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Open Access Research article

Do highly divergent loci reside in genomic regions affecting reproductive isolation? A test using next-generation sequence data in Timema stick insects

Patrik Nosil1*, Thomas L Parchman2, Jeffrey L Feder3 and Zach Gompert2

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80303, USA

2 Department of Botany, University of Wyoming, Laramie, WY, 82071, USA

3 Department of Biology, Notre Dame University, South Bend, IN, 11111, USA

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BMC Evolutionary Biology 2012, 12:164  doi:10.1186/1471-2148-12-164

Published: 31 August 2012

Additional files

Additional file 1:

Figure S1. TMap of the eight study populations examined by Nosil et al. [44]. The current study examines all populations except R12A and R12C. See text for details.

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Additional file 2:

Figure S2. The relationship between the number of outlier loci (on log10 scale) and the geographic distance between populations (on log10 scale), for geographically separated and geographically adjacent population pairs (filled and unfilled circles, respectively). Both the effects of geographic distance itself, and of geographic arrangement (separated versus adjacent) were statistically significant. The thick arrow labels the point at which zero gene flow between population pairs was achieved, where gene flow was estimated from genomic data using Approximate Bayesian Computation. Also shown is a picture of the study organism. Modified from Nosil et al. [44].

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Additional file 3:

Figure S3. The distribution of FST values under different degrees of geographic separation. The top panel shows the distribution of FST values across individual loci. The bottom panel presents a barplot of the distribution of point estimates for logit(FST) across the genome. The dashed black line is the genome-wide distribution of logit(FST) (i.e., the Gaussian normal hierarchical prior for locus-specific logit(FST)). The vertical red line in each pane denotes the 95th quantile of the genome-wide distribution, which was used to delimit high FST outliers. In all instances, some outlier loci were detected but the FST distribution tended to be the most ‘L-shaped’ for geographically-adjacent pairs and became less ‘L-shaped’ with increasing geographic separation of populations. Modified from Nosil et al. [44].

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Additional file 4:

Figure S4. Results of genomic clines analyses for the population pair MR. a) the 95% credible intervals for genomic cline parameters α. Loci are sorted by the point estimate of α and 95% CI's that do not include zero are shown in black (i.e., introgression for these loci is significantly different than the genome-wide average). There are over 30,000 lines, thus individual 95% CI’s are difficult to see. b) Genomic clines for 1000 representative loci. Black lines denote clines with α values whose CI do not include zero. Grey lines denote loci whose α values had CI that did include zero. c) The correlation between FST and α. See text and Tables 1, and 2 for statistics.

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Additional file 5:

Figure S5. The correlation coefficient for the relationship between locus-specific FSTand locus-specific absolute α values (y-axis) for loci with FST values above certain thresholds (x-axis). Open circles are HV. Closed circles are MR. Numbers of loci that had FST values above each threshold are as follows (0.02: 38304; 0.04: 38304; 0.06: 21937; 0.08: 5680; 0.10: 2922; 0.12: 1548; 0.14: 858; 0.16: 477; 0.18: 282).

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