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. Author manuscript; available in PMC: 2011 Mar 16.
Published in final edited form as: Evolution. 2010 Dec;64(12):3443–3460. doi: 10.1111/j.1558-5646.2010.01092.x

Table 3.

Summary of the analyses of polymorphism, frequency spectrum tests of neutrality, recombination and divergence in O. c. algirus (alg.) and O. c. cuniculus (cun.).

Locus Polymorphism Frequency spectrum tests of neutrality Recombination Divergence
Mean π (%)1 Mean θ (%)2 Mean DT3 Mean DFL4 Mean γ (%)5 Mean ρ (%)6 Mean Dxy (%)7
X-linked* (19,282 bp) All 0.595 0.620 −0.038 −0.307 0.62 1.40 3.689
alg 0.420 0.471 −0.577 −0.473 1.42 1.56
cun 0.358 0.381 −0.271 −0.243 0.51 0.89
Autosomal* (16,007 bp) All 0.691 0.939 −0.974 −0.952 1.46 2.42 4.093
alg 0.633 0.777 −0.774 −0.501 1.13 2.07
cun 0.617 0.677 −0.390 −0.359 1.34 1.83
Overall* (35,289 bp) All 0.632 0.743 −0.399 −0.556 0.95 1.79 3.837
alg 0.502 0.589 −0.641 −0.484 1.28 1.77
cun 0.458 0.495 −0.317 −0.288 0.93 1.28
*

Unweighted average values across 27 X-linked loci, 17 autosomal loci, or 44 combined loci are given in each row.

1

The average number of pairwise differences in a sample (Nei 1987).

2

The proportion of segregating sites in a sample (Watterson 1975).

4

Fu and Li’s D* (Fu and Li 1993).

5

Maximum likelihood estimate of the population recombination parameter between adjacent sites (Hey and Wakeley 1997).

6

Composite likelihood method to estimate the population recombination parameter between adjacent sites, employing a finite sites mutation model (Hudson 2001).

7

Dxy is the average nucleotide divergence (Nei 1987) between all rabbit haplotypes and Lepus granatensis.