Phylogenetic analysis of the hard pines (Pinus subgenus Pinus , Pinaceae) from chloroplast DNA restriction site analysis

1996 ◽  
Vol 83 (4) ◽  
pp. 489-498 ◽  
Author(s):  
A. B. Krupkin ◽  
A. Liston ◽  
S. H. Strauss
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Restriction Site ◽  
Site Analysis ◽  
Restriction Site Analysis ◽  
Dna Restriction

Evolution of Endemic Sideritis (Lamiaceae) in Macaronesia: Insights from a Chloroplast DNA Restriction Site Analysis

2000 ◽  
Vol 25 (4) ◽  
pp. 633 ◽  
Author(s):  
Janet C. Barber ◽  
Javier Francisco Ortega ◽  
Arnoldo Santos-Guerra ◽  
Aguedo Marrero ◽  
Robert K. Jansen
Keyword(s):  
Chloroplast Dna ◽  
Restriction Site ◽  
Site Analysis ◽  
Restriction Site Analysis ◽  
Dna Restriction

Phylogenetic relationships and infraspecific variation in Canadian Arctic Poa based on chloroplast DNA restriction site data

2001 ◽  
Vol 79 (6) ◽  
pp. 679-701 ◽  
Author(s):  
Lynn J Gillespie ◽  
Ruben Boles
Keyword(s):  
Chloroplast Dna ◽  
Phylogenetic Relationships ◽  
Restriction Site ◽  
Canadian Arctic ◽  
Classification Systems ◽  
Infraspecific Variation ◽  
Site Analysis ◽  
Restriction Site Analysis ◽  
Infraspecific Taxa ◽  
Dna Restriction

Infraspecific variation and phylogenetic relationships of Canadian Arctic species of the genus Poa were studied based on chloroplast DNA (cpDNA) variation. Restriction site analysis of polymerase chain reaction amplified cpDNA was used to reexamine the status of infraspecific taxa, reconstruct phylogenetic relationships, and reexamine previous classification systems and hypotheses of relationships. Infraspecific variation was detected in three species, but only in Poa hartzii Gand. did it correspond to infraspecific taxa where recognition of subspecies ammophila at the species level is supported. Additional variation in P. hartzii ssp. hartzii is hypothesized to be the result of hybridization with Poa glauca in the High Arctic and subsequent introgression resulting in repeated transfer of P. glauca DNA. The variation in Poa pratensis L. had a geographical rather than taxonomic basis, and is hypothesized to correspond to indigenous arctic versus introduced extra-arctic populations. In P. glauca Vahl cpDNA variation was detected only in western Low Arctic and boreal populations and may represent greater variation where the species survived the Pleistocene glaciations. Cladistic parsimony analysis of cpDNA restriction site data mostly confirms recent infrageneric classification systems. Poa alpina L., along with the non-arctic Poa annua L. and Poa sect. Sylvestres, formed the basalmost clades. The remaining taxa group into two main clades: one consisting of Poa sects. Poa, Homalopoa, Madropoa and Diocopoa; the second, of Poa sects. Secundae, Pandemos, Abbreviatae and Stenopoa. Poa sect. Poa, comprising Poa arctica R. Br. and P. pratensis, is a strongly supported monophyletic group, not closely related to P. alpina. Poa hartzii is confirmed as a member of a paraphyletic or weakly supported P. sect. Secundae. Poa glauca and Poa abbreviata R. Br. are distinct members within a generally unresolved Poa. sect. Stenopoa-Abbreviatae complexKey words: Poa, Canadian arctic, chloroplast DNA, restriction site analysis, infraspecific variation, phylogeny.

scholarly journals PHYLOGENETIC ANALYSIS OF CHLOROPLAST DNA RESTRICTION SITE DATA AT HIGHER TAXONOMIC LEVELS: AN EXAMPLE FROM THE ASTERACEAE

Evolution ◽  
1990 ◽  
Vol 44 (8) ◽  
pp. 2089-2105 ◽  
Author(s):  
Robert K. Jansen ◽  
Kent E. Holsinger ◽  
Helen J. Michaels ◽  
Jeffrey D. Palmer
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Restriction Site ◽  
Dna Restriction

Relationships among native and introduced North American species of Hordeum, based on chloroplast DNA restriction-site variation

