DOI: 10.5061/dryad.r8ns3
title: Data from: Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

description: 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, Peromyscus leucopus, 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.
description: FASTA file of CAP3
 assemblyAssembly in fasta format
 of white-footed mouse 454 cDNA libraries from in and around New York City
 (NYC) using the CAP3 assembler with default setting.Assembly_P.leucopus_CAP3_12APRIL2013.fastaFASTA file of Newbler cDNA assemblyAssembly in fasta format of white-footed mouse 454 cDNA sequence reads from in and around New York City (NYC) using the Newbler assembly program with the cDNA option.Assembly_P.leucopus_NewblercDNA_05NOV2012.fastaFASTA file of Newbler genome assemblyAssembly in fasta format of white-footed mouse 454 cDNA sequence reads from in and around New York City (NYC) using the Newbler assembly program with the large genome option.Assembly_P.leucopus_NewblerGenome_15APRIL2012.fastaSequence alignment file (SAM) of 454 reads from Central Park populationSequence alignment file of fastq files from Central Park 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.SequenceAlignment_P.leucopus_CentralPark_07DEC2012.samSequence alignment file (SAM) of 454 reads from Flushing Meadows populationSequence alignment file (SAM) of fastq files from Flushing Meadows 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.SequenceAlignment_P.leucopus_FlushingMeadows_07DEC2012.samSequence alignment file (SAM) of 454 reads from Harriman State Park populationSequence alignment file (SAM) of fastq files from Harriman State Park 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.SequenceAlignment_P.leucopus_HarrimanPark_07DEC2012.samSequence alignment file (SAM) of 454 reads from New York Botanical Garden populationSequence alignment file (SAM) of fastq files from New York Botanical Garden 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.SequenceAlignment_P.leucopus_NewYorkBotanicalGarden_07DEC2012.samSequence alignment file (SAM) of 454 reads from Ridgewood Reservoir populationSequence alignment file (SAM) of fastq files from Ridgewood Reservoir sequencing. Fastq Files were aligned to Newbler cDNA assembly.SequenceAlignment_P.leucopus_RidgewoodReservoir_07DEC2012.samBLAST and gene ontology annotations for white-footed mouse cDNA sequencesOutput file from software program BLAST2GO. Must be opened in BLAST2GO. Contains full BLAST and GO annotations for Newber assembly of all Peromyscus leucopus 454 sequencesAnnotations_P.leucopus_01MAY2012.datVCF (variant call format) file of SNPs identified in NYC white-footed miceVariant call format file of SNPs generated using the SAMTOOLS mpileup function. All populations were used to make probabilistic SNP calls.SNP_P.leucopus_CP_FM_NYBG_RR_HP_07DEC2012.vcfResults of Ka / Ks calculations for each white-footed mouse population pairExcel spreadsheet of results from KAKS_Calculator. Each population pair was compared and the 10 comparisons are displayed in separate tabs.KAKS_P.leucopus_26FEB2013.xls