Dataset Information

The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum).

ABSTRACT: BACKGROUND: Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation. RESULTS: We used 454 pyrosequencing to identify 2,980 putative SNPs in the eastern tiger salamander (Ambystoma tigrinum tigrinum) transcriptome, then constructed analytical models to estimate SNP frequency. The model which considered only contig length (i.e., the method employed in most published papers) was evaluated with very poor likelihood. Our most robust model considered read depth as well as contig length, and was 7.5?×?10?? times more likely than the length-only model. Using this novel modeling approach, we estimated SNP frequency in protein-coding (mRNA) and non-coding transcripts (e.g., small RNAs). We found little difference in SNP frequency in the contigs, but we found a trend of a higher frequency of SNPs in long contigs representing non-coding transcripts relative to protein-coding transcripts. These results support the hypothesis that long non-coding transcripts are less conserved than long protein-coding transcripts. CONCLUSIONS: A modeling approach (i.e., using multiple model construction and model selection approaches) can be a powerful tool for identifying selection on specific functional sequence groups by comparing the frequency and distribution of polymorphisms.

SUBMITTER: Eo SH

PROVIDER: S-EPMC3416719 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum).

Eo Soo Hyung SH Dewoody J Andrew JA

BMC genomics 20120620

<h4>Background</h4>Next-generation sequencing methods have contributed to rapid progress in the fields of genomics and population genetics. Using this high-throughput and cost-effective technology, a number of studies have estimated single nucleotide polymorphism (SNP) frequency by calculating the mean number of SNPs per unit sequence length (e.g., mean SNPs/kb). However, both read length and contig depth are highly variable and thus raise doubt about simple methods of SNP frequency estimation.< ...[more]

PMID: 22716167

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Project description:Animals live in heterogeneous environments must navigate in order to forage or capture food, defend territories, and locate mates. These heterogeneous environments have a variety of substrates that differ in their roughness, texture, and other properties, all of which may alter locomotor performance. Despite such natural variation in substrate, many studies on locomotion use noncompliant surfaces that either are unrepresentative of the range of substrates experienced by species or underestimate maximal locomotor capabilities. The goal of this study was to determine the role of forefeet and hindfeet on substrates with different properties during walking in a generalized sprawling tetrapod, the tiger salamander (Ambystoma tigrinum). Adult salamanders (n = 4, SVL = 11.2-14.6 cm) walked across level dry sand (DS), semi-soft plaster of Paris (PoP), wet sand (WS), and a hard, noncompliant surface (table)-substrates that vary in compliance. Trials were filmed in dorsal and anterior views. Videos were analyzed to determine the number of digits and surface area of each foot in contact with the substrate. The surface area of the forelimbs contacting the substrate was significantly greater on DS and PoP than on WS and the table. The surface area of the hindlimbs contacting the substrate was significantly greater on DS than on all other substrates. There were no significant differences in the time that the fore- or hindfeet were in contact with the substrate as determined by the number of digits. We conclude that salamanders modulate the use of their feet depending on the substrate, particularly on DS which is known to increase the mechanical work and energy expended during locomotion owing to the fluid nature of its loose particles. More studies are needed to test a wider range of substrates and to incorporate behavioral data from field studies to get a better understanding of how salamanders are affected by different substrates in their natural environment.

Project description:BackgroundLoss of pond habitat is catastrophic to aquatic larval amphibians, but even reduction in the amount of time a breeding site holds water (hydroperiod) can influence amphibian development and limit reproductive success. Using the landscape variation of a glacial valley in the Greater Yellowstone Ecosystem as the context for a natural experiment, we examined variation in growth pattern and life history of the salamander Ambystoma tigrinum melanostictum and determined how these developmental characteristics varied with hydroperiod over several summers.ResultsIn ponds that dried early in the season, maximum larval size was reduced relative to the sizes achieved in permanent ponds. Ephemeral ponds were associated with early metamorphosis at small body sizes, while permanent ponds facilitated longer larval periods and later metamorphosis. Paedomorphosis resulted from indefinite metamorphic postponement, and was identified only in the most permanent environments. Patterns of growth and allometry were similar between ponds with different hydroperiods, but considerable life history variation was derived from modulating the timing of and size at metamorphosis. Considering maximum rates of growth and inferring the minimum size at metamorphosis across 25 ponds over the course of three years, we calculated that hydroperiods longer than three months are necessary to support these populations through metamorphosis and/or reproductive maturity.ConclusionsLandscape heterogeneity fosters life history variation in this natural population. Modulation of the complex ambystomatid life cycle allows this species to survive in unpredictable environments, but current trends towards rapid pond drying will promote metamorphosis at smaller sizes and could eliminate the paedomorphic phenotype from this region. Metamorphosis at small size is has been linked to altered fitness traits, including reduced survival and fecundity. Thus, widespread environmental truncation of larval periods may lead to decreased population persistence. We found that the hydroperiods of many ponds in this region are now shorter than the developmental period required for larvae to reach the minimum size for metamorphosis; these locations serve as reproductive sinks that may be detrimental for persistence of the species in the region.

Dataset Information

The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum).

Publications

The effects of contig length and depth on the estimation of SNP frequencies, and the relative abundance of SNPs in protein-coding and non-coding transcripts of tiger salamanders (Ambystoma tigrinum).

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