Generic affinities among crocodilians as revealed by DNA fingerprinting with a Bkm-derived probe.

Abstract

Genetic fingerprint profiles have been succesfublly used for estabishing biological relationships, in linkage analysis, and in studies ofpopulato structure but have not so far been used for ascertalning phylogenetic relationships among related groups of species and genera. This Is largely because these proffles are thought to evolve too rapidly to be informative over large time intervals. However, we show here that among the Crocodilla, whose phylogeny is a debated Issue, these profiles can provide phylogenetically useful formation.By using the probe Bkm-2(8), DNA gerprints with distinct bands distributed in the size range 0.5-23.0 kb were obtained for individuals of 18 species belonging to seven of the eight genera of crocodiflans. These genetic profiles showed hidividual-, species-, and restriction enzyme-specific patterns. In addition, string differences were observed in the copy number of Bkm-related sequences in genomes of different crocodiflan species. The qualitative data from DNA flngirpit proffles, and quantitae data on copy number variation in Bkm-related sequences, suggest that these genera belong to two distinct groups, one of which includes Aligator, Paeosuchuis, and Caiman; the other incudes Crocodylus, Osteolkemus, Tomistoma, and Gavialis. A close relationship between Tomistoma and Gabals is also suggested by these results.Crocodilians are the sole living reptilian representatives of the subclass Archosauria, a highly successful group in the Mesozoic era both in numbers and in diversity. At present, only 8 of the 124 described genera have survived and all of these belong to the same suborder, Eusuchia (1). According to most systematists, there are only 21 extant species, 11 of which belong to Crocodylus, which is by far the largest genus.The natural affinities among living crocodilians have so far been determined primarily on the basis of comparative morphology and paleontological records. However, the resolving power of these approaches has not been adequate to solve certain problematic and confusing relationships within the order Crocodilia. The commonality in life-style of many of the crocodilian taxa may have led to similar adaptative strategies-e.g., convergent skull morphology and head shape. Such convergence in characters, although considered phylogenetically important, has made interpretation of the systematic relationships in crocodilians difficult (2). This has led to the use of other approaches such as cytogenetic parameters (3, 4), analysis ofcoevolving crocodilian-parasite lineages (5), biochemical and immunological studies of proteins (6-8), and Southern blot and DNA sequence analyses of mitochondrial and nuclear ribosomal DNA (9-11) to resolve the natural affinities and evolutionary history of the living crocodilians.On the basis of the approaches described above, there is general agreement in aing Osteolaemus with Crocodylus and the caimans (Caiman, Melanosuchus, Paleosuchus) as the nearest sister taxa ofAlligator, whereas opinion is divided on the affinities of the two gha...

Data Set Incongruence and the Phylogeny of Crocodilians

“…In addition to the data sets evaluated here, still more uncombinable data exist in the form of blood protein allozymes, hemoglobin peptide fingerprints, transferrin immunodiffusion distances (Densmore, 1983), and DNA fingerprints from a Bkmderived probe (Aggarawal et al, 1994). However, these studies did not produce results useful to the goals of this study.…”

Mitogenomic Analyses Place the Gharial (Gavialis gangeticus) on the Crocodile Tree and Provide Pre-K/T Divergence Times for Most Crocodilians

“…This molecular relationship was originally identified by Densmore (1983) in an extensive immunological study that included all recent crocodilian species. Other molecular studies, such as RFLP data (Densmore and White 1991), fingerprint analysis (Aggarwal et al 1994), and analyses of a portion (267 nt including gaps) of the mitochondrial (mt) 12S rRNA gene (Gatesy et al 1993) have suggested the same relationships. However, some of the molecular studies (e.g., Gatesy et al 1993;Hass et al 1992;Poe 1996) did not include an outgroup, were not statistically testable (Densmore and White 1991), or used problematic methods like UPGMA for tree construction (Aggarwal et al 1994).…”

Two new genomes in the Oryza complex identified on the basis of molecular divergence analysis using total genomic DNA hybridization

“…Some of these are based on thermal denaturation profiles of DNA (Sibley and Ahlquist 1986;King and Ingrouille 1987), restriction fragment length polymorphisms (RFLPs) of nuclear sequences (Wang et al 1992), multilocus mini-and microsatellite-specific repeat sequences (Rayburn and Gill 1987;Aggarwal et al 1994), and total genomic DNA hybridization both on Southern blots and in situ (Anamthawat-Jonsson et al 1990). Among these, RFLPs and multilocus probes provide useful information, but these involve considerable effort in isolating and cloning genome-specific sequences.…”