Weighting schemes for molecular data

LONE AAGESEN; REINHEIMER RENATA

Congreso; Hennig XXX; 2011

The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Here we explore the two alignment parameters, gap cost versus base change costs, in analyses of DNA sequences of unequal lengths. We apply different gap and base change costs to the TCP-gene family data set in which the homology among sequences are unknown. Reliable homology assessments among the different duplicates of the TCP sequences are required before comparative studies aimed to analyze TCP genes function can be perform.         The TCP genes are a plant specific family of transcription factors with a highly conservative 59-amino acid motive that initiates gene transcription by binding to promoter regions of the DNA. During the evolution of land plants the TCP family has developed through duplication and diversification. Whole genome sequencing in plant species has lead to the discovery of a high number of TCP genes that counts five members in the Lycophyta but more than 20 members in Eudicots such as Oryza (rice) and Vitis (grapevine). Current knowledge divides the TCP gene family into two clades of which members of class II genes are known to control development of lateral branching and floral symmetry. The TCP class I genes are less known, and homology assessments among the members of class I is lacking. Class I TCP sequences are much more variable than Class II sequences, in the region flanking the conserved motive. This variability has so far hampered alignment of the sequences and consequently phylogenetic analysis of TCP class I genes are lacking. We analyze the TCP class I genes within a dynamic holomology framework. Homology assessments are complicated both by homoplastic changes in the sequences as well as sequence length differences of up to1248 bp. We analyze both the amino-acid sequences as well as the nucleotide sequences, searching for clades that are robust to changes in alignment parameter costs. Clades that survive a wide array of cost changes are considered best candidates for future comparative studies of TCP gene function.