DnaSAM: Software to perform neutrality testing for large datasets with complex null models

Eckert, Andrew J.; Liechty, John D.; Tearse, Brandon R.; Pande, B. N.; Neale, David B.

doi:10.1111/j.1755-0998.2009.02768.x

Cited by 23 publications

(31 citation statements)

References 26 publications

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“…Haplotype analysis was performed as described in Campoli et al (2013). Nucleotide diversity π was calculated for the coding region using DnaSAM v. 20100621 (Eckert et al 2010). …”

Section: Methodsmentioning

confidence: 99%

Mapping-by-Sequencing IdentifiesHvPHYTOCHROME Cas a Candidate Gene for theearly maturity 5Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

et al. 2014

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Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering.

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“…Haplotype analysis was performed as described in Campoli et al (2013). Nucleotide diversity π was calculated for the coding region using DnaSAM v. 20100621 (Eckert et al 2010). …”

Section: Methodsmentioning

confidence: 99%

Mapping-by-Sequencing IdentifiesHvPHYTOCHROME Cas a Candidate Gene for theearly maturity 5Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

et al. 2014

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“…Significance of all tests was determined in DnaSAM [73] using 10 3 simulations that assumed a neutral model and no recombination. Because D , H , and EW differ in their sensitivities to demographic history, background selection, and recombination, the DHEW compound test [32] was also performed using the Perl script provided with DnaSAM [73].…”

Section: Methodsmentioning

confidence: 99%

Detecting Selection in the Blue Crab, Callinectes sapidus, Using DNA Sequence Data from Multiple Nuclear Protein-Coding Genes

Yednock

Neigel

2014

PLoS ONE

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The identification of genes involved in the adaptive evolution of non-model organisms with uncharacterized genomes constitutes a major challenge. This study employed a rigorous and targeted candidate gene approach to test for positive selection on protein-coding genes of the blue crab, Callinectes sapidus. Four genes with putative roles in physiological adaptation to environmental stress were chosen as candidates. A fifth gene not expected to play a role in environmental adaptation was used as a control. Large samples (n>800) of DNA sequences from C. sapidus were used in tests of selective neutrality based on sequence polymorphisms. In combination with these, sequences from the congener C. similis were used in neutrality tests based on interspecific divergence. In multiple tests, significant departures from neutral expectations and indicative of positive selection were found for the candidate gene trehalose 6-phosphate synthase (tps). These departures could not be explained by any of the historical population expansion or bottleneck scenarios that were evaluated in coalescent simulations. Evidence was also found for balancing selection at ATP-synthase subunit 9 (atps) using a maximum likelihood version of the Hudson, Kreitmen, and Aguadé test, and positive selection favoring amino acid replacements within ATP/ADP translocase (ant) was detected using the McDonald-Kreitman test. In contrast, test statistics for the control gene, ribosomal protein L12 (rpl), which presumably has experienced the same demographic effects as the candidate loci, were not significantly different from neutral expectations and could readily be explained by demographic effects. Together, these findings demonstrate the utility of the candidate gene approach for investigating adaptation at the molecular level in a marine invertebrate for which extensive genomic resources are not available.

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“…Genomic windows along the linkage map were defined in 5-cM bins with a step size of 2 cM. All calculations were conducted using DnaSAM (Eckert et al 2010c) and the libsequence, analysis, and gestimator C++ libraries (Thornton 2003). The latter C++ library uses the method of Comeron (1995) to calculate nonsynonymous (K a ) and synonymous (K s ) divergences, with the average across pairwise comparisons between ingroup and outgroup sequences being presented for each statistic when multiple sequences were available from the outgroup.…”

Section: Discussionmentioning

confidence: 99%

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

et al. 2013

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A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for .7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the .1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.A primary goal of population and quantitative genetics is to understand the genetic architecture of ecologically relevant traits (Stinchcombe and Hoekstra 2008; Barrett and Hoekstra 2011;Neale and Kremer 2011). A primary step on the path to this goal is to link genetic with phenotypic variation, either through linkage mapping of quantitative trait loci using pedigrees or through linkage disequilibrium mapping in natural populations (Lander and Schork 1994), with the latter currently being the most utilized. A multitude of studies ranging across a diverse set of taxa have discovered myriad genotype-phenotype correlations (Hindorff et al. 2009;Ingvarsson and Street 2011;Neale and Kremer 2011). Each discovered variant, however, often explains only a small fraction of the heritable phenotypic variance, thus being consistent with a polygenic model for the genetic architecture of complex traits (Lynch and Walsh 1998). Concomitant with the discovery of these associations are population genomic scans documenting deviations from expectations derived using the neutral theory (Nielsen 2005). Such scans have also discovered large numbers of loci putatively underlying phenotypic traits in many different taxa (e.g., Pollinger et al. 2005;Pritchard et al. 2010;Hufford et al. 2012), but in this case the link between genotype and phenotype is not explicit. A natural question thus arises about how much overlap exists between the lists gen...

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DnaSAM: Software to perform neutrality testing for large datasets with complex null models

Cited by 23 publications

References 26 publications

Mapping-by-Sequencing IdentifiesHvPHYTOCHROME Cas a Candidate Gene for theearly maturity 5Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

Mapping-by-Sequencing IdentifiesHvPHYTOCHROME Cas a Candidate Gene for theearly maturity 5Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

Detecting Selection in the Blue Crab, Callinectes sapidus, Using DNA Sequence Data from Multiple Nuclear Protein-Coding Genes

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

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