Bootstrapping analysis gives a way to judge the strength of support for nodes on phylogenetic trees.

In 2010 an analysis of available genetic data, mapping them to phylogenetic trees, gave " firm quantitative support for the unity of life.

# the science of phylogenetics and its methods ( phylogenetic analysis = cladistic analysis ), although sometimes the term is restricted to maximum parsimony ;

Both the first method for cladistic analysis and the school of taxonomy originated in the work of the German entomologist Willi Hennig, who referred to it as " phylogenetic systematics " ( also the title of his 1966 book ); the use of the terms cladistics and clade was popularized by other researchers.

The outcome of a cladistic analysis is a cladogram – a tree-shaped diagram ( dendrogram ) that represents a phylogenetic hypothesis, a hypothesis on evolutionary relationships.

Although traditionally such cladograms were generated largely on the basis of morphological characters and originally calculated by hand, genetic sequencing data and computational phylogenetics are now very commonly used in phylogenetic analysis.

Datasets are tables consisting of molecular, morphological, ethological and / or other characters and a list of operational taxonomic units ( OTUs ) which may be genes, individuals, populations, species, or larger taxa that are presumed to be monophyletic and that are presumed to form, all together, one large clade ; phylogenetic analysis reconstructs the branching pattern within that clade.

In the 1980s, phylogenetic analysis of the phocids has led to a few conclusions about the interrelatedness of the various genera.

Molecular phylogenetic analysis of Fringillidae, " New World nine-primaried oscines " ( Aves: Passeriformes ).

( 2006 ) conducted a molecular phylogenetic analysis of 12 of the above 17 species using DNA sequence from three genes: 12S rRNA, cytochrome b, and von Willebrand factor.

The following phylogenetic tree is from a cladistic analysis of DNA that was published in 2011.

Daphniphyllum was always thought to have an anomalous combination of characters and it was placed in several different orders before molecular phylogenetic analysis showed it to belong to Saxifragales.

* TNT (" Tree analysis using New Technology "), a phylogenetic software package

* Evolution of the mammalian placenta revealed by phylogenetic analysis

Based on phylogenetic analysis these two genotypes appear to have originated in West Africa and was introduced first into Brazil.

Recent phylogenetic studies based on cpDNA restriction site analysis and gene sequencing strongly suggest that the Cannabaceae sensu stricto arose from within the former Celtidaceae family, and that the two families should be merged to form a single monophyletic family, the Cannabaceae sensu lato.

and phylogenetic analysis suggests that they are more derived than either of these groups.

All the data are then organized into a " taxon-character matrix ", which is the base to perform phylogenetic analysis.

Basidiomycota that reproduce asexually ( discussed below ) can be recognized as members of this phylum by gross similarity to others, by the formation of a distinctive anatomical feature ( the clamp connection-see below ), cell wall components, and definitively by phylogenetic molecular analysis of DNA sequence data.

* Ross J, Jiang H, Kanost MR, Wang Y. Serine proteases and their homologs in the Drosophila melanogaster genome: an initial analysis of sequence conservation and phylogenetic relationships.

* DNA sequence analysis and phylogenetic estimates suggest that nuclear DNA contains genes that probably came from plastids.

While it is one of the most profound evolutionary changes known, it is also one of the best understood, largely thanks to a number of amazing fossil finds in the late 20th century combined with improved phylogenetic analysis.

A recent study of Convolvulaceae species, Ipomoea asarifolia, and its associated fungi showed the presence of a fungus, identified by DNA sequencing of 18s and ITS ribosomal DNA and phylogenetic analysis to be closely related to fungi in the family Clavicipitaceae, was always associated with the presence of ergoline alkaloids in the plant.

In 2007 the American Ornithologists ' Union's North American checklist moved Cathartidae back into the lead position in Falconiformes, but with an asterisk that indicates it is a taxon " that is probably misplaced in the current phylogenetic listing but for which data indicating proper placement are not yet available ".

In 2007 the American Ornithologists ' Union's North American checklist moved Cathartidae back into the lead position in Falconiformes, but with an asterisk that indicates it is a taxon " that is probably misplaced in the current phylogenetic listing but for which data indicating proper placement are not yet available ".

Recent phylogenetic evidence indicates that it is the closest relative of the vervet monkey ( Chlorocebus aethiops ), suggesting nomenclatural revision.

A comparative phylogenetic approach in the Australian Wet Tropics indicates that regional patterns of species distribution and diversity are largely determined by local extinctions and subsequent recolonizations corresponding to climatic cycles.

A recent phylogenetic analysis by May-Collado & Agnarsson ( 2006 ) indicates that two species traditionally assigned to the genus Lagenorhynchus, the Hourglass Dolphin L. cruciger and Peale's Dolphin L. australis are actually phylogenetically nested among the species of Cephalorhynchus, and they suggest that these two species should be transferred to the genus Cephalorhynchus.

