Article Figures & Data
Figures
- Figure 1.—
Restriction map of furrowed and location of the region sequenced in this study. R1–R42 are EcoRI restriction fragments described by Chen et al. (2000). The R1 fragment covers part of the 5′-untranslated region (UTR) and exons 1–9; R9/R42 covers exon 12, the 3′-UTR, and 3′ flanking region. A 5.1-kb region (1.2 kb of R1 and 3.9 kb of R9 and R42) corresponding to the 5.7-kb fw fragment of Chen et al. (2000)(−600 bp of 5′ sequence) was amplified in three separate PCR reactions and subjected to direct sequencing.
- Figure 2.—
Representative polymorphism at fw. Length polymorphisms are not shown. The standard sequence is based on the inferred ancestral sequence as determined by D. pallidosa. All nucleotides shown as letters represent the derived state of the polymorphism. Polymorphisms distinguishing the northern haplotype class (sites 1504 of R1 and 687, 969, 3994, and 4106 of R9/R42) are highlighted in blue. Note that site 1004 of R1 is not diagnostic of this haplotype class because it is not completely linked to these sites (see CH population). Polymorphisms distinguishing the southern haplotype class (sites 1854 and 2961 of R9/R42) are highlighted in red. Coordinates of the R1, and R9 and R42 (combined), fragments correspond to those given by the accession nos. AF185289 and AF185290, respectively.
- Figure 3.—
Geographic distribution of fw haplotype frequencies.
- Figure 4.—
Relationship of nontransformed haplotype frequency and population latitude (measured as distance from the equator). Regressions (r2) and slopes (m) are based on transformed frequencies: northern r2 = 0.841 (P < 0.0001), m = 10.224; southern r2 = 0.669 (P < 0.001), m = −10.115.
- Figure 5.—
Summary of clinal variation at fw for all populations. Only sites with significant clinal variation are shown (see Table 4). Shaded boxes refer to significant clinal variation at site Y that cannot be explained by linkage to site X.
- Figure 6.—
Comparison of the migration-drift parameter, ΘP (Vogl et al. 2003), at fw and 10 neutral loci.
Tables
- TABLE 1
Population samples of D. ananassae used in this study
Sampling location Country Abbreviation No. of isofemale lines Collection date Chennai India CH 9 2000 Puri India PUR 8 2000 Bhubaneswar India BBS 9 2000 Kathmandu Nepal KATH 10 2000 Mandalay Myanmar MAN 10 1994 Chiang Mai Thailand CNX 10 2002 Bangkok Thailand BKK 8 2002 Kota Kinabalu, Borneo Malaysia KK 8 2002 Bogor, Java Indonesia BOG 16 2001 Darwin and Kakadu Australia DAR 9 1995 Cebu Philippines CEB 9 2002 Manila Philippines MNL 10 2002 Kumejima, Okinawa Japan KMJ 10 2000 - TABLE 2
Summary of polymorphism at fw
Population Diversity, π̂ Diversity, θ̂ Tajima's D Divergence CH 0.00140 0.00132 0.32 0.00563 PUR 0.00068 0.00065 0.26 0.00556 BBS 0.00049 0.00070 −1.36 0.00574 KATH 0 0 — 0.00591 MAN 0.00023 0.00022 0.10 0.00585 CNX 0.00110 0.00089 1.04 0.00563 BKK 0.00132 0.00114 0.80 0.00541 KK 0.00077 0.00098 −1.07 0.00507 BOG 0.00034 0.00082 −2.28** 0.00502 DAR 0.00077 0.00093 −0.80 0.00530 CEB 0.00053 0.00077 −1.49 0.00511 MNL 0.00077 0.00112 −1.44 0.00585 KMJ 0.00013 0.00022 −1.56 0.00592 ↵** P < 0.01.
Nucleotide diversity π̂ was estimated accordting to Nei (1987), and θ̂ according to Watterson (1975). The value of D was obtained by Tajima's (1989) method.
- TABLE 3
Results of pairwise HKA tests between fw and 10 neutral loci
Population Significant comparisons with fw Total significant comparisons P CH 0 4 1 PUR 5 5 7.2E-05 BBS 4 4 0.00062 KATH 10 10 3.4E-11 MAN 9 16 1.6E-05 CNX 1 1 0.18 BKK 2 3 0.08 KK 2 2 0.0303 BOG 0 0 1 DAR 3 3 0.00457 CEB 4 4 0.00062 MNL 1 1 0.18 KMJ 7 9 1.9E-05 The HKA test was performed for all pairwise comparisons between loci [11 loci (fw + 10 neutral loci) → 55 comparisons], for each of the 13 sampled populations. For each population, the probability of observing at least i significant tests at the fw locus given that n paired tests were performed and k were significant between the l loci was calculated using Equation 1 (see materials and methods). Populations in italics indicate that the number of comparisons deviating from the neutral expectation was significantly higher than expected for this population.
