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Bérard S, Nicolas F, Buard J, Gascuel O, Rivals E. A Fast and Specific Alignment Method for Minisatellite Maps. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or gene regulation regions, like for the cystatin B gene, and be associated or implicated in diseases: the Creutzfeld-Jakob disease and the myoclonus epilepsy type 1, for our examples. When it affects neutrally evolving regions, the polymorphism in length ( i.e., in number of copies) of minisatellites proved useful in population genetics. Motivation In these tandem repeat sequences, different mutational mechanisms let the number of copies, as well as the copies themselves, vary. Especially, the interspersion of events of tandem duplication/contraction and of punctual mutation makes the succession of variant repeats much more informative than the sole allele length. To exploit this information requires the ability to align minisatellite alleles by accounting for both punctual mutations and tandem duplications. Results We propose a minisatellite maps alignment program that improves on previous solutions. Our new program is faster, simpler, considers an extended evolutionary model, and is available to the community. We test it on the data set of 609 alleles of the MSY1 (DYF155S1) human minisatellite and confirm its ability to recover known evolutionary signals. Our experiments highlight that the informativeness of minisatellites resides in their length and composition polymorphisms. Exploiting both simultaneously is critical to unravel the implications of variable minisatellites in the control of gene expression and diseases. Availability Software is available at http://atgc.lirmm.fr/ms_align/
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Affiliation(s)
| | - François Nicolas
- LIRMM, UMR 5506 CNRS-Université de Montpellier II, Montpellier, France
| | - Jérôme Buard
- Institut de Génétique Humaine, UPR-CNRS 1142, Montpellier, France
| | - Olivier Gascuel
- LIRMM, UMR 5506 CNRS-Université de Montpellier II, Montpellier, France
| | - Eric Rivals
- LIRMM, UMR 5506 CNRS-Université de Montpellier II, Montpellier, France
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2
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Hallast P, Balaresque P, Bowden GR, Ballereau S, Jobling MA. Recombination dynamics of a human Y-chromosomal palindrome: rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions. PLoS Genet 2013; 9:e1003666. [PMID: 23935520 PMCID: PMC3723533 DOI: 10.1371/journal.pgen.1003666] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/07/2013] [Indexed: 11/19/2022] Open
Abstract
The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9–8.4×10−4 events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages. The sex-determining role of the human Y chromosome makes it male-specific, and always present in only a single copy. This solo lifestyle has endowed it with some bizarre features, among which are eight large DNA units constituting about a quarter of the chromosome's length, and containing many genes important for sperm production. These units are called palindromes, since, taking into account the polarity of the DNA strands, the sequence is the same read from either end of the unit. We investigated the details of a process (gene conversion) that transfers sequence variants in one half of a palindrome into the other, thereby maintaining >99.9% similarity between the halves. We analysed patterns of sequence variants within one palindrome in a set of Y chromosomes whose evolutionary relationships are known. This allowed us to identify past gene conversion events, and to demonstrate a bias towards events that eliminate new variants, and retain old ones. Gene conversion has therefore acted during human evolution to retard sequence change in these regions. Analysis of the chimpanzee and gorilla versions of the palindrome shows that the dynamic processes we see in human Y chromosomes have a deep evolutionary history.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | | | - Georgina R. Bowden
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Stéphane Ballereau
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Mark A. Jobling
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail:
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3
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Abouelhoda MI, Giegerich R, Behzadi B, Steyaert JM. Alignment of minisatellite maps based on run-length encoding scheme. J Bioinform Comput Biol 2009; 7:287-308. [PMID: 19340916 DOI: 10.1142/s0219720009004060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 09/27/2008] [Accepted: 10/23/2008] [Indexed: 11/18/2022]
Abstract
Subsequent duplication events are responsible for the evolution of the minisatellite maps. Alignment of two minisatellite maps should therefore take these duplication events into account, in addition to the well-known edit operations. All algorithms for computing an optimal alignment of two maps, including the one presented here, first deduce the costs of optimal duplication scenarios for all substrings of the given maps. Then, they incorporate the pre-computed costs in the alignment recurrence. However, all previous algorithms addressing this problem are dependent on the number of distinct map units (map alphabet) and do not fully make use of the repetitiveness of the map units. In this paper, we present an algorithm that remedies these shortcomings: our algorithm is alphabet-independent and is based on the run-length encoding scheme. It is the fastest in theory, and in practice as well, as shown by experimental results. Furthermore, our alignment model is more general than that of the previous algorithms, and captures better the duplication mechanism. Using our algorithm, we derive a quantitative evidence that there is a directional bias in the growth of minisatellites of the MSY1 dataset.
