Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker

Abstract

The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.

Characterization of a Highly Repetitive Sequence Conserved Among the North American Morone Species

“…Phylogeny based on tandemly repetitive sequences has been demonstrated for many species such as vultures (Keyser et al, 1996), passerine birds (Quinn et al, 1992), parrots (Madsen et al, 1992), and cetacenas (Gretarsdottir and Arnason, 1992). In the cetaceans, the evolution of the highly repetitive DNA was congruent with and tightly correlated to the accepted phylogeny based on morphologic characters.…”

A Harp Seal × Hooded Seal Hybrid

“…Restriction enzyme analysis and gel electrophoresis were performed according to Guglich et al (1994). Digested DNA from the adult female attending the pup, the seal pup, and harp and hooded seal controls was analyzed by Southern Blotting using radioactively labeled genomic harp seal DNA (50 ng) (Feinburg and Vogelstein 1983, Westneat et al 1988, Quinn et al 1992. Random primer extension with 50 pCi alpha 3*P {dCTP] (Dupont/NEN, Inc.) produced specific activities of > 1.0 X lo8 cpm/kg.…”

Polyploid-specific repetitive DNA sequences from triploid ginbuna (Japanese silver crucian carp, Carassius auratus langsdorfi).

“…Satellite DNAs have been sequenced and analyzed for a wide variety of organisms including various vertebrates. Although the function of satellite DNAs remains yet to be defined, their repetition frequency, sequence composition and genomic organization are useful information for specifying a species or a population and for determining the evolutionary status of the genome in question (Macgregor and Sessions, 1986;Bogenberger et al, 1987;Quinn et al, 1992;Wijers et al, 1993;Mizuno et al, 1995).…”