stepnogo Predkavkaz’ya i Severnogo Kavkaza: problemy mezhetnicheskikh otnoshenii (History and Culture of the Peoples of the Steppe Ciscaucasia and Northern Caucasus: Problems of Interethnic Relations)
- B N Protsenko
Istoriya donskogo kazachestva v povestvovaniyakh i rasskazakh, v pyati tomakh (The History of the Don Cossacks in the Narratives and Stories in Five Volumes)
- M P Astapenko
Astapenko, M.P., Istoriya donskogo kazachestva v pov
estvovaniyakh i rasskazakh, v pyati tomakh (The History
of the Don Cossacks in the Narratives and Stories in
Five Volumes), Rostov on Don: Terra, 2000, vol. 1.
Донские казаки в прошлом и настояя щем
- Ю Г Волков
Волков Ю.Г. Донские казаки в прошлом и настояя
щем. Ростоввн/Д: ГинГо, 1998. 540 с.
Оппозиция " свой–чужой " и ментаа литет донских казаков // История и культура нароо дов степного Предкавказья и Северного Кавказа: проблемы межэтнических отношений: Сб. научн. статей. РостоввнааДону
- Б Н Проценко
Проценко Б.Н. Оппозиция " свой–чужой " и ментаа
литет донских казаков // История и культура нароо
дов степного Предкавказья и Северного Кавказа:
проблемы межэтнических отношений: Сб. научн.
статей. РостоввнааДону, 1999. С. 211–221.
История донского казачества в повествованиях и рассказах
- М П Астапенко
Астапенко М.П. История донского казачества в
повествованиях и рассказах. В 5 т. Ростов н/Д:
Терра, 2000. Т. 1. 700 с.
Геоинформационные технологии в ге ногеографии // Современная географическая кар тография / Под ред
- С М Кошель
Кошель С.М. Геоинформационные технологии в ге
ногеографии // Современная географическая кар
тография / Под ред. Лурье И.К. и Кравцовой В.И.
Москва: Дата+, 2012. С. 158-166.
Генетическая генеалогия: история и методология
- Е Я Тетушкин
Тетушкин Е.Я. Генетическая генеалогия: история и
методология // Генетика. 2011. Т. 47. № 5. С. 581–
596.
Information technologies in genogeog raphy, in Sovremennaya geograficheskaya kartografiya (Modern Geographic Cartography
- Koshel
Koshel', S.M., Information technologies in genogeog
raphy, in Sovremennaya geograficheskaya kartografiya
(Modern Geographic Cartography), Lur'e, I.K. and
Kravtsova, V.I., Eds., Moscow: Data+, 2012, pp. 158-166.
Popuu lation and segregation data on 17 YYSTRs: results of a GEPPISFG collaborative study
- P Sanchezzdiz
- C Alves
- E Carvalho
SanchezzDiz, P., Alves, C., Carvalho, E., et al., Popuu
lation and segregation data on 17 YYSTRs: results of a
GEPPISFG collaborative study, Int. J. Legal. Med.,
2008, vol. 122, pp. 529–533. doi 10.1007/s0041440088
02655z
Popu lation and segregation data on 17 Y STRs: results of a GEP ISFG collaborative study
- P Sanchez Diz
- C Alves
- E Carvalho
Sanchez Diz, P., Alves, C., Carvalho, E., et al., Popu
lation and segregation data on 17 Y STRs: results of a
GEP ISFG collaborative study, Int. J. Legal. Med.,
2008, vol. 122, pp. 529-533. doi 10.1007/s00414 008
0265 z
Y chromosome haplotype reference database (YHRD): update
- S Willuweit
- L Roewer
Willuweit, S. and Roewer, L., Y chromosome haplotype
reference database (YHRD): update, Forensic Sci. Int.
Genet., 2015, vol. 15, pp. 43-48. doi 10.1016/j.fsi
gen.2014.11.024
Донские казаки в прошлом и настоя щем. Ростов н/Д: ГинГо
- Ю Г Волков
Волков Ю.Г. Донские казаки в прошлом и настоя
щем. Ростов н/Д: ГинГо, 1998. 540 с.
свой-чужой" и мента литет донских казаков // История и культура наро дов степного Предкавказья и Северного Кавказа: проблемы межэтнических отношений: Сб. научн. статей. Ростов на Дону
- Б Н Проценко
- Оппозиция
Проценко Б.Н. Оппозиция "свой-чужой" и мента
литет донских казаков // История и культура наро
дов степного Предкавказья и Северного Кавказа:
проблемы межэтнических отношений: Сб. научн.
статей. Ростов на Дону, 1999. С. 211-221.
- M Nei
Nei M. Molecular Evolutionary Genetics. N.Y.: Co
lumbia Univ. Press, 1987. 512 p.
Muta tion rates at Y chromosome specific microsatellites
- L Gusmao
- P Sanchez Diz
- F Calafell
Gusmao, L., Sanchez Diz, P., Calafell, F., et al., Muta
tion rates at Y chromosome specific microsatellites, Hum.
Mutat., 2005, vol. 26, pp. 520-528. doi 10.1002/humu.
20254
Y chromo somal diversity in Lebanon is structured by recent his torical events
- P A Zalloua
- Y Xue
- J Khalife
Zalloua, P.A., Xue, Y., Khalife, J., et al., Y chromo
somal diversity in Lebanon is structured by recent his
torical events, Am. J. Hum. Genet., 2008, vol. 82,
pp. 873-882. doi 10.1016/j.ajhg.2008.01.020
Identify ing genetic traces of historical expansions: Phoenician footprints in the Mediterranean
- P A Zalloua
- D E Platt
- M El Sibai
Zalloua, P.A., Platt, D.E., El Sibai, M., et al., Identify
ing genetic traces of historical expansions: Phoenician
footprints in the Mediterranean, Am. J. Hum. Genet.,
2008, vol. 83, pp. 633-642. doi 10.1016/j.ajhg.2008.
10.012
Donskie kazaki v proshlom i nastoyash chem (Don Cossacks in the Past and Present)
- Yu G Volkov
Volkov, Yu.G., Donskie kazaki v proshlom i nastoyash
chem (Don Cossacks in the Past and Present), Rostov
on Don: GinGo, 1998.
Opposition "us them" and the men tality of the Don Cossacks, in Istoriya i kul'tura narodov stepnogo Predkavkaz'ya i Severnogo Kavkaza: problemy mezhetnicheskikh otnoshenii (History and Culture of the Peoples of the Steppe Ciscaucasia and Northern Cau casus: Problems of Interethnic Relations)
- B N Protsenko
Protsenko, B.N., Opposition "us them" and the men
tality of the Don Cossacks, in Istoriya i kul'tura narodov
stepnogo Predkavkaz'ya i Severnogo Kavkaza: problemy
mezhetnicheskikh otnoshenii (History and Culture of the
Peoples of the Steppe Ciscaucasia and Northern Cau
casus: Problems of Interethnic Relations), Rostov on
Don, 1999, pp. 211-221.
Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non significant genetic distances between populations
- L Roewer
- S Willuweit
- C Kruger
Roewer, L., Willuweit, S., Kruger, C., et al., Analysis of
Y chromosome STR haplotypes in the European part of
Russia reveals high diversities but non significant
genetic distances between populations, Int. J. Legal
Med., 2008, vol. 122, no. 3, pp. 219-223. doi
10.1007/s00414 007 0222 2
The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time
- L A Zhivotovsky
- P A Underhill
- C Cinnioglu
- L.A. Zhivotovsky
Mitochondrial portraits of human populations using median networks
- H J Bandelt
- P Forster
- B C Sykes
- H.J. Bandelt