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Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis. Mutat Res 2008; 648:46-53. [PMID: 18929582 PMCID: PMC2599865 DOI: 10.1016/j.mrfmmm.2008.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 09/03/2008] [Accepted: 09/12/2008] [Indexed: 11/21/2022]
Abstract
Mutation at most human minisatellites is driven by complex interallelic processes that give rise to a high degree of length polymorphism and internal structural variation. MSY1, the only highly variable minisatellite on the non-recombining region of the Y chromosome, is constitutively haploid and therefore precluded from interallelic interactions, yet maintains high diversity in both length and structure. To investigate the basis of its mutation processes, an unbiased structural analysis of >500 single-molecule MSY1 PCR products from matched sperm and blood samples from a single donor was undertaken. The overall mutation frequencies in sperm and blood DNAs were not significantly different, at 2.68% and 1.88%, respectively. Sperm DNA showed significantly more length mutants than blood DNA, with mutants in both tissues involving small-scale (1–3 repeat units in a 77 repeat progenitor allele) increases or decreases in repeat block lengths, with no gain or loss bias. Isometric mutations altering structure but not length were found in both tissues, and involved either the apparent shift of a boundary between repeat unit blocks (a ‘boundary switch’) or the conversion of a repeat within a block to a different repeat type (‘modular structure’ mutant). There was a significant excess of boundary switch mutants and deficit of modular structure mutants in sperm. A comparison of mutant structures with phylogenetically matched alleles in population samples showed that alleles with structures resembling the blood mutants were unlikely to arise in populations. Mutation seems likely to involve gene conversion via synthesis-dependent strand annealing, and the blood-sperm differences may reflect more relaxed constraint on sister chromatid alignment in blood.
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5
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Abstract
Human proteins containing polyalanine tracts tend to have runs of other amino acids and their open reading frames (ORFs) display a biased codon usage. Their alanine, glycine, proline, and histidine content strongly correlates with the GC content of the third codon base, suggesting that the compositional specificity of these proteins is dictated to a great extent by the evolution of their ORFs.
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Affiliation(s)
- Julie Cocquet
- INSERM E0021 and U361, Reproduction et Physiopathologie Obstétricale, Hôpital Cochin, 75014 Paris, France
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Brion M, Salas A, González-Neira A, Lareu MV, Carracedo A. Insights into Iberian population origins through the construction of highly informative Y-chromosome haplotypes using biallelic markers, STRs, and the MSY1 minisatellite. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2003; 122:147-61. [PMID: 12949835 DOI: 10.1002/ajpa.10231] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To investigate the diversity of Y chromosomes in the Iberian Peninsula and the North African population of Maghreb, we constructed superhaplotypes on the basis of 10 biallelic markers, 7 microsatellites, and 1 minisatellite located in the nonrecombining portion of the human Y chromosome. The analysis of extremely high MSY1 variability was performed by reducing the MVR-codes to modular structures. Y-STRs and MSY1 data provide information about the relationship between closely related populations such as those of Iberia. Analysis of biallelic markers allowed us to identify 7 of 12 haplogroups defined by those polymorphisms. The haplogroup background showed clear differences between Iberian populations and the North African one. The use of differently mutating Y-chromosome markers allowed us to infer different population events at different time scales: the Paleolithic background of the Iberian Peninsula, the Neolithic fingerprint on Y-chromosome lineages, and the Iron Age influence in the populations of Iberia. Implications of our results for the highly debated origin of Basques are also discussed.
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Affiliation(s)
- M Brion
- Unit of Genetics, Institute of Legal Medicine, University of Santiago de Compostela, E-15782 Santiago de Compostela, Galicia, Spain
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8
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Jin ZB, Huang XL, Nakajima Y, Yukawa N, Osawa M, Takeichi S. Haploid allele mapping of Y-chromosome minisatellite, MSY1 (DYF155S1), to a Japanese population. Leg Med (Tokyo) 2003; 5:87-92. [PMID: 12935536 DOI: 10.1016/s1344-6223(03)00042-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The present study analyses the human Y-chromosome minisatellite locus, MSY1 (DYF155S1), in 205 Japanese males of 191 pedigrees using the minisatellite variant repeat (MVR) mapping system. The internal haploid structures of the detected alleles considerably varied and consisted of three major repeat units: types 2, 3 and 4. A comparison of the haploid profiles of the MVR codes identified 185 distinct alleles, of which only five were shared. We did not detect a type 1 repeat unit, and variations were frequent at the 5' end of the minisatellite locus. Within an analysis of 24 paternally linked DNA samples donated by ten families, no mutational events were identified even over two generation gaps. Furthermore, we applied this mapping system to a paternity test in which the alleged father was missing.
