Hello everyone,

I want to calculate genetic distances between intron allele sequences, but within these sequences is there a minisatellite, where a 19-bp motif may duplicate 2-6 times. I previously used K2P (Kimura-2-parameter) distances for Mantel tests and phylogeny constructions, but a reviewer commented that "since there are many gaps (i.e. indels) in the alignments, K2P can't effectively reflect such variations. In addition, repeat number variation can be faster than SNPs and using K2P or other measures without taking into account that repeat number variation is a single event and not multiple indels could generate very misleading distances and phylogenies. Thus, I believe the authors should modify their evolutionary model of intron sequence variation and reanalyze the data".

Do you know what model I should use to calculate genetic distances? My alignment is attached.

Any comments are welcome.

Yongjie Zhang

>A
GTTCGTGCCGTGTGGA-CCCCGAAGTGCCGGGTGGACCCCCGAA--------------------------------------------------------------------------------GCTTGTCCGGGCCACCACTGACGAGACTGGCGCGTTAG
>B
GTTCGTGCCGTGTGGA-CCCCGAAGTGCCGGGTGGACCCCCGAA--------------------------------------------------------------------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>C
GTTCGTGCCGTGTGGATCCCCGAAGTGCCGGGTGGACCCCCGAA--------------------------------------------------------------------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>D
GTTCGTGCCGTGTGGATCCCCGAAGTGCCGGGTGGACCCCCGAAGCGCCGTGTGGA-CCCCGAA------------------------------------------------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>E
GTTCGTGCCGGGTGGATCCCCGAAGTGCCGGGTGGATCCCCGAAGCGCCGGCCGGACCCCCGAA------------------------------------------------------------GCTTGCCCGGGCCGCCACTGACGAGACTGGCGTGTTAG
>F
GTTCGTGCCGTGTGGA-CCCCGAAGTTCCGGGTGGACCCCCGAAGTGCCGGGTGGA-CCCCGAAGTGCCGTGTGGACCCCCGAA----------------------------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>G
GTTCGTGCCGTGTGGATCCCCGAAGTGCCGGGTGGACCCCCGAAGCGCCGTGTGGA-CCCCGAAGTGCCGTGTGGACCCCCGAA----------------------------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>H
GTTCGTGCCGTGTGGATCCCCAAAGTGCCGGGTGGACCCCGGAAGTGCCGTGTGGA-CCCCGAAGTGCCGTGTGGACCCCCGAA----------------------------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>I
GTTCGTGCCGTGTGGACCCCCGAAGTGCCGGGTGGATCCCCGAAGTGCCGGGTGGATCCCCGAAGCGCCGGCCGGACCCCCGAA----------------------------------------GCTTGCCCGGGCCGCCACTGACGAGACTGGCGTGTTAG
>J
GTTCGTGCCGTGTGGA-CCCCGAAGTGCCGTGTGGA-CCCCGAAGTTCCGGGTGGACCCCCGAAGTGCCGGGTGGA-CCCCGAAGTGCCGTGTGGACCCCCGCA--------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>K
GTTCGTGCCGTGTGGA-CCCCGAAGTGCCGTGTGGA-CCCCGAAGTTCCGGGTGGACCCCCGAAGTGCCGGGTGGA-CCCCGAAGTGCCGTGTGGACCCCCGAA--------------------GCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG
>L
GTTCGTGCCGTGTGGA-CCCCGAAGTGCCGGGTGGACCCCCGAAGTTCCGGGTGGATCCCCAAAGTGCCGGGTGGACCCCCGAAGCGCCGGGTGGACCCCCGAA--------------------GCTTGCCCGGGCCGCCACTGACGAACCTGGCGTGTTAG
>M
GTTCGTGCCGTGTGGA-CCCCGAAGTGCCGTGTGGA-CCCCGAAGTGCCGTGTGGA-CCCCGAAGTTCCGTGTGGACCCCCGAAGTGCCGGGTGGA-CCCCGAAGTGCCGTGTGGACCCCCGAAGCTTGTCCGGGCCGCCACTGACGAGACTGGCGCGTTAG