Fig 1.
Guppy reference genome strain.
Female (top) and male (bottom) from the inbred Guanapo strain.
Table 1.
Overview of assembly and annotation for the female guppy genome.
Fig 2.
Sequence characteristics for each linkage group.
Linkage groups are indicated on the outside. Small numbers indicate distances along each linkage group in Mb. Estimates for nucleotide diversity, π, GC content, and genic (exons and introns) and repeat density are averaged in 50 kb windows. Note that repeats can be located in genic regions.
Fig 3.
Distribution of anchored scaffolds along linkage groups.
Grey outlined boxes denote scaffolds with at least two markers. Scaffolds in the forward orientation are solid grey and in the reverse orientation are dashed light grey. Black outlined boxes and horizontal black bars denote scaffolds with just one marker and unknown orientation. Spacing between scaffolds was set arbitrarily to 500 kb.
Fig 4.
Whole genome alignment between Guppy and Medaka.
Circos plot of syntenic relationship between guppy (left) and medaka (right) chromosomes. Minimum block length 500 bp. Light grey lines indicate non-syntenic alignment blocks or blocks not assigned to any guppy linkage group (UN).
Fig 5.
Evolutionary rates along X-chromosome (LG12) and autosomes.
Density plots (A) of the rates of nonsynonymous (dN), (B) synonymous substitutions per nucleotide (dS) and (C) the ratios of dN and dS (dN/dS) between LG12 (red dashed lines) and autosomes (black dashed lines).
Table 2.
Characteristics of autosomes and X chromosome (LG12).
Estimates are from 50 kb windows across each linkage group. Measurements are dN (rate of nonsynonymous substitutions per nonsynonymous site), dS (rate of synonymous substitutions per synonymous site) and the ratio of dN/dS (mean estimates are approximated by ΣdN/ΣdS), π (nucleotide diversity within populations). Coverage was estimated using pooled resequencing data and is shown as average coverage per base. Statistical testing was carried out using non-parametrical Mann-Whitney U test (n.s., not significant, ***, p < 0.001).
Fig 6.
Inference of population size changes over time.
PSMC results for the high-predation population for each individual. Each color represents a single individual. Time scale on the x-axis is calculated assuming a mutation rate of 4.89x10-8 bp-1 generation-1 and a generation time of 0.5 years.
Fig 7.
Bootstrapped inference of population size change over time.
Plots of bootstrapped PSMC results for single individuals representing the high-predation population (GH13). The solid red line depicts the average estimate, the light red lines the 50 bootstrap results. Time scale on the x-axis is calculated assuming a mutation rate of 4.89x10-8 bp-1 generation-1 and a generation time of 0.5 years.