- TABLE 4
Summary of clinal variation of polymorphic sites at fw and 10 neutral loci
r2 Locus Site Frequency Slope All populations India SE Asia Easternmost fw 834 0.07 9.79 NS — — 0.821* (25) 1004 0.53 8.84 0.782*** NS 0.886* 0.812* 1504 0.49 10.46 0.857*** 0.929* 0.886* 0.812* 687 0.49 10.46 0.857*** 0.929* 0.886* 0.812* 969 0.49 10.46 0.857*** 0.929* 0.886* 0.812* 1069 0.19 8.9 0.305* NS NS — 1854 0.44 −10.57 0.693*** — 0.987** NS 2292 0.06 −6.05 NS 0.589* — — 2961 0.44 −10.57 0.693*** — 0.987** NS 3994 0.49 10.46 0.857*** 0.929* 0.886* 0.812* 4023 0.05 −11.8 NS 0.948* — — 4106 0.49 10.46 0.857*** 0.929* 0.886* 0.812* 1 4 0.07 −22.65 NS NS NS 0.808* (35) 10 0.14 6.81 NS NS NS 0.850* 14 0.19 5.74 NS NS NS 0.825* 53 0.14 −20.91 0.335* NS NS NS 2 28 0.05 21.56 NS — — 0.890* (63) 47 0.12 −23.67 0.283* NS NS NS 48 0.10 −48.77 0.424* — NS NS 80 0.78 5.46 NS — 0.933** NS 83 0.88 10.27 0.290* — 0.857* NS 89 0.02 −94.96 0.270* — 0.852* — 90 0.05 −5.48 NS — 0.852* NS 94 0.02 77.84 0.308* NS — — 3 3 0.31 5.35 NS 0.928* NS NS (60) 8 0.01 114.99 0.280* — — — 9 0.01 104.11 0.251* — — — 11 0.15 3.96 NS 0.994* NS NS 13 0.05 10.80 NS — 0.840* NS 18 0.01 114.99 0.280* — — — 47 0.01 114.99 0.280* — — — 52 0.81 −1.16 NS NS NS 0.802* 53 0.80 −2.78 NS NS NS 0.802* 4 72 0.07 23.81 NS — NS 0.795* (34) 5 2 0.18 −18.56 NS 0.936* NS NS (27) 13 0.05 −57.94 0.343* — NS NS 6 7 0.18 28.16 0.398* NS NS NS (10) 7 10 0.10 8.36 NS NS NS 0.821* (19) 20 0.01 −126.33 0.370** — — — 8 8 0.03 −50.13 0.305* — NS — (15) 9 22 0.91 18.28 0.454** — NS 0.959** (29) 25 0.33 −4.82 NS 0.931* NS NS 10 7 0.01 −129.66 0.356* — 0.852* — (34) 21 0.25 12.62 0.315* 0.943* NS NS 23 0.86 4.74 NS 0.935* NS NS 39 0.27 13.13 0.303* NS NS NS 46 0.16 10.41 NS NS NS 0.874* 58 0.37 −10.48 0.313* NS NS NS ↵* P < 0.05;
↵** P < 0.01;
↵*** P < 0.001.
The numbers of polymorphic sites analyzed for clinal variation (singletons were eliminated) at each locus are indicated in parentheses in column 1. Only sites displaying significant clinal variation in one or more subsets (see below) are shown. The frequency of individual sites is calculated for the entire pooled sample, on the basis of the derived state of the polymorphism as determined by the outgroup D. pallidosa. The slopes are computed from transformed data based on the entire pooled sample. Regressions (r2) of transformed allele frequencies on latitude were performed for all the populations combined, as well as the following subsets: India (KATH, BBS, PUR, and CH), SE Asia (MAN, CNX, BKK, and BOG), and Easternmost (KMJ, MNL, CEB, KK, BOG, and DAR). Polymorphic sites monomorphic or occurring only once in individual subsets are indicated by dashes. NS, no significant clinal variation.
- TABLE 5
Probability of obtaining the observed or lower values of FST under the background selection model
k = 100 k = 500 Population 1 Population 2 Region of comparison R = 0 R = 0.1 R = 0 R = 0.1 KATH MAN N-N 0.068 0.057 0.070 0.032 KATH BBS N-N 0.039 0.027 0.039 0.012 KATH KMJ N-N 0.080 0.077 0.080 0.078 MAN BBS N-N 0.025 0.029 0.025 0.005 MAN KMJ N-N 0.051 0.035 0.050 0.019 KATH BOG N-S 0.522 0.536 0.525 0.556 MAN DAR N-S 0.456 0.458 0.461 0.437 BBS DAR N-S 0.516 0.498 0.509 0.473 BBS BOG N-S 0.747 0.766 0.737 0.770 KMJ KK N-S 0.342 0.322 0.332 0.299 DAR BOG S-S 0.107 0.074 0.107 0.030 DAR CEB S-S 0.048 0.034 0.045 0.017 DAR KK S-S 0.065 0.046 0.065 0.019 BOG CEB S-S 0.056 0.038 0.057 0.013 BOG KK S-S 0.064 0.039 0.069 0.012 Significant comparisons are shown in italics. N, North; S, South.
