Restriction-Site Variation and Molecular Systematics of New World Leaf-Nosed Bats

1992 ◽  
Vol 73 (1) ◽  
pp. 29-42 ◽  
Author(s):  
R. A. Van Den Bussche
Keyword(s):  
Molecular Systematics ◽  
New World ◽  
Restriction Site ◽  
Restriction Site Variation ◽  
Site Variation

scholarly journals Hierarchical Analysis of Nucleotide Diversity in Geographically Structured Populations

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 629-639 ◽  
Author(s):  
Kent E Holsinger ◽  
Roberta J Mason-Gamer
Keyword(s):  
Nucleotide Diversity ◽  
Restriction Site ◽  
Rooted Tree ◽  
Structured Populations ◽  
Hierarchical Analysis ◽  
Restriction Site Variation ◽  
Hierarchical Levels ◽  
Site Variation ◽  
The Mean ◽  
Mean Time

Abstract Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of Nei's nucleotide diversity statistics and show that our modification has the same properties as Wright's  F  ST. We compare its statistical properties with several other F  ST estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.

More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 402-407 ◽  
Author(s):  
L E Talbert ◽  
L Y Smith ◽  
N K Blake
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Restriction Site ◽  
Cereal Crop ◽  
Crop Species ◽  
Wheat Evolution ◽  
D Genome ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Copy Dna

Allohexaploid bread wheat is grown on more acreage than any other cereal crop, yet variation at the DNA level seems to be less than that observed in many diploid crop species. A common explanation for the small amount of DNA-level variation is that a severe bottleneck event resulted from the polyploidization events that gave rise to hexaploid wheat, whereby wheat was genetically separated from its progenitors. In this report, we test the extent of the bottleneck separating wheat from its D-genome progenitor, Triticum tauschii, by comparative DNA sequence analysis. Restriction site variation of low-copy DNA sequences amplified by PCR showed an average of 2.9 and 2.4 alleles per primer set in T. tauschii and wheat, respectively. Two different restriction patterns were present in T. tauschii for DNA amplified with a primer set for the A1 locus. Both alleles were also present in wheat. Alleles at the A1 locus were cloned and 527 bp of sequence obtained from 12 and 13 diverse accessions of wheat and T. tauschii, respectively. Average genetic distance among the wheat alleles was similar to that among the T. tauschii alleles (0.0127 and 0.0133, respectively). Nucleotide differences indicated that two distinct alleles existed in T. tauschii, both of which were present in wheat. These data suggest that hexaploid wheat formed at least twice, and that the bottleneck separating wheat from T. tauschii may be less constrictive than previously supposed.Key words: wheat, evolution, DNA.

Phylogenetic Implications of Ribosomal DNA Restriction Site Variation in the Plant Family Onagraceae

1990 ◽  
Vol 77 (3) ◽  
pp. 523 ◽  
Author(s):  
Jorge V. Crisci ◽  
Elizabeth A. Zimmer ◽  
Peter C. Hoch ◽  
George B. Johnson ◽  
Christy Mudd ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Restriction Site ◽  
Plant Family ◽  
Restriction Site Variation ◽  
Phylogenetic Implications ◽  
Site Variation ◽  
Dna Restriction

Mitochondrial DNA restriction site variation in Tasmanian populations of Orange Roughy (Hoplostethus atlanticus), a deep-water marine teleost

1989 ◽  
Vol 40 (1) ◽  
pp. 1 ◽  
Author(s):  
JR Ovenden ◽  
AJ Smolenski ◽  
RWG White
Keyword(s):  
Mitochondrial Dna ◽  
West Coast ◽  
East Coast ◽  
Restriction Site ◽  
The West ◽  
Orange Roughy ◽  
Site Change ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Hoplostethus Atlanticus

The orange roughy, Hoplostethus atlanticus, forms the basis of an important trawl fishery in Australia and New Zealand which is currently being over-exploited. To gain information about the stock structure of an Australian orange roughy population, ten restriction enzymes were used to survey the restriction- site variation in the mitochondrial genome of 23 individuals collected from the east coast and 26 individuals collected from the west coast of Tasmania. The mean diversity between all 49 genomes was a low 0.19%. Of the eleven haplotypes identified, only one was present in both the east and west coast samples. Four haplotypes were found only in the east coast sample and six were found only in the west coast sample. Eight haplotypes were related to the haplotype found on both coasts by the gain or loss of one restriction site. One haplotype collected in the east coast sample was related to one other east coast haplotype by one site change. One haplotype collected from the west coast was related to a west coast haplotype by one site change. If this pattern is confirmed by further mitochondrial DNA studies, it could be inferred that gene flow between the orange roughy populations on the east and west coasts of Tasmania is low.

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