Chloroplast DNA Transgresses Species Boundaries and Evolves at Variable Rates in the California Closed-Cone Pines (Pinus radiata, P. muricata, and P. attenuata)

Hong, Young Pyo; Krupkin, Alex B.; Strauss, Steven H.

doi:10.1006/mpev.1993.1031

Cited by 56 publications

(68 citation statements)

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“…dubia occurred as between-population differences (0 = 0.61). A similar pattern of relatively high genetic diversity primarily partitioned between populations was also observed in H. vulgare where 8 = 0.67 (Milligan, 1991, from data in Neale, 1988 and in bishop pine (0 >0.80;Hong et at., 1993). In contrast, extremely low between-population differentiation (0 = 0.02) for cpDNA haplotypes was found in the highly polymorphic T pratense, a pattern which is suggestive of panmixia (Milligan, 1991).…”

Section: Intraspecific Polymorphismsupporting

confidence: 68%

“…(Scowcraft, 1979;Palmer & Zamir, 1982). More recent and thorough analyses of intraspecific cpDNA variation suggest that polymorphism is common, but that the level of variation depends upon the particular species (Hong et a!., 1993). In the present study, extensive variation was found within P dubia and P maculata.…”

Section: Intraspecific Polymorphismsupporting

confidence: 52%

“…California (Hong et a!., 1993). The amount of genetic difference between haplotypes within species may be small as is often observed, but in P dubia and Coreopsis grandijiora (Mason et a!., 1994) haplotypes differed by as many as 14 and 19 mutations, respectively.…”

Section: Intraspecific Polymorphismmentioning

confidence: 91%

“…The species-specific nature of cpDNA variation should not be surprising; levels of polymorphism depend upon the mutation rate and effective population size. Although the chioroplast genome is thought to evolve slowly, little is known about its mutation rate other than that there is an apparently higher rate for length variants compared to point mutations (Hong et al, 1993). In contrast, extensive data exist that show that species differ in all components (e.g.…”

Section: Intraspecific Polymorphismmentioning

confidence: 99%

“…Population analyses based upon the chloroplast genome are beginning to be applied to problems in intraspecific phylogeography in plants (Soltis et al, 1992;Hooglander et al, 1993;Mayer & Soltis, 1994) in ways analogous to the use of mitochondrial DNA (mtDNA) in studies of animals (Avise et a!., 1987). In addition, data from cpDNA have been used to examine population structure within species (Neale et al, 1988;Milligan, 1991;Soltis et a!., 1992;McCauley, 1994;Petit et a!., 1994), haplotype diversity within and between populations (Milligan, 1991;Hong et a!., 1993;Byrne & Moran, 1994), and to search for correlations between chloroplast variation and morphological (Terauchi et a!., 1991) or breeding system (Wolff & Schaal, 1992) characteristics.…”

Section: Introductionmentioning

confidence: 99%

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A population genetic analysis of chloroplast DNA in Phacelia

et al. 1996

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Hierarchical sampling from populations, incipient and recognized varieties within Phacelia dubia and P maculata has revealed high levels of intraspecific polymorphism in chloroplast DNA. Much of the variation is partitioned between populations as evidenced by populationspecific variants at fixation in all three populations of P dubia var. interior and in both populations of P maculata. Nine of 16 populations were polymorphic for cpDNA haplotypes. A total of 16 haplotypes was found in a sample of 106 individuals; the most common occurred in eight of the 16 populations and in 31 per cent of the individuals in the entire sample. A phylogenetic analysis revealed four basic plastome types. The two major groups of plastomes were separated by four independent base-pair mutations which suggests an ancient split in the evolution of plastid genomes. Representatives from each major plastome division were found in each of five populations spanning two allopatric varieties of P dubia. The geographical distribution of haplotypes and lack of evidence for recent admixture argue against migration as a source of the polymorphism. It is more likely that the current taxonomic varieties are descendants of a polymorphic common ancestor.

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Section: Intraspecific Polymorphismsupporting

confidence: 68%

Section: Intraspecific Polymorphismsupporting

confidence: 52%

Section: Intraspecific Polymorphismmentioning

confidence: 91%

Section: Intraspecific Polymorphismmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A population genetic analysis of chloroplast DNA in Phacelia

et al. 1996

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Multi‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

Gernandt

Dugua

Vázquez‐Lobo

et al. 2018

American J of Botany

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

Krupkin

Liston

Strauss

1996

American J of Botany

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Phylogenetic analysis of plastid DNA restriction site and rearrangement mutations suggests a number of major revisions to taxonomy and phylogenetic concepts in the hard pines. Total genomic DNA from 18 species that sampled all nine subsections was digested with 19 restriction enzymes, blotted, and probed with 70% of the Douglas‐fir (Pseudotsuga menziesii) chloroplast genome, or, with clones encompassing the entire chloroplast genome of Pinus contorta. A total of 204 site mutations and five rearrangement mutations were generated, of which 126 were phylogenetically informative. Wagner parsimony analyses revealed 11 clades that were strongly supported by bootstrap and decay index analyses. All North American species except P. resinosa formed a distinct monophyletic group that was strongly separated from the Eurasian species. Within the Eurasian clade subsect. Sylvestres was polyphyletic; its Mediterranean species were closely allied with members of sect. Pinea. Sect. Pinea appeared polyphyletic as well; both species of its subsect. Leiophyllae showed a close affinity to Mesoamerican pines of subsect. Oocarpae in sect. Pinus. Within the North American pines subsects. Ponderosae and Oocarpae were polyphyletic. Despite its shallow fossil record, subsect. Contortae emerged as a sister group to all of the North American pines apart from P. resinosa, which was allied with Eurasian species of subsect. Sylvestres. The remaining North American subsections formed two groups: a poorly resolved clade with subsects. Ponderosae and Sabinianae, and sequentially nested clades represented by: P. radiata; P. taeda; representatives of subsects. Oocarpae and Ponderosae from Mesoamerica, and subsect. Leiophyllae. We present estimates of divergence times for each of these major clades based on molecular clocks calibrated using two hard pine fossil observations.

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Chloroplast DNA Transgresses Species Boundaries and Evolves at Variable Rates in the California Closed-Cone Pines (Pinus radiata, P. muricata, and P. attenuata)

Cited by 56 publications

References 0 publications

A population genetic analysis of chloroplast DNA in Phacelia

A population genetic analysis of chloroplast DNA in Phacelia

Multi‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

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

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