Genetic diversity and population structure based on mitochondrial
markers
To perform the genetic analyses, we edited and aligned COI and cytb sequences using CodonCode Aligner 4.0.4 (CodonCode Corporation,
Dedham, MA) and carefully checked the chromatograms for ambiguities and
sequences to detect the presence of any stop codons, as well as
alignment gaps.
Because mitochondrial sequences are linked within the same genome, COI
and cyt b sequences were concatenated for the analyses. First, to
analyze the genetic variation within the species and understand the
relationship among haplotypes, we calculated the average p distances
using MEGA 5.2 (Tamura et al. 2011) and generated haplotype networks
using the median joining algorithm implemented in PopART 1.0
(< http://popart.otago.ac.nz >), respectively. We
conducted an analysis of molecular variance (AMOVA) in Arlequin 3.5
(Excoffier and Lischer 2010) to explore the distribution of genetic
variation within T. ruficapillus and specifically test whether
there are differences in the frequency of mitochondrial haplotypes among
subspecies. The ΦST values between pairs of subspecies
were computed using uncorrected genetic distance matrices between
haplotypes and significance was tested through 2,000 random
permutations.