DNA-DNA hybridization is among a class of comparative techniques in molecular biology that produce distance data (versus character data) and that can be analyzed to produce phylogenetic reconstructions only using phenetic tree-building algorithms. In DNA-DNA hybridization, the percent similarity of DNA between two species is estimated by the reduction in hydrogen bonding between nucleotides of imperfectly complemented heteroduplex DNA, (i.e., double stranded DNAs that are experimentally produced from single strands of two different species) compared with perfectly matched homoduplex DNA (both strands of DNA from the same species).
This revolutionary reordering was initially widely accepted by North American ornithologists, and the American Ornithologists' Union adopted some of its provisions. In other parts of the world its adoption has been more deliberative: it has been a respected major influence on existing classification schemes but hardly any authority adopted it in its entirety. Today, the Sibley-Ahlquist taxonomy has fallen out of use; cladistic analyses have questioned its very methodological foundations and most of the proposed major changes (with one notable exception) are today considered to be false.
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The resulting arrangement differs greatly from the more traditional approach used in the Clements taxonomy. More recently published phylogenetic reconstructions based on cladistic and maximum likelihood analyses of DNA sequences lend credence to some of the DNA-DNA hybridization-based taxonomy, e.g. the recognition of palaeognathous birds as monophyletic and sister to all others, and the recognition that fowl and waterfowl (Galloanserae, initially named "Galloanseri") are one anothers' closest relatives and sister to the remainder of all birds, Neoaves. However, new studies also categorically reject many of the rearrangements in the Sibley-Ahlquist classification, e.g., the all-encompassing order Ciconiiformes, placement of buttonquails at the base of Neoaves, and the monophyly of the Corvida as well as the Passerae, to name a few.
Even DNA-DNA hybridization studies produced later on in other laboratories disagree with some of Sibley and Ahlquist's results, e.g., inclusion of the limpkin in the sungrebe family, and the placement of flamingos near storks rather than next to grebes.
The major changes at order level are as follows:
Some of these changes are minor adjustments. For instance, instead of putting the swifts, treeswifts, and hummingbirds in the same order that includes nothing else, Sibley and Ahlquist put them in the same superorder that includes nothing else, consisting of one order for the hummingbirds and another for the swifts and treeswifts. In other words, they still regard the swifts as the hummingbirds' closest relatives.
Other changes are much more drastic. The penguins were traditionally regarded as distant from all other living birds. For instance, Wetmore put them in a superorder by themselves, with all other non-ratite birds in a different superorder. Sibley and Ahlquist, though, put penguins in the same superfamily as divers (loons), tubenoses, and frigatebirds. According to their view, penguins are closer to those birds than herons are to storks.
The new research suggested that the ducks and gallinaceous birds are each other's closest relatives and together form the basal lineage of neognathous (non-ratite) birds, distinct from the others which are collectively called Neoaves. The ratites and tinamous are followed by the ducks and their allies and the pheasants and their allies. Penguins, grebes and divers are placed with other groups that were traditionally considered more modern.
A more recent paper by van Tuinen, Sibley, and Hedges looked in more detail at the early ancestry of bird groups. The traditional view of avian evolution places ratites and tinamous at the base of the tree of modern birds (Neornithes), followed by old marine groups such as the penguins, grebes and divers.
The Galloanseres (waterfowl and landfowl) have found widespread acceptance and roundabout support. The ancientness was splendidly confirmed with the 2005 report on Vegavis iaai, an essentially modern but most peculiar waterfowl that lived near Cape Horn some 66-68 million years ago, still in the age of the dinosaurs.
On the other hand, penguins, grebes, divers, and so on (colloquially sometimes called "higher waterbirds") are still considered very ancient neoavian orders - quite possibly together with the shorebirds (waders) which seem a bit older still, the most ancient ones. The supposed distinctness of the storks and herons as well as at least the supposed degree of closeness of penguins to frigatebirds have been refuted. They, as well as the "Ciconiiformes" assemblage, appear to be due to the shortcomings, both methodological and analytical, of DNA-DNA hybridization.
Today, no major ornithological organization uses the Sibley-Ahlquist taxonomy anymore. The AOU, starting in the late 1990s, moved away from advocating the Sibley-Ahlquist taxonomy and today advocates the Howard-Moore taxonomy as baseline. Compared to the main competitor, the Clements taxonomy (which at that time was based on simple qualitative analyses of morphology), it can be stated that most of the changes suggested by Sibley and Ahlquist - with the notable exception of the Galloanserae - are erroneous and caused by the flawed methodology.