Recent phylogenetic research, based on leaf arrangement, leaf anatomical characters and stipules, indicates that there are at least two subgenera in Artocarpus:

Typically, a branch length of a phylogenetic tree is expressed as the expected number of substitutions per site ; if the evolutionary model indicates that each site within an ancestral sequence will typically experience x substitutions by the time it evolves to a particular descendant's sequence then the ancestor and descendant are considered to be separated by branch length x.

For this reason, scientists had long believed that mesonychids were the direct ancestor of Cetacea, but the discovery of well preserved hind limbs of archaic cetaceans, as well as more recent phylogenetic analyses now indicates that cetaceans are more closely related to hippopotamids and other artiodactyls than they are to mesonychids, and this result is consistent with many molecular studies.

Based on phylogenetic research, the latest ( 2009 ) revision of the APG classification groups together these three families under the conserved name of Amaryllidaceae.

For these and other reasons, phylogenetic nomenclature has been developed ; it is still controversial.

While taxonomists using molecular phylogenetic techniques find strong support for the order, there remain questions about the morphological relationships of the Quillajaceae and Surianaceae to the rest of the order, due in part to limited research on these families.

Since 1993, the circumscriptions of these two subfamilies have been changed in light of phylogenetic studies of DNA sequences.

The relationships of these families were uncertain until 2011, when they were resolved in a molecular phylogenetic study based on two nuclear genes and ten chloroplast genes.

Discoverers would name these as separate species ( listed below ), and came up with several phylogenetic schemes for how they were related to each other.

Anthropologist John D. Hawks expresses the view that rather than explaining human traits simply and parsimoniously, it actually requires two explanations for each trait-first that proximity to water drove human evolution enough to significantly change the human phenotype and second that there was significant evolutionary pressure beyond mere phylogenetic inertia to maintain these traits ( which would not be adaptive on dry land ) and points out that exaptation is not an adequate reply.

In general, the output tree of a phylogenetic analysis is an estimate of the characters phylogeny ( i. e. a gene tree ) and not the phylogeny of the taxa ( i. e. species tree ) from which these characters were sampled, though ideally, both should be very close.

Northwest Caucasian languages have been suggested as being related to the Northeast Caucasian languages and both are often merged under the blanket term " North Caucasian languages "; several linguists, notably Sergei Starostin, posit a phylogenetic link between these two families.

However, various groups that lack these traits may be considered excavates based on genetic evidence ( primarily phylogenetic trees of molecular sequences ).

In 2008, a study that included molecular phylogenetic analysis of museum specimens in the genera Moho and Chaetoptila, both extinct genera endemic to the Hawaiian islands, argued that these five species were not members of the Meliphagidae and instead belong to their own distinct family, the Mohoidae.

The different so-called " natural " or " monophyletic " groups form nested units, and only these are given phylogenetic names.

However, three of these genera are not supported as monophyletic by recent phylogenetic studies ( Jackman et al.

Formerly the Monogenea were included in Trematoda on the basis that these worms are also vermiform parasites, but modern phylogenetic studies have raised this group to the status of a sister class within the Platyhelminthes, along with the Cestoda.

Comparative psychology refers to the scientific study of the behavior and mental processes of non-human animals, especially as these relate to the phylogenetic history, adaptive significance, and development of behavior.

Molecular phylogenetic analyses have proven these three are all distinctive and separate species ; other taxa formerly believed to be unique species or subspecies, such as B. betulicola, B. chippewaensis, B. persoonii, B. quercicola and B. venturii, are now known to be part of a B. edulis species complex with a wide morphological, ecological and geographic range, and that the genetic variability in this complex is low.

A clade consisting of these three phyla is strongly supported by phylogenetic analyses based upon a number of different proteinsThese phyla also branch in the same position based upon conserved signature indels in a number of important proteins.

Few phylogenetic studies of these parasites have been done, and their the relationship to their mosquito hosts is still being determined.

The megamouth shark ( Megachasma pelagios ) was placed as the next-closest relative to these taxa, though the phylogenetic position of that species has yet to be resolved with confidence.

Of the several potential causes for this constant redefinition the greatest is probably that little is known about its intergeneric relationships or a lack of phylogenetic understanding enhanced by the other problems of conflicting clues from morphological characters, the large size of the tribe, the absence of a precise delimitation or circumscription of Senecio and the naturalness of these assemblages combined with the imprecise boundaries of the different species themselves.

Since the mid-1990s these more sophisticated tree-and network-based phylogenetic methods have been used to investigate the relationships between languages and to determine approximate dates for proto-languages.