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.
FASTA file of CAP3 assembly
Assembly 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.fasta
FASTA file of Newbler cDNA assembly
Assembly 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.fasta
FASTA file of Newbler genome assembly
Assembly 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.fasta
Sequence alignment file (SAM) of 454 reads from Central Park population
Sequence alignment file of fastq files from Central Park 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.
SequenceAlignment_P.leucopus_CentralPark_07DEC2012.sam
Sequence alignment file (SAM) of 454 reads from Flushing Meadows population
Sequence alignment file (SAM) of fastq files from Flushing Meadows 454 sequencing. Fastq Files were aligned to Newbler cDNA assembly.
SequenceAlignment_P.leucopus_FlushingMeadows_07DEC2012.sam
Sequence alignment file (SAM) of 454 reads from Harriman State Park population
Sequence 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.sam
Sequence alignment file (SAM) of 454 reads from New York Botanical Garden population
Sequence 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.sam
Sequence alignment file (SAM) of 454 reads from Ridgewood Reservoir population
Sequence alignment file (SAM) of fastq files from Ridgewood Reservoir sequencing. Fastq Files were aligned to Newbler cDNA assembly.
SequenceAlignment_P.leucopus_RidgewoodReservoir_07DEC2012.sam
BLAST and gene ontology annotations for white-footed mouse cDNA sequences
Output file from software program BLAST2GO. Must be opened in BLAST2GO. Contains full BLAST and GO annotations for Newber assembly of all Peromyscus leucopus 454 sequences
Annotations_P.leucopus_01MAY2012.dat
VCF (variant call format) file of SNPs identified in NYC white-footed mice
Variant 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.vcf
Results of Ka / Ks calculations for each white-footed mouse population pair
Excel 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