In compiling this, the authors used a variety of phylogenetic information including molecular analysis, anatomical analysis, shell morphology and shell microstructure as well as bio-geographic, paleobiogeographic and stratigraphic information.
A ribosomal DNA study of Acer species in 2006 placed A. nipponicum along with the related A.caudatum near the base of the phylogenetic trees recovered.
AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic datasets.
The debate between Wells and Zalloua was whether haplogroup J2 (M172) should be identified as that of the Phoenicians or that of its "parent" haplogroup M89 on the YDNA phylogenetic tree.
Preliminary phylogenetic studies in 2006 using molecular and morphological evidence have suggested that the genus forms three natural species confined to the southeastern United States.
Study of the internal transcribed spacer region (ITS) of nuclear ribosomal DNA, combined with morphological data, have yielded a better-resolved phylogenetic hypothesis, confirming the distinctiveness of the above-named genera.
As a result of numerous molecular phylogenetic studies based on various chloroplast DNA (cpDNA) loci, it was shown to be more closely related to members of the Orobanchaceae.
Phylogenetic studies published by Jack Garrick in 1982 and Leonard Compagno in 1988, based on morphology, placed the bignose shark in the "obscurus group" of Carcharhinus, centered on the dusky shark (C. obscurus) and the Galapagos shark (C. galapagensis).
In 2006, Leticia de Almeida Leao Vaz and colleagues published a phylogenetic analysis, based on genomic DNA, of the Brazilian large-eyed stingray and three other common stingrays found off Brazil: the southern stingray (D. americana), the longnose stingray (D. guttata), and the roughtail stingray (D. centroura).
Phylogenetic analysis of DNA sequence data shows that within the Pezizales order, Caloscypha fulgens belongs in an evolutionary lineage with the families Helvellaceae, Morchellaceae, and Tuberaceae.
However in 2009, in an article titled "A phylogenetic classification of the land plants to accompany APG III," Mark W. Chase and James L. Reveal proposed a much broader sense for the Equisetopsida class name.
The phylogenetic analysis conducted by the author indicated that such defined Euhelopodidae, in addition to Euhelopus itself, contained genera Qiaowanlong, Erketu, Daxiatitan, Tangvayosaurus and Phuwiangosaurus as well.
In addition to the groups mentioned in the table above, the genus Malawimonas is generally considered to be a member of Excavata owing to its typical excavate morphology, and phylogenetic affinity to excavate groups in some molecular phylogenies.
In terms of the broader evolutionary relationships between the giant freshwater whipray and the rest of the family Dasyatidae, a 2012 phylogenetic analysis based on mitochondrial DNA reported that it was most closely related to the porcupine ray (Urogymnus asperrimus), and that they in turn formed a clade with the mangrove whipray (H. granulata) and the tubemouth whipray (H. lobistoma).
Phylogenetic analysis of the mitochondrial 16S ribosomal RNA gene and a range of other anomuran crustaceans, using Bayesian inference, places this species from the East Scotia Ridge as a sister taxon to Kiwa hirsuta, with a sequence divergence from this species of 6.45%, which is consistent for within-genus divergence in squat lobsters.
Phylogenetic analyses have indicated the Ibaliidae have spread from the eastern Palearctic and northern Asian regions in early Cretaceous.
RBP3 (Retinol-binding protein 3 = Interphotoreceptor retinoid-binding protein = Interstitial retinol-binding protein), an eye protein commonly used as a phylogenetic marker.
Other concentrations include the Chilean species of the widespread genus Berberis, the usage of computer models in evaluating methods of phylogenetic analysis, and serving on a committee of botanists (including D.J. Pinkava) working on a new manual of the vascular plants of Arizona to replace the aging Arizona Flora by Kearney and Peebles (last updated in 1960).
The development of DNA sequencing at the end of the twentieth century had a profound impact on the research of phylogenetic relationships within the family.
According to the result of a pilot phylogenetic analysis, the freshwater Mesocottus is a sister lineage to the Cottus clade.
The reconstruction of two highly unusual archaeal genomes by de novo metagenomic assembly of multiple, deeply sequenced libraries via multi-locus phylogenetic analyses, from surface waters of Lake Tyrrell, a hypersaline lake in north-west Victoria, Australia, has led to the creation of a major novel euryarchaeal lineage, distantly related to halophilic archaea of class Halobacteria.
16S rRNA phylogenetic analysis has been used to identify a member of Neisseria from closely related genera, but this method is unable to distinguish amongst the various species that compose the genus Neisseria.
Omega-atracotoxin is an insect-specific neurotoxin of Blue mountains funnel-web spiders whose phylogenetic specificity derives from its ability to antagonise insect, but not vertebrate, voltage-gated calcium channels.
Paul Sereno, for example, considered the family Omnivoropterygidae to be invalid because it is redundant and was not given a phylogenetic definition.
Along with examination of conserved synteny, conserved operon structure, or "Rosetta Stone" domain fusions, comparing phylogenetic profiles is a designated a "post-homology" technique, in that the computation essential to method begins after it is determined which proteins are homologous to which.
A shortcoming of current formats for describing phylogenetic trees (such as Nexus and Newick/New Hampshire) is a lack of a standardized means to annotate tree nodes and branches with distinct data fields (which in the case of a basic species tree might be: species names, branch lengths, and possibly multiple support values).
In 1976 Seemannia was synonymized under the genus Gloxinia by gesneriad specialist Hans Wiehler but has more recently been revived following phylogenetic and morphological research on relationships of Gloxinia and related genera, which suggested that Wiehler's generic concept of Gloxinia was overly broad and polyphyletic.
Therizinosauridae was first given a phylogenetic definition by Paul Sereno in 1998, who defined it as all dinosaurs closer to Erlikosaurus than to Ornithomimus.
When herpetologist G. K. Noble examined Allophryne, he suggested it was closely related to glassfrogs, a hypothesis later confirmed by recent phylogenetic studies, which have found Allophryne is the sister taxon of the glassfrog clade Centroleninae.
Apparently among modern phylogenetic systematists, Wagner is alone in having been mentioned in a Hollywood film (A New Leaf, starring Elaine May and Walter Matthau).
Andrzej Elżanowski (2001) of the Institute of Zoology of the University of Wrocław, Poland, determined the differences resulted from a "phylogenetic reduction rather than individual variation."