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Affiliation(s)
- Zheng-Bin Jin
- Department of Forensic Medicine, Tokai University School of Medicine, Kanagawa 259-1193, Isehara, Japan
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9
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Brión M, Cao R, Salas A, Lareu MV, Carracedo A. New method to measure minisatellite variant repeat variation in population genetic studies. Am J Hum Biol 2002; 14:421-8. [PMID: 12112563 DOI: 10.1002/ajhb.10057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The classical analysis of minisatellite variant repeat (MVR) variation using modular structures is limited by the lack of knowledge of the mutational process involved in the evolution of most of the minisatellites. In this study a new method to measure MVR variation and to calculate genetic distances using MVR codes is proposed. The method is based on the statistical similarity of MVR patterns and considers the complete variability of the minisatellite, enabling meaningful comparisons of closely related populations. As an example, the method has been applied to analyze variation in MSY1 (DYF155S1) in five sets of data from European and North African populations.
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Affiliation(s)
- M Brión
- Institute of Legal Medicine, University of Santiago de Compostela, E-15705 Santiago de Compostela, Galicia, Spain
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10
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Flores C, Larruga J, González A, Hernández M, Pinto F, Cabrera V. The Origin of the Canary Island Aborigines and Their Contribution to the Modern Population: A Molecular Genetics Perspective. CURRENT ANTHROPOLOGY 2001. [DOI: 10.1086/323819] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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McLain DK. Evolution of transcript structure and base composition of rDNA expansion segment D3 in ticks. Heredity (Edinb) 2001; 87:544-57. [PMID: 11869345 DOI: 10.1046/j.1365-2540.2001.00943.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four to thirty-two copies of the rDNA 28S gene expansion segment D3 and flanking H14 stem were sequenced in six species of ticks (Ixodes: Ixodidae: Acari). Sequence match among species varied from 66% to 97%. Sequence length averaged 130 bases in I. persulcatus across eight Eurasian sites and averaged 186 bases in five other species across 19 Eurasian and North American sites. The difference in length represents one or more deletions totalling about 60 bases that correspond to stems S3 or S4 of the folded transcript. The typical transcript conformation was observed as one possible low energy structure in the five species of longer D3. The structure entails a basal loop with four stem/loop structures, S1-S4 (moving 5' to 3') atop stem H14. A secondary structure lacking S4 but possessing all other putative standard features of the D3 transcript is possible with the shorter I. persulcatus sequences. Interspecific sequence differences occur at higher frequency in loops and bulges vs. complementary pairing regions of stems. Insertion/deletion events (indels) and base substitutions accounted equally for sequence differences. Indels are flanked by similar sequences, suggesting that they occur by slippage during replication. The D3 of Ixodes species is composed of a degenerate set of subrepeats. Thus, unequal exchange among subrepeats may have caused the reduction in length of the I. persulcatus D3. Compensatory base substitution and compensatory insertion/deletion events are indicated by the failure of mutations to affect secondary structure. Transversions accounted for 64% of sequence differences and were biased toward the gain of G and U and the loss of A and C. This bias could re-establish intramolecular base pairing when disrupted by insertions or deletions that shift one side of a stem relative to the other. The distribution of sequence differences, biased substitution, and conservation of transcript conformation in D3 suggest selective constraint.
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Affiliation(s)
- D K McLain
- Biology Department, PO Box 8042, Georgia Southern University, Statesboro, GA 30460, USA.
