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Unfortunately the sensitivity has been affected by unaccounted noise and systematics since the beginning.
The identification of orthologous sequences is especially relevant for molecular systematics, since the addition of easily amplified and phylogenetically informative sequences to current datasets allows for the independent testing of phylogenetic hypotheses using as much data as possible.
Our focus on the chloroplast genome is driven by its phylogenetic informativeness at essentially all taxonomic scales and its relative ease of amplification (e.g., Downie and Palmer, 1992; Graham and Olmstead, 2000; Moore et al., 2007; Parks et al., 2009; Moore et al., 2010), which have made the chloroplast the workhorse of molecular plant systematics since the beginning of the field.
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The older systematists particularly and most vociferously Mayr and the paleontologist George Gaylord Simpson (both, by the way, former members of the AMNH staff)—pointed out that systematics had long since been based on the evolutionary relationships of species and higher taxa.
That long branch attraction can be a serious problem in phylogenetic inference has long been known to the systematics community, ever since this phenomenon was first explored by Felsenstein [ 37].
This locus has been considered as a "gold standard" for bacterial molecular systematics (Janda and Abbott 2007) since the days of DNA-DNA hybridization, but in spite of its functional and sequence conservation, it is now apparent that in the case of Mycobacterium as a genus, it does not reflect genome-level evolution.
The furor engendered by the upstart arrival of Hennig's ideas has long since died down and phylogenetic systematics is now the de facto order of the day.
Consensus methods in systematics date back to [ 6]; since then, many consensus methods have been designed.
In memory of the late Jan Bergström in the 40th year since his publication of Organization, life, and systematics of trilobites[ 90].
However, evolutionary biology has itself evolved since then as it incorporated advances in genetics, paleontology, and systematics (Huxley 1942), and later in other fields like developmental biology, molecular biology, and genomics (Pigliucci and Muller 2010).
A monophyletic origin of carnivory in Lamiales has been discussed since the introduction of molecular phylogenetics to the field of angiosperm systematics (see chapter on Lamiales in [ 90]).
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