A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unli...

Geological evolution of the Indian and Pacific Ocean basins, including the Tethys Sea, is relevant to the evolution and distribution of Indo-Pacific freshwater fishes. Area cladograms derived from phylogenetic analyses of atherinomorph fishes are compared, in part, with those for plant bugs, cicadas and bats. Geologically and biologically composite islands in the Indo-Australian archipelago suc...

We conducted the first comprehensive phylogenetic analysis of Psephenidae, based on 143 morphological characters of adults, larvae and pupae and coded for 34 taxa, representing three outgroups and 31 psephenid genera, including four undescribed ones. A strict consensus tree calculated (439 steps, consistency index 1⁄4 0.45, retention index1⁄4 0.75) from the two most-parsimonious cladograms indi...

Evolutionary trees communicate both the diversity and unity of life, a central important scientific concept, as highlighted by Vision Change undergraduate biology education movement. cladograms are diagrams viewed biologists Rosetta Stone-like in how well they convey an enormous amount information with clarity precision. However, majority undergraduates introductory courses find non-li...

The evolutionary divergence of the galling habit of aphids (Homoptera: Fordinae) that induce different gall types on Pistacia spp. (Anacardiaceae) trees in the Mediterranean region was examined. The phylogenetic cladogram of the aphids that was based on sequences of mitochondrial genes (COI and COII) was constructed. Placing gall traits on the single parsimony cladogram suggests that gall types...

This study identified the genetic diversity of amylase-producing lactic acid bacteria from brown rice (Oryza nivara) Wakawondu cultivar based on 16S rRNA gene. The ten strains were isolated fermented washing water; two isolates, SBM3D and SBM4A, displayed strong amylase activity. isolates had same characteristics according to both morphological biochemical examination. effect fermentation time ...

SUMMARY We implement a program that incorporates polymorphic sites data, haplotype frequency arrays, and other factors, into cladogram estimation.

The first comprehensive combined molecular and morphological phylogenetic analysis of the major groups of termites is presented. This was based on the analysis of three genes (cytochrome oxidase II, 12S and 28S) and worker characters for approximately 250 species of termites. Parsimony analysis of the aligned dataset showed that the monophyly of Hodotermitidae, Kalotermitidae and Termitidae wer...

A fully resolved cladogram for 19 species in the Charis cleonus group of riodinid butterflies, which have closely parapatric ranges throughout the Amazon basin, is used to derive an area cladogram for the region. This represents the first comprehensive species-level analysis using insects and results in a hypothesis of Amazonian area relationships that is the most detailed to date. The Charis a...