Table 3 Linkage disequilibrium estimate (D’) and associated estimation error for syntenic markers in 13 nine-spined stickleback populations and five habitat types (marine, lake, pond, river, and coastal freshwater) using 109 microsatellite markers
Data SetPhysical Distance Interval (Syntenic)Overall (Syntenic)
0−5 Mb5.001−10 Mb10.001−15 Mb15.001−20 Mb>20 Mb
Hel (M)0.557 (0.020)0.549 (0.024)0.500 (0.039)0.492 (0.051)0.649 (0.117)0.544 (0.014)
Sbol (M)0.557 (0.020)0.553 (0.024)0.534 (0.037)0.578 (0.048)0.519 (0.095)0.553 (0.014)
Lev (M)0.559 (0.020)0.590 (0.026)0.551 (0.037)0.571 (0.043)0.579 (0.103)0.570 (0.014)
Kro (L)0.509 (0.021)0.504 (0.021)0.445 (0.039)0.442 (0.048)0.373 (0.101)0.491 (0.013)
Ska (L)0.651 (0.050)0.539 (0.050)0.596 (0.090)0.959 (0.042)0.700 (0.174)0.631 (0.033)
Por (L)0.630 (0.031)0.716 (0.035)0.564 (0.068)0.615 (0.088)0.541 (0.147)0.648 (0.021)
L1 (L)0.551 (0.031)0.428 (0.042)0.536 (0.074)0.453 (0.101)0.471 (0.279)0.506 (0.023)
Rah (L)0.646 (0.027)0.672 (0.029)0.719 (0.051)0.616 (0.082)0.677 (0.053)0.663 (0.018)
Byn (P)0.553 (0.046)0.636 (0.056)0.628 (0.105)0.608 (0.102)0.767 (0.149)0.605 (0.032)
Pyo (P)0.804 (0.064)0.710 (0.101)0.579 (0.421)1.000 (0.000)0.781 (0.051)
Rbol (P)0.537 (0.022)0.599 (0.023)0.526 (0.038)0.455 (0.042)0.522 (0.085)0.551 (0.014)
Ryt (P)0.631 (0.041)0.604 (0.052)0.577 (0.092)0.521 (0.105)0.768 (0.232)0.612 (0.029)
Mat (R)0.509 (0.021)0.562 (0.027)0.532 (0.041)0.426 (0.043)0.580 (0.122)0.527 (0.015)
Marine (averagea)0.558 (0.001)0.564 (0.013)0.528 (0.015)0.547 (0.028)0.582 (0.038)0.556 (0.008)
Lake (averagea)0.597 (0.037)0.572 (0.069)0.572 (0.058)0.617 (0.121)0.552 (0.080)0.588 (0.047)
Pond (averagea)0.631 (0.070)0.637 (0.029)0.578 (0.024)0.646 (0.141)0.686 (0.082)0.637 (0.058)
CF (averagea)0.518 (0.009)0.555 (0.028)0.501 (0.028)0.441 (0.009)0.492 (0.062)0.523 (0.017)
Marine (combinedb)0.433 (0.017)0.450 (0.021)0.393 (0.033)0.357 (0.035)0.406 (0.082)0.428 (0.012)
Lake (combinedb)0.507 (0.017)0.486 (0.018)0.469 (0.028)0.451 (0.042)0.503 (0.111)0.491 (0.011)
Pond (combinedb)0.530 (0.022)0.578 (0.023)0.553 (0.037)0.531 (0.046)0.547 (0.069)0.550 (0.014)
CF (combinedb)0.383 (0.017)0.397 (0.021)0.332 (0.020)0.357 (0.039)0.413 (0.094)0.380 (0.011)
River0.509 (0.021)0.562 (0.027)0.532 (0.041)0.426 (0.043)0.580 (0.122)0.527 (0.015)
  • M, marine; L, lake; P, pond; R, river; CF, Coastal freshwater, including Kro, Rbol, and Mat. The population abbreviations are defined in Table 1. The value in the brackets is the estimation error associated to the mean D’ value, obtained by dividing the SD of D’ value by the square root of the number of marker pairs used to measure LD in each distance bin (Table S7).

  • a D′ value is directly obtained from the averaged D′ value of relevant populations.

  • b D′ value is calculated from the combined original haplotype data of relevant populations.