Table 2.
Genes Identified in Overlapping Selective Sweep Regions
| Regions | Scaffold | Selection Analyses/Cluster Identities | SNP Position | |iHS|/XPEHH | Candidate Genes under Selection |
|---|---|---|---|---|---|
| 1 | RCO7_scaffold001 | (a) XP-EHH—cluster 1 versus Cluster 3 | 962864 | 4.785 | (a) RCO7_01115 (transcription factor Som1) |
| (b) iHS—cluster 3 | 963272 | 4.343 | RCO7_01116 (phthalate 4,5-dioxygenase oxygenase reductase subunit) | ||
| RCO7_01117 (uncharacterized protein) | |||||
| 2 | RCO7_scaffold003 | (a) XP-EHH—cluster 2 versus Cluster 3 | 624918 | 3.564 | RCO7_02480 (ubiquitin-conjugating enzyme E2) |
| (b) iHS—cluster 3 | 624918 | 4.6574 | RCO7_02479 (MON2) | ||
| 3 | RCO7_scaffold012 | (a) XP-EHH—cluster 2 versus cluster 3 | 1822306 | −3.977 | (a) RCO7_02695 (uncharacterized protein) |
| (b) iHS—cluster 2 | 1823054 | 8.694 | RCO7_02696 (mediator complex subunit 7 (MED7)) | ||
| 1823058 | 8.694 | RCO7_02697 (Type 2 phosphatidic acid phosphatase (PAP2)) | |||
| 4 | RCO7_scaffold020 | (a) XP-EHH—cluster 2 versus cluster 1 | 647275 | −4.251 | RCO7_14617 (uncharacterized protein) |
| (b) iHS—cluster 2 | 646208 | 8.834 | (a) RCO7_03084 (uncharacterized protein) | ||
| 5 | RCO7_scaffold001 | (a) XPEHH—cluster2 versus cluster1 | 1026013 | 3.914 | RCO7_01132 (G-protein alpha chain) |
| (b) XPEHH—cluster1 versus cluster3 | 1025700 | 4.130 | |||
| 6 | RCO7_scaffold009 | (a) XPEHH—cluster 2 versus cluster 3 | 205732 | −4.091 | (a) intergenic |
| (b) XPEHH—cluster 1 versus cluster 3 | 204366 | −4.684 | (b) RCO7_06601 (Cu/Zn superoxide dismutase) | ||
| 7 | RCO7_scaffold002 | (a) XPEHH—cluster 2 versus cluster 1 | 818548 | −3.749 | RCO7_04583 (transmembrane protein with MARVEL domain) |
| (b) XPEHH—cluster 2 versus cluster 3 | 818548 | −3.574 | RCO7_04584 (domain of unknown function DUF2012) |
Note.—Regions 1–4 show selective sweep regions identified by both integrated haplotype score (|iHS|) and cross-population extended haplotype homozygosity (XP-EHH) analyses. Regions 5–7 show selective sweep regions identified in two separate XP-EHH analyses. Genes were reported if they were within 5,000 bp of the most significant single nucleotide polymorphism (SNP) locus (top 0.05%). For each XP-EHH selection analyses, the genetic cluster in which selection was detected is shown in bold. Gene names shown in bold are genes found in the overlap of both selection analyses. Gene names labelled with either (a) or (b) refer to which selection analyses identified these genes (see third column).