483 research outputs found
A Genomic Approach for Distinguishing between Recent and Ancient Admixture as Applied to Cattle
Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We developed a metric, scaled block size (SBS), which uses the nonrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient types of admixture, and applied it to the reconstruction of admixture in cattle. Cattle are descendants of 2 independently domesticated lineages, taurine and indicine, which diverged more than 200 000 years ago. Several breeds have hybrid ancestry between these divergent lineages. Using 47 506 single-nucleotide polymorphisms, we analyzed the genomic architecture of the ancestry of 1369 individuals. We focused on 4 groups with admixed ancestry, including 2 anciently admixed African breeds (n = 58; n = 43), New World cattle of Spanish origin (n = 51), and known recent hybrids (n = 46). We estimated the ancestry of chromosomal regions for each individual and used the SBS metric to differentiate the timing of admixture among groups and among individuals within groups. By comparing SBS values of test individuals with standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed cattle. We also estimated ancestry at the chromosomal scale. The X chromosome exhibits reduced indicine ancestry in recent hybrid, New World, and western African cattle, with virtually no evidence of indicine ancestry in New World cattle.
Key words: cattle, chromosome painting, hybridization, introgressionGraduate Program in Ecology, Evolution, and Behavior at the University of Texas at Austin; Texas EcoLabs; Texas Longhorn Cattleman’s Foundation; National Science Foundation BEACON (Cooperative Agreement DBI–0939454); Extreme Science and Engineering Discovery Environment (XSEDE), National Science Foundation (OCI–1053575)
How do SNP ascertainment schemes and population demographics affect inferences about population history?
Background: The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using F and principal components analysis (PCA).
Results: Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group polymorphism decreases estimates of F between groups. Subpopulation-biased selection of SNPs changes the weighting of principal component axes and can affect inferences about proportions of admixture and population histories using PCA. PCA-based inferences of population relationships are largely congruent across types of ascertainment bias, even when ascertainment bias is strong.
Conclusions: Analyses of ascertainment bias in genomic data have largely been conducted on human data. As genomic analyses are being applied to non-model organisms, and across taxa with deeper divergences, care must be taken to consider the potential for bias in ascertainment of variation to affect inferences. Estimates of F, time of separation, and population divergence as estimated by principal components analysis can be misleading if this bias is not taken into account
Elevated titre of antihuman shock protein 60 predicts an adverse medium-term prognosis in patients with unstable angina
Article Efficient Sequencing of Anuran mtDNAs and a Mitogenomic Exploration of the Phylogeny and Evolution of Frogs
Abstract Anura (frogs and toads) constitute over 88% of living amphibian diversity but many important questions about their phylogeny and evolution remain unresolved. For this study, we developed an efficient method for sequencing anuran mitochondrial DNAs (mtDNAs) by amplifying the mitochondrial genome in 12 overlapping fragments using frog-specific universal primer sets. Based on this method, we generated 47 nearly complete, new anuran mitochondrial genomes and discovered nine novel gene arrangements. By combining the new data and published anuran mitochondrial genomes, we assembled a large mitogenomic data set (11,007 nt) including 90 frog species, representing 39 of 53 recognized anuran families, to investigate their phylogenetic relationships and evolutionary history. The resulting tree strongly supported a paraphyletic arrangement of archaeobatrachian (=nonneobatrachian) frogs, with Leiopelmatoidea branching first, followed by Discoglossoidea, Pipoidea, and Pelobatoidea. Within Neobatrachia, the South African Heleophrynidae is the sister-taxon to all other neobatrachian frogs and the Seychelles-endemic Sooglossidae is recovered as the sister-taxon to Ranoidea. These phylogenetic relationships agree with many nuclear gene studies. The chronogram derived from two Bayesian relaxed clock methods (MultiDivTime and BEAST) suggests that modern frogs (Anura) originated in the early Triassic about 244 Ma and the appearance of Neobatrachia took place in the late Jurassic about 163 Ma. The initial diversifications of two species-rich superfamilies Hyloidea and Ranoidea commenced 110 and 133 Ma, respectively. These times are older than some other estimates by approximately 30-40 My. Compared with nuclear data, mtDNA produces compatible time estimates for deep nodes (>150 Ma), but apparently older estimates for more shallow nodes. Our study shows that, although it evolves relatively rapidly and behaves much as a single locus, mtDNA performs well for both phylogenetic and divergence time inferences and will provide important reference hypotheses for the phylogeny and evolution of frogs
Quantum mechanics of lattice gas automata. I. One particle plane waves and potentials
Classical lattice gas automata effectively simulate physical processes such
as diffusion and fluid flow (in certain parameter regimes) despite their
simplicity at the microscale. Motivated by current interest in quantum
computation we recently defined quantum lattice gas automata; in this paper we
initiate a project to analyze which physical processes these models can
effectively simulate. Studying the single particle sector of a one dimensional
quantum lattice gas we find discrete analogues of plane waves and wave packets,
and then investigate their behaviour in the presence of inhomogeneous
potentials.Comment: 19 pages, plain TeX, 14 PostScript figures included with epsf.tex
(ignore the under/overfull \vbox error messages), two additional large
figures available upon reques
From quantum cellular automata to quantum lattice gases
A natural architecture for nanoscale quantum computation is that of a quantum
cellular automaton. Motivated by this observation, in this paper we begin an
investigation of exactly unitary cellular automata. After proving that there
can be no nontrivial, homogeneous, local, unitary, scalar cellular automaton in
one dimension, we weaken the homogeneity condition and show that there are
nontrivial, exactly unitary, partitioning cellular automata. We find a one
parameter family of evolution rules which are best interpreted as those for a
one particle quantum automaton. This model is naturally reformulated as a two
component cellular automaton which we demonstrate to limit to the Dirac
equation. We describe two generalizations of this automaton, the second of
which, to multiple interacting particles, is the correct definition of a
quantum lattice gas.Comment: 22 pages, plain TeX, 9 PostScript figures included with epsf.tex
(ignore the under/overfull \vbox error messages); minor typographical
corrections and journal reference adde
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