Figure 1.
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.
Figure 2.
Transcriptome alignment to reference rodent genomes.
Number and distribution of contigs from P. leucopus transcriptome (Newbler cDNA assembly) that aligned to each chromosome of the. (a) Rattus norvegicus. Blue = total number of genes per chromosome for Rattus. Red = number of aligned Peromyscus isotigs per Rattus chromosome. (b) Mus musculus. Blue = total number of genes per chromosome for Mus. Red = number of aligned Peromyscus isotigs per Mus chromosome.
Figure 3.
Annotation of final reference transcriptome.
Number of assembled P. leucopus contigs from four different tissue types that had significant hits with known proteins on BLASTX, and GO term annotations from reference databases using Blast2Go; Blue = Total number of contigs, Red = BLASTX hits, Green = number of annotated contigs.
Figure 4.
Over-represented GO terms from pairwise tissue comparisons (FDR ≤0.05).
(a) Comparison of brain transcriptome to liver and gonad. (b) Comparison of liver to brain and gonad. (c) Comparison of gonad to liver and brain.
Figure 5.
Non-synonymous (pN) SNP substitutions plotted vs. synonymous (pS) substitutions for 354 genes.
Each circle represents one unique assembled contig. (a) Pairwise comparisons for all urban populations. (b) Pairwise comparisons for urban to rural populations. The dashed line denotes pN / pS = 1, and circles above the line (pN / pS > 1) indicate candidates for positive selection. The solid line shows the slope for pN / pS = 0.5.
Figure 6.
Location and number of individuals collected from five populations in the NYC metropolitan area.
Urban populations are in shades of blue; light blue = male; dark blue = female. Rural population in orange and brown; orange = male; brown = female. Areas shaded red on the map indicate degree of urbanization (i.e. impermeable surface cover such as roads and rooftops) and green areas indicate vegetation cover from the 2006 National Landcover Database (CP = Central Park; NYBG = New York Botanical Gardens; RR = Ridgewood Reservoir; FM = Flushing Meadows-Willow Lake; HP = Harriman State Park).