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

Abstract:

: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.

journal_name

Mol Biol Evol

authors

Ramakrishnan U,Mountain JL

doi

10.1093/molbev/msh212

subject

Has Abstract

pub_date

2004-10-01 00:00:00

pages

1960-71

issue

10

eissn

0737-4038

issn

1537-1719

pii

msh212

journal_volume

21

pub_type

杂志文章
  • Gene products of Escherichia coli: sequence comparisons and common ancestries.

    abstract::Sequences of 1,862 chromosomally encoded Escherichia coli K12 proteins were examined to identify genes likely to have arisen by duplication of genes in an ancestral chromosome. The criteria for sequence relatedness were an alignment of at least 100 amino acid residues and a PAM distance (number of accepted point mutat...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040291

    authors: Labedan B,Riley M

    更新日期:1995-11-01 00:00:00

  • Sequential evolution of a symbiont inferred from the host: Wolbachia and Drosophila simulans.

    abstract::This study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. Specifically, a global sample of 1,442 Drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh028

    authors: Ballard JW

    更新日期:2004-03-01 00:00:00

  • Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.

    abstract::Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn148

    authors: Burgess R,Yang Z

    更新日期:2008-09-01 00:00:00

  • Evolution of trypsinogen activation peptides.

    abstract::The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msg183

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

    更新日期:2003-11-01 00:00:00

  • The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.

    abstract::Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and cha...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa122

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

    更新日期:2020-10-01 00:00:00

  • Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution.

    abstract::Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition,...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025972

    authors: Nedelcu AM,Lee RW

    更新日期:1998-06-01 00:00:00

  • A Robust ANOVA Approach to Estimating a Phylogeny from Multiple Genes.

    abstract::In this article, we address the issue of estimating the phylogenetic tree based on sequence data across a set of genes. Recognizing that the individual gene trees may not all share the same evolutionary history due to lateral gene transfer or differences in rates of evolution for instance, we develop a robust algorith...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msv084

    authors: Xu X,Dunn KA,Field C

    更新日期:2015-08-01 00:00:00

  • Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

    abstract::We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produc...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh018

    authors: Bryant D,Moulton V

    更新日期:2004-02-01 00:00:00

  • Archaic Adaptive Introgression in TBX15/WARS2.

    abstract::A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely rela...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msw283

    authors: Racimo F,Gokhman D,Fumagalli M,Ko A,Hansen T,Moltke I,Albrechtsen A,Carmel L,Huerta-Sánchez E,Nielsen R

    更新日期:2017-03-01 00:00:00

  • A graphical method for detecting recombination in phylogenetic data sets.

    abstract::Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025722

    authors: McGuire G,Wright F,Prentice MJ

    更新日期:1997-11-01 00:00:00

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

    abstract::Frequent positive selection is a hallmark of genes involved in the adaptive immune system of vertebrates, but the incidence of positive selection for genes underlying innate immunity in vertebrates has not been well studied. The toll-like receptors (TLRs) of the innate immune system represent the first line of defense...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq104

    authors: Wlasiuk G,Nachman MW

    更新日期:2010-09-01 00:00:00

  • Making the impossible possible: rooting the tree of placental mammals.

    abstract::Untangling the root of the evolutionary tree of placental mammals has been nearly an impossible task. The good news is that only three possibilities are seriously considered. The bad news is that all three possibilities are seriously considered. Paleontologists favor a root anchored by Xenarthra (e.g., sloths and ante...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mst118

    authors: Teeling EC,Hedges SB

    更新日期:2013-09-01 00:00:00

  • Endogenous lentiviral elements in the weasel family (Mustelidae).

    abstract::Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mss126

    authors: Han GZ,Worobey M

    更新日期:2012-10-01 00:00:00

  • Amino Acid metabolism conflicts with protein diversity.

    abstract::The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. O...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu228

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

    更新日期:2014-11-01 00:00:00

  • Structural molecular components of septate junctions in cnidarians point to the origin of epithelial junctions in eukaryotes.

    abstract::Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu265

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

    更新日期:2015-01-01 00:00:00

  • Genetic diversity patterns in the SR-BI/II locus can be explained by a recent selective sweep.

    abstract::The human scavenger receptor class B type I (SR-BI and splice variant SR-BII) plays a central role in HDL cholesterol metabolism and represents a candidate gene for a number of related diseases. We examined the genetic diversity of its coding and flanking regions in a sample of 178 chromosomes from individuals of Euro...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh074

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

    更新日期:2004-04-01 00:00:00

  • Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History.

    abstract::A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msz271

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

    更新日期:2020-03-01 00:00:00

  • The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium.

    abstract::At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msg032

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

    更新日期:2003-02-01 00:00:00

  • Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior.

    abstract::The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn,...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh194

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

    更新日期:2004-09-01 00:00:00

  • c-Myb is an evolutionary conserved miR-150 target and miR-150/c-Myb interaction is important for embryonic development.

    abstract::Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn165

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

    更新日期:2008-10-01 00:00:00

  • A New Formulation of Random Genetic Drift and Its Application to the Evolution of Cell Populations.

    abstract::Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx161

    authors: Chen Y,Tong D,Wu CI

    更新日期:2017-08-01 00:00:00

  • Paralogy and orthology in the MALVACEAE rpb2 gene family: investigation of gene duplication in hibiscus.

    abstract::A sample of the second largest subunit of low-copy nuclear RNA polymerase II (rpb2) sequences from Malvaceae subfamily Malvoideae suggests that rpb2 has been duplicated early in the subfamily's history. Hibiscus and related taxa possess two rpb2 genes, both of which produce congruent phylogenetic patterns that are lar...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh144

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

    更新日期:2004-07-01 00:00:00

  • Genome-Wide Analysis in Brazilians Reveals Highly Differentiated Native American Genome Regions.

    abstract::Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental ad...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msw249

    authors: Mychaleckyj JC,Havt A,Nayak U,Pinkerton R,Farber E,Concannon P,Lima AA,Guerrant RL

    更新日期:2017-03-01 00:00:00

  • Gene Tree Discordance Does Not Explain Away the Temporal Decline of Convergence in Mammalian Protein Sequence Evolution.

    abstract::Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, howev...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx109

    authors: Zou Z,Zhang J

    更新日期:2017-07-01 00:00:00

  • 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

    doi:10.1093/molbev/msl042

    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.

    abstract::Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of th...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msy148

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

    更新日期:2018-10-01 00:00:00

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

    abstract::DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known ins...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa214

    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

    更新日期:2021-01-23 00:00:00

  • Genome-wide patterns of expression in Drosophila pure species and hybrid males.

    abstract::One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogam...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msg119

    authors: Michalak P,Noor MA

    更新日期:2003-07-01 00:00:00

  • Heterotypy in the N-terminal region of growth/differentiation factor 5 (GDF5) mature protein during teleost evolution.

    abstract::Heterotypy is now recognized as a generative force in the formation of new proteins through modification of existing proteins. We report that heterotypy in the N-terminal region of the mature growth/differentiation factor 5 (GDF5) protein occurred during evolution of teleosts. N-terminal length variation of GDF5 was f...

    journal_title:Molecular biology and evolution

    pub_type: 信件,评审

    doi:10.1093/molbev/msn041

    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.

    abstract::Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a003777

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

    更新日期:2001-12-01 00:00:00