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Table 2 Historical population expansion by clade

From: Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni

 

Upland

Lowland

Southeastern

Mean (obs.)

11.796

5.858

10.000

Ï„

11.250 (5.356 – 22.945)

2.180 (0.534 – 4.627)

3.000 (0.430 – 3.160)

θ0

4.945

0.002

0.219

θ1

4.962

4.003

0.290

SSD

0.047 P = 0.458

0.044 P = 0.056

0.155 P = 0.030

Raggedness Index

0.045 P = 0.640

0.142 P = 0.107

0.667 P = 0.620

t (MYA)

0.793 (0.378 – 1.618)

0.154 (0.038 – 0.326)

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Fu's F

2.686 P = 0.880

-1.547 P = 0.324

8.007 P = 0.99

Tajima's D

-1.707 P > 0.05

-0.834 P > 0.01

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  1. Mismatch analysis parameters by clade: mean number of observed differences; expansion parameter τ (with upper and lower bounds at α = 0.05); θ is the substitution rate before (0) and after (1) the expansion; SSD tests the validity of a stepwise expansion model based on the sum of squares deviations between the observed and expected mismatch, with probability values (P). Non-significant mismatch values suggest population expansion. Raggedness Index is calculated similarly, and with probability values (P). Non-significant raggedness values suggest population expansion. Time since lineage expansion (t) is calculated from τ = 2μt, where μ = 1.0%/MYR for 709 bp. Under a model of sudden population expansion, Fu's F and Tajima's D are expected to be significantly negative. Some parameters are not estimated for the Southeastern Clade because of small sample sizes.