Intra-species differences in population size shape life history and genome evolution
- Max Planck Institute for Biology of Ageing, Germany
- Czech Academy of Sciences, Institute of Vertebrate Biology, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Czech Republic
- CECAD, University of Cologne, Germany
Figures
Figure 1 with 2 supplements
Demography and natural occurrence of turquoise killifish populations.
(a) Inferred ancestral effective population size (Ne) (using PSMC’) on y-axis and past generations on x-axis in GNP (red, orange), NF414 (black, grey) and NF303 (blue). Inset: unrooted neighbor …
Figure 1—figure supplement 1
Altitude, climate classification and genetic differentiation of studied samples.
(a) Altitude elevation map with studied samples. (b) Climate classification based on Koeppen-Geiger index combined with a high-resolution river map. (c) Unrooted neighbor joining tree based on …
Figure 1—figure supplement 2
Map positions of the populations used in this study and of those used in the QTL study (Valenzano et al., 2015).
The distance between population ‘GRZ’ (from QTL study) and population ‘GNP’ is <30 Km, while the distance between population ‘MZM-0703’ (from QTL study) and population ‘NF414’ is 70 Km.
Figure 2
Genomic regions of high and low genetic divergence between pairs of turquoise killifish populations.
Left) Genomic regions with high or low genetic differentiation between turquoise killifish populations identified with an FST outlier approach. Z-transformed FST values of all pairwise comparisons …
Figure 3
Synteny and sex chromosome evolution in turquoise killifish.
(a) Synteny circos plots based on 1-to-1 orthologous gene location between the new turquoise killifish assembly (black chromosomes) and platyfish (Xiphophorus maculatus, colored chromosomes, left …
Figure 4 with 2 supplements
Genome-wide signatures of natural and relaxed selection in turquoise killifish populations.
Asymptotic McDonald-Kreitman alpha (MK α) analysis based on derived frequency bins using as outgroups (a) Nothobranchius orthonotus and (b) Nothobranchius rachovii. Population GNP is shown in red, …
Figure 4—figure supplement 1
Simulated models with the inferred negative distribution of fitness effects.
Simulated demographic models are shown on the left and the inferred negative distribution of fitness effects are shown on the right (large population in blue, small population in red). Models differ …
Figure 4—figure supplement 2
Mean Consurf score per variant based on derived frequency bins.
(a) Mean Consurf score based on derived frequency bins in non-synonymous (left) and synonymous (right) sites using Nothobranchius orthonotus as outgroup, including all available sites (upper panel) …
Figure 5
Pathway enrichment in genes under adaptive and neutral evolution in turquoise killifish populations.
(a) Distribution of direction of selection (DoS) represented with median of distribution for population GNP (red), NF414 (grey) and NF303 (blue). Left panel shows DoS distribution computed using Noth…
Author response image 1
Additional files
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Supplementary file 1
file 1A.
Geographical and environmental statistics file 1B. Sequencing and mapping statistics file 1C. Genome-wide genetic differentiation file 1D. FST outlier high genetic differentiation NF414 vs. NF303 file 1E. FST outlier high genetic differentiation NF303 vs. GNP file 1F. FST outlier high genetic differentiation NF414 vs. GNP file 1G. FST outlier low genetic differentiation file 1H. Distribution of fitness effects file 1I. Pathway overrepresentation DoS file 1J. FST outlier genes differentially expressed with age file 1K. Pairwise Wilcoxon rank sum test P values for Consurf score with N. orthonotus as outgroup file 1L. Pairwise Wilcoxon rank sum test P values for Consurf score with N. rachovii as outgroup
- https://cdn.elifesciences.org/articles/55794/elife-55794-supp1-v2.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/55794/elife-55794-transrepform-v2.pdf
