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The unholy trinity: taxonomy, species delimitation and DNA barcoding
TLDR
A phylogenetic systematic framework for an improved barcoder as well as a taxonomic framework for interweaving classical taxonomy with the goals of ‘DNA barcoding’ are presented.
Multiple sources of character information and the phylogeny of Hawaiian drosophilids.
TLDR
The data suggest that significant incongruence among data partitions may be isolated to specific relationships and the "false" signal creating this incongrience is most likely to be overcome by a simultaneous analysis.
Tempo and mode of sequence evolution in mitochondrial DNA of HawaiianDrosophila
TLDR
The mtDNAs of flies and mammals are alike in the shape of the curve relating the percentage of positions at which there are differences in protein-coding regions to the time of divergence, and the low percentage of hypervariable sites may be a consequence of a functional constraint associated with the low content of guanine and cytosine in fly mtDNA.
Adaptive Evolution of Genes and Genomes
TLDR
The author concludes with a chapter that places modern molecular evolutionary studies in the context of Neo-Darwinism and characterises evolutionary biology as `a boat that the authors continually repair while remaining a ̄oat in it' (after Otto Neurath, p. 234).
Oil palm genome sequence reveals divergence of interfertile species in old and new worlds
TLDR
The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
Assessing the relative contribution of molecular and morphological characters in simultaneous analysis trees.
TLDR
Despite the significant incongruence found for nearly half the studies, the PBS indices suggest both types of data contribute positively to the combined analyses and that, when standardized by the number of phylogenetically informative characters, morphology data generally provide equal or greater support than do the molecular data.
Molecular phylogeny of Acipenserinae.
TLDR
The phylogenetic tree obtained for combined data is the first comprehensive treatment of phylogeny within the Acipenserinae and shows congruence between ploidy and the branching patterns of the sturgeon species.
caos software for use in character‐based DNA barcoding
TLDR
Here, a set of software tools is presented that implement the previously described Characteristic Attribute Organization System for both diagnostic identification and diagnostic‐based classification.
Alignment-ambiguous nucleotide sites and the exclusion of systematic data.
TLDR
A replicable methodology in which the comparison of several multiple sequence alignments can be used to eliminate regions of unstable sequence alignment is explored.
Class-level relationships in the phylum Cnidaria: molecular and morphological evidence.
TLDR
Analysis of class-level relationships based on 18S ribosomal DNA sequences, mitochondrial 16S rDNA sequence, mitochondrial genome structure, and morphological characters unifies the classes possessing a medusa stage, leaving the holobenthic Anthozoa basal within the phylum.
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