An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae)

TY - JOUR

T1 - An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae)

AU - Petersen, Gitte

AU - Seberg, Ole

AU - Aagesen, Lone

AU - Frederiksen, Signe Elisabeth

PY - 2004

Y1 - 2004

N2 - The ability of the program POY, implementing optimization alignment, to deal with major indels is explored and discussed in connection with a phylogenetic analysis of the genus Secale based on partial Adhl sequences. The Adhl sequences used span exon 2-4. Nearly all variation is found in intron 2 and intron 3, which form the basis for the phylogenetic analyses. Both in some ingroup and outgroup taxa intron 3 has a major duplication. Previous phylogenetic analyses have repeatedly confirmed monophyly of both Secale and Hordeum, the latter being part of the outgroup. However, optimization alignment only recovers both genera as monophyletic when knowledge of the duplication is incorporated in the analysis. The phylogenetic relationships within Secale are not clearly resolved. Subspecific taxa of Secale strictum have identical sequences and they are confined to a monophyletic group. However, the two subspecific taxa of Secale cereale do not form a monophyletic group, and the position of Secale sylvestre is uncertain.

AB - The ability of the program POY, implementing optimization alignment, to deal with major indels is explored and discussed in connection with a phylogenetic analysis of the genus Secale based on partial Adhl sequences. The Adhl sequences used span exon 2-4. Nearly all variation is found in intron 2 and intron 3, which form the basis for the phylogenetic analyses. Both in some ingroup and outgroup taxa intron 3 has a major duplication. Previous phylogenetic analyses have repeatedly confirmed monophyly of both Secale and Hordeum, the latter being part of the outgroup. However, optimization alignment only recovers both genera as monophyletic when knowledge of the duplication is incorporated in the analysis. The phylogenetic relationships within Secale are not clearly resolved. Subspecific taxa of Secale strictum have identical sequences and they are confined to a monophyletic group. However, the two subspecific taxa of Secale cereale do not form a monophyletic group, and the position of Secale sylvestre is uncertain.

U2 - 10.1016/S1055-7903(03)00206-9

DO - 10.1016/S1055-7903(03)00206-9

M3 - Journal article

SN - 1055-7903

VL - 30

SP - 733

EP - 742

JO - Molecular Phylogenetics and Evolution

JF - Molecular Phylogenetics and Evolution

IS - 3

ER -