Construction of Phylogenetic Trees

Abstract

known responses in the visual system to show typical adaptation properties. This suggests that the site of visual adaptation may be in the bi-polarcell layer, the presumed locus of b-wave generation. Recent electron microscopic studies have demonstrated reciprocal synapses between the bipolar terminals and amacrine processes, and it is suggested that such a ;synaptic arrangement could account for visual adaptation by a mechanism of inhibitory feedback on the bipolar cells. known responses in the visual system to show typical adaptation properties. This suggests that the site of visual adaptation may be in the bi-polarcell layer, the presumed locus of b-wave generation. Recent electron microscopic studies have demonstratedreciprocal synapses between the bipolar terminals and amacrine processes, and it is suggested that such a ;synaptic arrangement could account for visual adaptation by a mechanism of inhibitory feedback on the bipolar cells.

High frequencies of alleles MICA*020 and MICA*027 in Amerindians and evidence of positive selection on exon 3

“…48 Both analyses were made with the software package Phylip. 49 The dendrogram was drawn using TreeView 1.6.6.…”

A reconsideration of the domestication geography of tetraploid wheats

“…The genetic relationships among the taxa considered were established using the phylogenetic analysis package PHYLIP (Felsenstein 1989) and the multivariate analysis system NTSYS (Rohlf 1998). For the phylogenetic analysis concerning AFLP allele frequencies in populations or groups of lines, ten independent trees were constructed as described (Heun et al 1997;Badr et al 2000), using CONTML and distance matrix methods (Fitch and Margoliash 1967;Saitou and Nei 1987), and employing various measures of genetic distance (Cavalli-Sforza and Edwards 1967;Nei 1972;Wright 1978;Reynolds et al 1983) calculated from AFLP allele frequency. To cluster single accessions (Fig.…”

“…c Genetic relationships of domesticated tetraploid wheats with wild T. dicoccoides groups sampled in different regions of the Fertile Crescent with origins already specified in b. Using programs of the PHYLIP package (1993), 10 independent trees were constructed as described (Heun et al 1997;Badr et al 2000) using CONTML (topology shown; Felsenstein 1981) and distance matrix methods (Fitch and Margoliash 1967;Saitou and Nei 1987) employing various measures of genetic distance (Cavalli-Sforza and Edwards 1967;Nei 1972;Wright 1978;Reynolds et al 1983) calculated from AFLP allele frequencies between groups of lines from the geographic regions indicated. The number of tree-buiding methods generating the same topologies is indicated at branches.…”

The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

“…Trees of the RecA sequences were generated using two parsimony methods (the protpars program in PHYLIP and the heuristic search algorithm of PAUP) and three distance methods (the least-squares method of De Soete (De Soete 1983) as implemented in GDE, and the Fitch-Margoliash (Fitch and Margoliash 1967) and neighbor-joining methods (Saitou and Nei 1987) as implemented in PHYLIP). Trees of the SS-rRNA sequences were generated using one parsimony method (the dnapars algorithm of PHYLIP) and the same three distance methods as used for the RecA trees.…”