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12
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Scozzari R, Cruciani F, Pangrazio A, Santolamazza P, Vona G, Moral P, Latini V, Varesi L, Memmi MM, Romano V, De Leo G, Gennarelli M, Jaruzelska J, Villems R, Parik J, Macaulay V, Torroni A. Human Y-chromosome variation in the western Mediterranean area: implications for the peopling of the region. Hum Immunol 2001; 62:871-84. [PMID: 11543889 DOI: 10.1016/s0198-8859(01)00286-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Y-chromosome variation was analyzed in a sample of 1127 males from the Western Mediterranean area by surveying 16 biallelic and 4 multiallelic sites. Some populations from Northeastern Europe and the Middle East were also studied for comparison. All Y-chromosome haplotypes were included in a parsimonious genealogic tree consisting of 17 haplogroups, several of which displayed distinct geographic specificities. One of the haplogroups, HG9.2, has some features that are compatible with a spread into Europe from the Near East during the Neolithic period. However, the current distribution of this haplogroup would suggest that the Neolithic gene pool had a major impact in the eastern and central part of the Mediterranean basin, but very limited consequences in Iberia and Northwestern Europe. Two other haplogroups, HG25.2 and HG2.2, were found to have much more restricted geographic distributions. The first most likely originated in the Berbers within the last few thousand years, and allows the detection of gene flow to Iberia and Southern Europe. The latter haplogroup is common only in Sardinia, which confirms the genetic peculiarity and isolation of the Sardinians. Overall, this study demonstrates that the dissection of Y-chromosome variation into haplogroups with a more restricted geographic distribution can reveal important differences even between populations that live at short distances, and provides new clues to their past interactions.
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Affiliation(s)
- R Scozzari
- Department of Genetics and Molecular Biology, University of Rome "La Sapienza,", Rome, Italy.
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13
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Blanco P, Shlumukova M, Sargent CA, Jobling MA, Affara N, Hurles ME. Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism. J Med Genet 2000; 37:752-8. [PMID: 11015452 PMCID: PMC1757162 DOI: 10.1136/jmg.37.10.752] [Citation(s) in RCA: 116] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The Y chromosome provides a unique opportunity to study mutational processes within the human genome, decoupled from the confounding effects of interchromosomal recombination. It has been suggested that the increased density of certain dispersed repeats on the Y could account for the high frequency of causative microdeletions relative to single nucleotide mutations in infertile males. Previously we localised breakpoints of an AZFa microdeletion close to two highly homologous complete human endogenous retroviral sequences (HERV), separated by 700 kb. Here we show, by sequencing across the breakpoint, that the microdeletion occurs in register within a highly homologous segment between the HERVs. Furthermore, we show that recurrent double crossovers have occurred between the HERVs, resulting in the loss of a 1.5 kb insertion from one HERV, an event underlying the first ever Y chromosomal polymorphism described, the 12f2 deletion. This event produces a substantially longer segment of absolute homology and as such may result in increased predisposition to further intrachromosomal recombination. Intrachromosomal crosstalk between these two HERV sequences can thus result in either homogenizing sequence conversion or a microdeletion causing male infertility. This represents a major subclass of AZFa deletions.
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Affiliation(s)
- P Blanco
- Human Molecular Genetics Group, University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, UK
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14
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Bao W, Zhu S, Pandya A, Zerjal T, Xu J, Shu Q, Du R, Yang H, Tyler-Smith C. MSY2: a slowly evolving minisatellite on the human Y chromosome which provides a useful polymorphic marker in Chinese populations. Gene 2000; 244:29-33. [PMID: 10689184 DOI: 10.1016/s0378-1119(00)00021-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We present the second human Y-specific minisatellite, MSY2 (DYS440). It consists of three or four copies of a 99-110bp repeat unit and is located about 1kb upstream of the DBY gene. The most common allele contains four units, but a three-unit allele has arisen on at least four occasions; in chimpanzees and orangutans, MSY2 contains only two units. It is therefore evolving slowly and provides a particularly useful polymorphic marker for Chinese populations.
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Affiliation(s)
- W Bao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
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15
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Bosch E, Calafell F, Santos FR, Pérez-Lezaun A, Comas D, Benchemsi N, Tyler-Smith C, Bertranpetit J. Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 1999; 65:1623-38. [PMID: 10577916 PMCID: PMC1288373 DOI: 10.1086/302676] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/1999] [Accepted: 09/08/1999] [Indexed: 11/03/2022] Open
Abstract
Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations-that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit.
