Microsatellite Length Differences Between Humans and Chimpanzees at Autosomal Loci Are Not Found at Equivalent Haploid Y Chromosomal Loci

Kayser, Manfred; Vowles, Edward J.; Kappei, Dennis; Amos, William

doi:10.1534/genetics.106.055632

Cited by 14 publications

(13 citation statements)

References 35 publications

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“…Our analysis was focused on the differences in short tandem repeats of mono-, di-and trinucleotide units. Several authors claim that the human repeats are on average longer than the chimpanzee ones (Kayser et al 2006;Vowles and Amos 2006;Webster et al 2002). Our results confirm this observation, but we concluded that the asymmetry is too weak to warrant the construction of two independent mutational probabilities and since the ancestral state of the repeats is not known we can only compile the mutational probabilities based on the relative differences.…”

Section: Replication Slippage Versus Point Mutationssupporting

confidence: 77%

Replication slippage versus point mutation rates in short tandem repeats of the human genome

2007

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Short tandem repeats (STRs) are subjected to two kinds of mutational modifications: point mutations and replication slippages. The latter is found to be the more frequent cause of STR modifications, but a satisfactory quantitative measure of the ratio of the two processes has yet to be determined. The comparison of entire genome sequences of closely enough related species enables one to obtain sufficient statistics by counting the differences in the STR regions. We analyzed human-chimpanzee DNA sequence alignments to obtain the counts of point mutations and replication slippage modifications. The results were compared with the results of a computer simulation, and the parameters quantifying the replication slippage probability as well as the probabilities of point mutations within the repeats were determined. It was found that within the STRs with repeated units consisting of one, two or three nucleotides, point mutations occur approximately twice as frequently as one would expect on the basis of the 1.2% difference between the human and chimpanzee genomes. As expected, the replication slippage probability is negligible below a 10-bp threshold and grows above this level. The replication slippage events outnumber the point mutations by one or two orders of magnitude, but are still lower by one order of magnitude relative to the mutability of the markers that are used for genotyping purposes.

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Section: Replication Slippage Versus Point Mutationssupporting

confidence: 77%

Replication slippage versus point mutation rates in short tandem repeats of the human genome

2007

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“…1998). The degree of polymorphism seems to be positively correlated with microsatellite length (Kayser et al . 2006).…”

Section: Resultsmentioning

confidence: 99%

Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics

et al. 2008

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Chimpanzees experienced a reduction of the allelic repertoire at the major histocompatibility complex (MHC) class I A and B loci, which may have been caused by a retrovirus belonging to the simian immunodeficiency virus (SIV) family. Extended MHC haplotypes were defined in a pedigreed chimpanzee colony. Comparison of genetic variation at microsatellite markers mapping inside and outside the Mhc region was carried out in humans and chimpanzees to investigate the genomic extent of the repertoire reduction. Multilocus demographic analyses underscored that chimpanzees indeed experienced a selective sweep that mainly targeted the chromosomal segment carrying the Mhc class I region. Probably due to genetic linkage, the sweep also affected other polymorphic loci, mapping in the close vicinity of the Mhc class I region genes. Nevertheless, although the allelic repertoire at particular Mhc class I and II loci appears to be limited, naturally occurring recombination events allowed the establishment of haplotype diversity after the sweep. However, recombination did not have sufficient time to erase the signal of the selective sweep.

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“…Unfortunately, using current algorithms, microsatellite sequences do not align well and, at first sight, might resemble sequences with no common ancestry; the above statistical approach, which assumes a “perfect” alignment (Margulies and Birney 2008), is thus inappropriate for microsatellites. An alternative approach, applied in recent studies of human–chimpanzee comparisons (Kayser et al 2006; Vowles and Amos 2006; Kelkar et al 2008), is to identify all microsatellites in each genome and find homologies by comparing positions in a pairwise whole-genome alignment. Although efficient, this task may become impractical when many genomes are compared and probably disproportionate when dealing with highly divergent species that are not expected to share many microsatellite sequences (e.g., human and chicken).…”

Section: Introductionmentioning

confidence: 99%

Conservation of Human Microsatellites across 450 Million Years of Evolution

Buschiazzo

Gemmell

2010

Genome Biology and Evolution

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The sequencing and comparison of vertebrate genomes have enabled the identification of widely conserved genomic elements. Chief among these are genes and cis-regulatory regions, which are often under selective constraints that promote their retention in related organisms. The conservation of elements that either lack function or whose functions are yet to be ascribed has been relatively little investigated. In particular, microsatellites, a class of highly polymorphic repetitive sequences considered by most to be neutrally evolving junk DNA that is too labile to be maintained in distant species, have not been comprehensively studied in a comparative genomic framework. Here, we used the UCSC alignment of the human genome against those of 11 mammalian and five nonmammalian vertebrates to identify and examine the extent of conservation of human microsatellites in vertebrate genomes. Out of 696,016 microsatellites found in human sequences, 85.39% were conserved in at least one other species, whereas 28.65% and 5.98% were found in at least one and three nonprimate species, respectively. An exponential decline of microsatellite conservation with increasing evolutionary time, a comparable distribution of conserved versus nonconserved microsatellites in the human genome, and a positive correlation between microsatellite conservation and overall sequence conservation, all suggest that most microsatellites are only maintained in genomes by chance, although exceptionally conserved human microsatellites were also found in distant mammals and other vertebrates. Our findings provide the first comprehensive survey of microsatellite conservation across deep evolutionary timescales, in this case 450 Myr of vertebrate evolution, and provide new tools for the identification of functional conserved microsatellites, the development of cross-species microsatellite markers and the study of microsatellite evolution above the species level.

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Microsatellite Length Differences Between Humans and Chimpanzees at Autosomal Loci Are Not Found at Equivalent Haploid Y Chromosomal Loci

Cited by 14 publications

References 35 publications

Replication slippage versus point mutation rates in short tandem repeats of the human genome

Replication slippage versus point mutation rates in short tandem repeats of the human genome

Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics

Conservation of Human Microsatellites across 450 Million Years of Evolution

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