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
Network of R1a and R1b1b STR haplotypes based on the data of all the markers.Median joining network of all the samples belonging to haplogroups R1a and R1b1b, based on the data of all the 24 markers used in this study. Open circles represent haplotypes of haplogroup R1a, black those of haplogroup R1b1b2, grey those of haplogroup R1b1b1. 13 nearly identical Altaian and Tuva samples form a separate branch within R1a, indicated by a red circle.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2748704&req=5

pone-0007276-g003: Network of R1a and R1b1b STR haplotypes based on the data of all the markers.Median joining network of all the samples belonging to haplogroups R1a and R1b1b, based on the data of all the 24 markers used in this study. Open circles represent haplotypes of haplogroup R1a, black those of haplogroup R1b1b2, grey those of haplogroup R1b1b1. 13 nearly identical Altaian and Tuva samples form a separate branch within R1a, indicated by a red circle.

Mentions: Due to their large sample sizes, in the case of sister haplogroups R1a (n = 82) and R1b1b (n = 33), combined data of all the markers was used to obtain a high resolution median joining network (Figure 3). Most haplotypes in this network are represented by a single individual. However, it is notable that inside haplogroup R1a (represented by open circles in Figure 3), several individual samples still exhibit identical haplotypes even at the resolution of 24 Y-STR markers. A separate branch of nearly identical Altaian and Tuva samples from haplogroup R1a can be seen to emerge (marked by a red circle in Figure 3), indicating that STR marker data can be used to point to potential intra-haplogroup subdivisions. This is further demonstrated by the clear separation of sister clades R1b1b2 (n = 20, represented by black circles in Figure 3) and R1b1b1 (n = 13, represented by grey circles) within haplogroup R1b1b. However, this division, as well as the high intrahaplogroup variability of R1b1b1, is not surprising, since unlike R1b1b2, R1b1b1 is a low frequency ancient haplogroup, the haplotype structure of which has apparently been significantly influenced by genetic drift.


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)

Network of R1a and R1b1b STR haplotypes based on the data of all the markers.Median joining network of all the samples belonging to haplogroups R1a and R1b1b, based on the data of all the 24 markers used in this study. Open circles represent haplotypes of haplogroup R1a, black those of haplogroup R1b1b2, grey those of haplogroup R1b1b1. 13 nearly identical Altaian and Tuva samples form a separate branch within R1a, indicated by a red circle.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0007276-g003: Network of R1a and R1b1b STR haplotypes based on the data of all the markers.Median joining network of all the samples belonging to haplogroups R1a and R1b1b, based on the data of all the 24 markers used in this study. Open circles represent haplotypes of haplogroup R1a, black those of haplogroup R1b1b2, grey those of haplogroup R1b1b1. 13 nearly identical Altaian and Tuva samples form a separate branch within R1a, indicated by a red circle.
Mentions: Due to their large sample sizes, in the case of sister haplogroups R1a (n = 82) and R1b1b (n = 33), combined data of all the markers was used to obtain a high resolution median joining network (Figure 3). Most haplotypes in this network are represented by a single individual. However, it is notable that inside haplogroup R1a (represented by open circles in Figure 3), several individual samples still exhibit identical haplotypes even at the resolution of 24 Y-STR markers. A separate branch of nearly identical Altaian and Tuva samples from haplogroup R1a can be seen to emerge (marked by a red circle in Figure 3), indicating that STR marker data can be used to point to potential intra-haplogroup subdivisions. This is further demonstrated by the clear separation of sister clades R1b1b2 (n = 20, represented by black circles in Figure 3) and R1b1b1 (n = 13, represented by grey circles) within haplogroup R1b1b. However, this division, as well as the high intrahaplogroup variability of R1b1b1, is not surprising, since unlike R1b1b2, R1b1b1 is a low frequency ancient haplogroup, the haplotype structure of which has apparently been significantly influenced by genetic drift.

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