Precision and accuracy of divergence time estimates from STR and SNPSTR variation.


:Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels of homoplasy and varying mutational properties, often leading to inaccurate inference of population divergence. A SNPSTR is a genetic system that consists of an STR polymorphism closely linked (typically < 500 bp) to one or more single-nucleotide polymorphisms (SNPs). SNPSTR systems are characterized by lower levels of homoplasy than are STR loci. Divergence time estimates based on STR variation (on the derived SNP allele background) should, therefore, be more accurate and precise. We use coalescent-based simulations in the context of several models of demographic history to compare divergence time estimates based on SNPSTR haplotype frequencies and STR allele frequencies. We demonstrate that estimates of divergence time based on STR variation on the background of a derived SNP allele are more accurate (3% to 7% bias for SNPSTR versus 11% to 20% bias for STR) and more precise than STR-based estimates, conditional on a recent SNP mutation. These results hold even for models involving complex demographic scenarios with gene flow, population expansion, and population bottlenecks. Varying the timing of the mutation event generating the SNP revealed that estimates of divergence time are sensitive to SNP age, with more recent SNPs giving more accurate and precise estimates of divergence time. However, varying both mutational properties of STR loci and SNP age demonstrated that multiple independent SNPSTR systems provide less biased estimates of divergence time. Furthermore, the combination of estimates based separately on STR and SNPSTR variation provides insight into the age of the derived SNP alleles. In light of our simulations, we interpret estimates from data for human populations.


Mol Biol Evol


Ramakrishnan U,Mountain JL




Has Abstract


2004-10-01 00:00:00














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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Labedan B,Riley M

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Burgess R,Yang Z

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    pub_type: 杂志文章


    authors: Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

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    pub_type: 杂志文章


    authors: Gluck-Thaler E,Haridas S,Binder M,Grigoriev IV,Crous PW,Spatafora JW,Bushley K,Slot JC

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    pub_type: 杂志文章


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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Xu X,Dunn KA,Field C

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bryant D,Moulton V

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    pub_type: 杂志文章


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    pub_type: 杂志文章


    authors: McGuire G,Wright F,Prentice MJ

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  • Adaptation and constraint at Toll-like receptors in primates.

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Wlasiuk G,Nachman MW

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Teeling EC,Hedges SB

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Han GZ,Worobey M

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    authors: Krick T,Verstraete N,Alonso LG,Shub DA,Ferreiro DU,Shub M,Sánchez IE

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    authors: Ganot P,Zoccola D,Tambutté E,Voolstra CR,Aranda M,Allemand D,Tambutté S

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    authors: Le Jossec M,Wambach T,Labuda D,Sinnett D,Levy E

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    pub_type: 杂志文章


    authors: Sprengelmeyer QD,Mansourian S,Lange JD,Matute DR,Cooper BS,Jirle EV,Stensmyr MC,Pool JE

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    journal_title:Molecular biology and evolution

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    authors: Akey JM,Zhang K,Xiong M,Jin L

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    journal_title:Molecular biology and evolution

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    authors: Mayrose I,Graur D,Ben-Tal N,Pupko T

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Lin YC,Kuo MW,Yu J,Kuo HH,Lin RJ,Lo WL,Yu AL

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    journal_title:Molecular biology and evolution

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    authors: Chen Y,Tong D,Wu CI

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    pub_type: 杂志文章


    authors: Pfeil BE,Brubaker CL,Craven LA,Crisp MD

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    journal_title:Molecular biology and evolution

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    authors: Zou Z,Zhang J

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  • The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr.

    abstract::A recent investigation found evidence that the transition of Arabidopsis thaliana from ancestral self-incompatibility (SI) to full self-compatibility occurred very recently and suggested that this occurred through a selective fixation of a nonfunctional allele (PsiSCR1) at the SCR gene, which determines pollen specifi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bechsgaard JS,Castric V,Charlesworth D,Vekemans X,Schierup MH

    更新日期:2006-09-01 00:00:00

  • Rapid Viral Symbiogenesis via Changes in Parasitoid Wasp Genome Architecture.

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Burke GR,Simmonds TJ,Sharanowski BJ,Geib SM

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  • Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation.

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Kyger R,Luzuriaga-Neira A,Layman T,Milkewitz Sandberg TO,Singh D,Huchon D,Peri S,Atkinson SD,Bartholomew JL,Yi SV,Alvarez-Ponce D

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Michalak P,Noor MA

    更新日期:2003-07-01 00:00:00

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    journal_title:Molecular biology and evolution

    pub_type: 信件,评审


    authors: Fujimura K,Terai Y,Ishiguro N,Miya M,Nishida M,Okada N

    更新日期:2008-05-01 00:00:00

  • SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited.

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    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bolivar I,Fahrni JF,Smirnov A,Pawlowski J

    更新日期:2001-12-01 00:00:00