Limits...
Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit.

Järve M, Zhivotovsky LA, Rootsi S, Help H, Rogaev EI, Khusnutdinova EK, Kivisild T, Sanchez JJ - PLoS ONE (2009)

Bottom Line: According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats.Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia. mari.jarve@ut.ee

ABSTRACT

Background: Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.

Principal findings: In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.

Conclusions: Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.

Show MeSH
Networks of STR haplotypes based on penta- and hexanucleotide STRs, with and without SNPs.Median joining networks of Y chromosome STR haplotypes with balanced sample sizes from each haplogroup. A network based on 9 penta- and hexanucleotide STR markers and SNPs; B network based solely on the data of the 9 penta- and hexanucleotide STR markers used in this study. Nodes are named according to the haplogroups of the samples. STR markers employed in network construction: DYS448, DYS596, Y PENTA 1, Y PENTA 2, DYS438, DYS594, DYS643, DYS645, DYF411S1.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2748704&req=5

pone-0007276-g001: Networks of STR haplotypes based on penta- and hexanucleotide STRs, with and without SNPs.Median joining networks of Y chromosome STR haplotypes with balanced sample sizes from each haplogroup. A network based on 9 penta- and hexanucleotide STR markers and SNPs; B network based solely on the data of the 9 penta- and hexanucleotide STR markers used in this study. Nodes are named according to the haplogroups of the samples. STR markers employed in network construction: DYS448, DYS596, Y PENTA 1, Y PENTA 2, DYS438, DYS594, DYS643, DYS645, DYF411S1.

Mentions: Haplogroups R1a and R1b1b were represented by the same samples as in Figures 1 and 2 (4 samples from R1a and 3 from R1b1b, marked with grey shading in Table S1).


Decreased rate of evolution in Y chromosome STR loci of increased size of the repeat unit.

Järve M, Zhivotovsky LA, Rootsi S, Help H, Rogaev EI, Khusnutdinova EK, Kivisild T, Sanchez JJ - PLoS ONE (2009)

Networks of STR haplotypes based on penta- and hexanucleotide STRs, with and without SNPs.Median joining networks of Y chromosome STR haplotypes with balanced sample sizes from each haplogroup. A network based on 9 penta- and hexanucleotide STR markers and SNPs; B network based solely on the data of the 9 penta- and hexanucleotide STR markers used in this study. Nodes are named according to the haplogroups of the samples. STR markers employed in network construction: DYS448, DYS596, Y PENTA 1, Y PENTA 2, DYS438, DYS594, DYS643, DYS645, DYF411S1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2748704&req=5

pone-0007276-g001: Networks of STR haplotypes based on penta- and hexanucleotide STRs, with and without SNPs.Median joining networks of Y chromosome STR haplotypes with balanced sample sizes from each haplogroup. A network based on 9 penta- and hexanucleotide STR markers and SNPs; B network based solely on the data of the 9 penta- and hexanucleotide STR markers used in this study. Nodes are named according to the haplogroups of the samples. STR markers employed in network construction: DYS448, DYS596, Y PENTA 1, Y PENTA 2, DYS438, DYS594, DYS643, DYS645, DYF411S1.
Mentions: Haplogroups R1a and R1b1b were represented by the same samples as in Figures 1 and 2 (4 samples from R1a and 3 from R1b1b, marked with grey shading in Table S1).

Bottom Line: According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats.Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Evolutionary Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia. mari.jarve@ut.ee

ABSTRACT

Background: Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.

Principal findings: In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.

Conclusions: Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies.

Show MeSH