1991 ◽  
Vol 69 (11) ◽  
pp. 2421-2426 ◽  
Author(s):  
Bernard R. Baum ◽  
L. Grant Bailey
Keyword(s):  
Chloroplast Dna ◽  
North American ◽  
Native Species ◽  
Restriction Site ◽  
North American Species ◽  
Central Position ◽  
Site Analysis ◽  
Site Variation ◽  
Dna Restriction ◽  
Cladistic Analyses

Restriction-site analysis of chloroplast DNA was carried out on a total of 13 North American species of Hordeum, 7 native and 6 introduced. Sites associated with polymorphic banding patterns were omitted so that only invariant sites within species were used in the analyses. A number of taxa whose species status is in dispute can indeed be supported at species rank, i.e., H. brachyantherum, H. californicum, H. pusillum, H. intercedens, H. marinum, and H. geniculatum. The maternal progenitor of H. arizonicum is H. pusillum, and this is further discussed in light of other possibilities. Both phenetic and cladistic analyses indicate a tripartite relationship whereby H. vulgare is distant from the group of H. leporinum, H. glaucum, and H. murinum and from a second group comprising the native species H. brachyantherum, H. californicum, H. arizonicum, H. jubatum, H. pusillum, H. intercedens, and H. depressum. Hordeum marinum and H. geniculatum occupy a central position in this relationship. Speculation that the putative ancient form of Hordeum resembled a H. murinum – H. geniculatum-like species is discussed. Key words: chloroplast DNA, Hordeum, phylogenetic relationships.

scholarly journals Phylogenetic Analysis of Chloroplast DNA Restriction Site Data at Higher Taxonomic Levels: An Example from the Asteraceae

Evolution ◽  
1990 ◽  
Vol 44 (8) ◽  
pp. 2089 ◽  
Author(s):  
Robert K. Jansen ◽  
Kent E. Holsinger ◽  
Helen J. Michaels ◽  
Jeffrey D. Palmer
Keyword(s):  
Phylogenetic Analysis ◽  
Chloroplast Dna ◽  
Restriction Site ◽  
Dna Restriction

scholarly journals An Economical Approach to Distinguish Genetically Needles of Limber from Whitebark Pine

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1060
Author(s):  
Franklin Alongi ◽  
Andrew J. Hansen ◽  
David Laufenberg ◽  
Robert E. Keane ◽  
Kristin Legg ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Dna Sequence ◽  
Restriction Site ◽  
Genetic Identification ◽  
Stand Age ◽  
Whitebark Pine ◽  
Site Analysis ◽  
Limber Pine ◽  
Restriction Site Analysis ◽  
Pine Trees

Whitebark pine is difficult to distinguish from limber pine when seed cones are not present. This is often the case because of young stand age, growth at environmental extremes, or harvesting by vertebrate species. Developing an economical genetic identification tool that distinguishes non-cone-bearing limber from whitebark pine, therefore, could aid many kinds of research on these species. Phylogenetic studies involving limber and whitebark pine suggest that chloroplast DNA sequences differ between these species. We therefore wanted to identify chloroplast loci that could differentiate limber from whitebark pine trees by taking an economical approach involving restriction-site analysis. We generated chloroplast DNA barcode sequences sampled from limber and whitebark pine trees that we identified using attached seed cones. We searched for nucleotide differences associated with restriction endonuclease recognition sites. Our analyses revealed that matK and the psbA-trnH spacer each readily amplified and harbored multiple DNA-sequence differences between limber and whitebark pine. The matK coding sequence of whitebark pine has a BsmAI restriction site not found in limber pine. The psbA-trnH spacer of limber pine has two PsiI restriction sites, neither of which is found in whitebark pine. DNA-sequence and restriction-site analysis of the psbA-trnH spacer from 111 trees showed complete congruence between visually and genetically identified limber (n = 68) and whitebark (n = 43) pine trees. We conclude that restriction site analysis of the chloroplast psbA-trnH spacer and matK involves both minimal technical expertize and research funds. These findings should be of value to foresters interested in species identification and distribution modeling, as well as the analysis of fossil pine pollen, given that gymnosperms transmit chloroplast DNA paternally.

Sign in / Sign up

Export Citation Format

Share Document