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Table 1 Topology of gene trees and summary of tests for positive selection and increased nonsynonymous rate in specific lineages

From: Adaptation and convergence in circadian‐related genes in Iberian freshwater fish

Topology of phylogenetic gene tree

Genes

Gene-wide test for positive selectiona

Branch test for positive selectionb

Site-level positive selectionc

Increased nonsynonymous rated

Positive selection?

Positive selection?

Branch of the gene tree under selection

Positive selection?e

(Sc, SpT, SpG) vs. (St, Sa) clades*,e

Convergent lineagese

Species tree

((Sc,SpT),SpG),(Sa,St)*

cry1ba

✖(–)

✔ (1)

per1a

✔ (6)

✔ (3)

per3

S. pyrenaicus (Almargem)

✔ (6)

✔ (3)

bmal2

✔ (5)

✔ (11)

Convergence (Sc,SpT),(St,(Sa,SpG))*

cry1aa

✔ (1)

✖(–)

cry1bb

✖(–)

✔ (11)

clockb

S. carolitertii

✔ (3)

✖(–)

clock2

✔ (1)

✔ (3)

Convergence ((Sc,SpT),St),(Sa,SpG)*

cry3

✔ (14)

✔ (12)

per1b

S. torgalensis

✔ (1)

✖(–)

per2

S. torgalensis +

S. aradensis

✔ (15)

✔ (1)

clocka

✔ (2)

✖(–)

bmal1a

✖(-)

✖(–)

Other topologies

cry1ab

✖(-)

cry2

✔ (1)

✔ (2)

bmal1b

✖(–)

  1. *Sc, Squalius carolitertii; SpT, Squalius pyrenaicus (Tagus population); SpG, Squalius pyrenaicus (Almargem population);
  2. St, Squalius torgalensis; Sa, Squalius aradensis.
  3. aBUSTED[78]; baBSREL[80, 81]; cMEME[79] and FUBAR[83]; dContrast-FEL[84]; eNumber of sites within parenthesis