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Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area.

Harris SE, Munshi-South J, Obergfell C, O'Neill R - PLoS ONE (2013)

Bottom Line: From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus.These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments.This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

View Article: PubMed Central - PubMed

Affiliation: Program in Ecology, Evolutionary Biology, & Behavior, The Graduate Center, City University of New York (CUNY), New York, New York, United States of America.

ABSTRACT
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscusleucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar "urban adapter." We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

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Frequency of contig lengths for three transcriptome assembly methods.Inset: Zoomed-in view of frequency of longer assembled contigs from 1,500–3,000 bp. Blue line = Newbler cDNA, Red line = Newbler genome, Green line = Cap3.
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pone-0074938-g001: Frequency of contig lengths for three transcriptome assembly methods.Inset: Zoomed-in view of frequency of longer assembled contigs from 1,500–3,000 bp. Blue line = Newbler cDNA, Red line = Newbler genome, Green line = Cap3.

Mentions: 454 Sequencing of four full plates of P. leucopus cDNA libraries made from liver, brain, and gonad tissue produced 3,052,640 individual reads with an average length of 309 ± 122 bp (median = 341, Interquartile Range (IQR) = 188 bp). While the initial Newbler genomic assembly and Cap3 assembly produced more contigs, the mean length and N50 for both sets of contigs were lower than the Newbler cDNA assembly (Table 1). The Cap3 assembly and the genomic assembly included a much higher proportion of shorter contigs than the cDNA assembly (Figure 1). Coverage was calculated for all three assemblies, and all had similar median read coverage per contig (Newbler Genomic, median = 4.7 reads, IQR = 4.6; Newbler cDNA, median = 4.9 reads, IQR = 4.1; Cap3, median = 5.0 reads, IQR = 7.0, Figure S1).


Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area.

Harris SE, Munshi-South J, Obergfell C, O'Neill R - PLoS ONE (2013)

Frequency of contig lengths for three transcriptome assembly methods.Inset: Zoomed-in view of frequency of longer assembled contigs from 1,500–3,000 bp. Blue line = Newbler cDNA, Red line = Newbler genome, Green line = Cap3.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3756007&req=5

pone-0074938-g001: Frequency of contig lengths for three transcriptome assembly methods.Inset: Zoomed-in view of frequency of longer assembled contigs from 1,500–3,000 bp. Blue line = Newbler cDNA, Red line = Newbler genome, Green line = Cap3.
Mentions: 454 Sequencing of four full plates of P. leucopus cDNA libraries made from liver, brain, and gonad tissue produced 3,052,640 individual reads with an average length of 309 ± 122 bp (median = 341, Interquartile Range (IQR) = 188 bp). While the initial Newbler genomic assembly and Cap3 assembly produced more contigs, the mean length and N50 for both sets of contigs were lower than the Newbler cDNA assembly (Table 1). The Cap3 assembly and the genomic assembly included a much higher proportion of shorter contigs than the cDNA assembly (Figure 1). Coverage was calculated for all three assemblies, and all had similar median read coverage per contig (Newbler Genomic, median = 4.7 reads, IQR = 4.6; Newbler cDNA, median = 4.9 reads, IQR = 4.1; Cap3, median = 5.0 reads, IQR = 7.0, Figure S1).

Bottom Line: From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus.These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments.This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

View Article: PubMed Central - PubMed

Affiliation: Program in Ecology, Evolutionary Biology, & Behavior, The Graduate Center, City University of New York (CUNY), New York, New York, United States of America.

ABSTRACT
Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscusleucopus, is a common resident of NYC's forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar "urban adapter." We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.

Show MeSH
Related in: MedlinePlus