Article Figures & Data
Figures
- Figure 1.—
Two cluster configurations from the three-states Potts–Dirichlet model. For ψ = 0.1, no spatial structure can be observed (the situation is close to the noninformative prior used by STRUCTURE). For ψ = 0.9, a number of nonnecessarily connected random clusters can be observed.
- Figure 2.—
Distributions of the number of clusters estimated by the HRMF model. Data sets were simulated from the prior distributions of the HMRF model. The vertical lines indicate the true number of populations.
- Figure 3.—
Estimated cluster configuration for the Scandinavian brown bear data set in North Sweden using the HMRF model (four clusters).
- Figure 4.—
Sampled geographical coordinates of 70 individuals from the Pakistan data set and the associated Dirichlet tiling. (The full sample was not shown but a similar spatial distribution was assumed for the 200 individuals.)
- Figure 5.—
The reconciliation illustrated. At the left of the ψ-axis, a clustering analysis does not account for the spatial continuity of allele frequencies and may detect more clusters than actually exist. At the right, the pure continuity hypothesis assumes no cluster. Here the vision is intermediate, with the main discontinuities confirmed, but some small clusters may be considered nonsignificant.
Tables
- TABLE 1
Proportions of individuals assigned to extra clusters given the number of estimated clusters
and their true number KTrue K = 1 0 0.02 0 0 0 True K = 2 — 0 0.0136 — 0.03 True K = 3 — — 0 0.0096 0.0267 — indicates cases that never occurred during the simulation study.
- TABLE 2
Error rate in coassignments (ERCA) for 200 simulated data sets (n = 100, L = 10, J𝓁 = 10) with Kmax = 2
Genetic structure: Spatial structure: Inbreeding FST ψ (ϕ1, ϕ2) Nonspatial model HMRF model GENELAND All All All 16.1 0.7 3.2 FST ≤ 0.08 All All 26.3 1.6 6.6 0.08 < FST ≤ 0.09 All All 7.6 0.6 1.4 0.09 < FST ≤ 0.1 All All 8 0.6 1.4 FST > 0.1 All All 8.3 0.2 1.1 All ψ ≤ 0.2 All 1.1 1 1.1 All 0.2 < ψ ≤ 0.4 All 1 0.8 1.6 All 0.4 < ψ ≤ 0.6 All 2.7 0.7 0.9 All 0.6 < ψ ≤ 0.8 All 28.2 0.4 4.7 All ψ > 0.8 All 42.4 0.5 6.9 All All (<0.06, <0.06) 17.2 0.3 0.7 All All (<0.06, >0.1) or (>0.1, <0.06) 10 0.5 1.9 All All (>0.1, >0.1) 12.3 1 1.5 FST ≤ 0.08 ψ ≤ 0.4 All 2.7 2.1 2.8 FST ≤ 0.08 0.6 < ψ ≤ 1 All 41.8 0.9 9.4 FST > 0.1 ψ ≤ 0.4 All 0.2 0.1 0.4 FST > 0.1 0.6 < ψ ≤ 1 All 23.7 0.3 2.4 The three models were initialized at Kmax = 2.
- TABLE 3
Latitudes and longitudes for the eight Pakistan samples (from Cann et al. 2002)
Sample name Latitude Longitude Sample size Brahui 30°–31° N 66°–67° E 25 Balochi 30°–31° N 66°–67° E 25 Hazara 33°–34° N 70° E 25 Makrani 26° N 62°–66° E 25 Shindi 24°–27° N 68°–70° E 25 Pathan 32°–35° N 69°–72° E 25 Kalash 35°–37° N 71°–72° E 25 Burusho 36°–37° N 73°–75° E 25