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Affiliation(s)
- Elena Bosch
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - Francesc Calafell
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - Fabrício R. Santos
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - Anna Pérez-Lezaun
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - David Comas
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - Noufissa Benchemsi
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - Chris Tyler-Smith
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
| | - Jaume Bertranpetit
- Unitat
de Biologia Evolutiva, Facultat de Ciències de la Salut i de la
Vida, Universitat Pompeu Fabra, Barcelona; Cancer Research
Campaign Chromosome Molecular Biology Group, Department of Biochemistry,
University of Oxford, Oxford; Departamento de Biologia Geral,
Instituto de Ciências Biológicas, Universidade Federal de
Minas Gerais, Belo Horizonte, Brazil; and Centre National de
Transfusion Sanguine, Rabat, Morocco
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16
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Jobling MA, Williams GA, Schiebel GA, Pandya GA, McElreavey GA, Salas GA, Rappold GA, Affara NA, Tyler-Smith C. A selective difference between human Y-chromosomal DNA haplotypes. Curr Biol 1998; 8:1391-4. [PMID: 9889101 DOI: 10.1016/s0960-9822(98)00020-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA analysis is making a valuable contribution to the understanding of human evolution [1]. Much attention has focused on mitochondrial DNA (mtDNA) [2] and the Y chromosome [3] [4], both of which escape recombination and so provide information on maternal and paternal lineages, respectively. It is often assumed that the polymorphisms observed at loci on mtDNA and the Y chromosome are selectively neutral and, therefore, that existing patterns of molecular variation can be used to deduce the histories of populations in terms of drift, population movements, and cultural practices. The coalescence of the molecular phylogenies of mtDNA and the Y chromosome to recent common ancestors in Africa [5] [6], for example, has been taken to reflect a recent origin of modern human populations in Africa. An alternative explanation, though, could be the recent selective spread of mtDNA and Y chromosome haplotypes from Africa in a population with a more complex history [7]. It is therefore important to establish whether there are selective differences between classes (haplotypes) of mtDNA and Y chromosomes and, if so, whether these differences could have been sufficient to influence the distributions of haplotypes in existing populations. A precedent for this hypothesis has been established for mtDNA in that one mtDNA background increases susceptibility to Leber hereditary optic neuropathy [8]. Although studies of nucleotide diversity in global samples of Y chromosomes have suggested an absence of recent selective sweeps or bottlenecks [9], selection may, in principle, be very important for the Y chromosome because it carries several loci affecting male fertility [10] [11] and as many as 5% of males are infertile [11] [12]. Here, we show that one class of infertile males, PRKX/PRKY translocation XX males, arises predominantly on a particular Y haplotypic background. Selection is, therefore, acting on Y haplotype distributions in the population.
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Affiliation(s)
- M A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
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Hurles ME, Irven C, Nicholson J, Taylor PG, Santos FR, Loughlin J, Jobling MA, Sykes BC. European Y-chromosomal lineages in Polynesians: a contrast to the population structure revealed by mtDNA. Am J Hum Genet 1998; 63:1793-806. [PMID: 9837833 PMCID: PMC1377652 DOI: 10.1086/302147] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
We have used Y-chromosomal polymorphisms to trace paternal lineages in Polynesians by use of samples previously typed for mtDNA variants. A genealogical approach utilizing hierarchical analysis of eight rare-event biallelic polymorphisms, seven microsatellite loci, and internal structural analysis of the hypervariable minisatellite, MSY1, has been used to define three major paternal-lineage clusters in Polynesians. Two of these clusters, both defined by novel MSY1 modular structures and representing 55% of the Polynesians studied, are also found in coastal Papua New Guinea. Reduced Polynesian diversity, relative to that in Melanesians, is illustrated by the presence of several examples of identical MSY1 codes and microsatellite haplotypes within these lineage clusters in Polynesians. The complete lack of Y chromosomes having the M4 base substitution in Polynesians, despite their prevalence (64%) in Melanesians, may also be a result of the multiple bottleneck events during the colonization of this region of the world. The origin of the M4 mutation has been dated by use of two independent methods based on microsatellite-haplotype and minisatellite-code diversity. Because of the wide confidence limits on the mutation rates of these loci, the M4 mutation cannot be conclusively dated relative to the colonization of Polynesia, 3,000 years ago. The other major lineage cluster found in Polynesians, defined by a base substitution at the 92R7 locus, represents 27% of the Polynesians studied and, most probably, originates in Europe. This is the first Y-chromosomal evidence of major European admixture with indigenous Polynesian populations and contrasts sharply with the picture given by mtDNA evidence.
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Affiliation(s)
- M E Hurles
- Department of Genetics, University of Leicester, UK
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