Chloroplast DNA sequences are a primary source of data for plant molecular systematic studies. A few key papers have provided the molecular systematics community with universal primer pairs for noncoding regions that have dominated the field, namely trnL-trnF and trnK/matK. These two regions have provided adequate information to resolve species relationships in some taxa, but often provide little resolution at low taxonomic levels. To obtain better phylogenetic resolution, sequence data from these regions are often coupled with other sequence data. Choosing an appropriate cpDNA region for phylogenetic investigation is difficult because of the scarcity of information about the tempo of evolutionary rates among different noncoding cpDNA regions. The focus of this investigation was to determine whether there is any predictable rate heterogeneity among 21 noncoding cpDNA regions identified as phylogenetically useful at low levels. To test for rate heterogeneity among the different cpDNA regions, we used three species from each of 10 groups representing eight major phylogenetic lineages of phanerogams. The results of this study clearly show that a survey using as few as three representative taxa can be predictive of the amount of phylogenetic information offered by a cpDNA region and that rate heterogeneity exists among noncoding cpDNA regions.

The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis

Ribosomal ITS sequences and plant phylogenetic inference.

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

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Genome evolution in polyploids

The number of angiosperm species for which nuclear DNA amount estimates have been made has nearly trebled since the last collected lists of such values were published, and therefore, publication of a more comprehensive list is overdue. This paper lists absolute nuclear DNA amounts for 753 angiosperm species. The data were assembled primarily for reference purposes, and so the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists whom, it is anticipated, will be among its major users. The paper also reviews aspects of the history, nomenclature, methods, accuracy and problems of nuclear DNA estimation in angiosperms. No attempt is made to reconsider those aspects of nuclear DNA estimation which have been fully revised previously, although the bibliography of such aspects is given. Instead, the paper is intended as a source of basic information regarding the terminology, practice and limitations of nuclear DNA estimation, especially by Feulgen microdensitometry, as currently practiced.

Nuclear DNA Amounts in Angiosperms

Nuclear DNA amounts have been estimated for more than 200 angiosperm species since the last collected list of such values for about 750 species was published by Bennett & Smith in 1976 (Phil. Trans. R. Soc. Lond. B 274, 227-274). These new estimates are either scattered in a wide range of scientific journals or, in many cases, unpublished; so they are not readily accessible. A publication, collecting these data in a single list is required. This paper contains a supplementary list of absolute DNA values, including estimates for 240 angiosperm species not listed by Bennett & Smith in 1976, as well as additional estimates for 41 species already listed by them. These data are assembled primarily for reference purposes. Consequently, the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists, who it is anticipated will be among the major users.

To evaluate the monophyly of Coelogyne (Epidendroideae; Orchidaceae) and reveal sectional relationships and relations to allied genera in subtribe Coelogyninae, we collected PCR (polymerase chain reaction) amplified restriction fragment length polymorphisms (RFLPs) from 11 plastid regions for 42 taxa (28 Coelogyne species and 14 representatives of other genera) and three outgroups from Bletiinae and Thuniinae. We also sequenced a large portion of the plastid trnK intron (mostly matK) and the nuclear ribosomal DNA internal transcribed spacers ITS1 and ITS2 (including the 5.8S gene). Separate phylogenetic analyses on each data set using maximum parsimony produced mainly congruent (except for the position of Panisea) but weakly supported clades. Parsimony analysis of the combined data clearly identified three main clades in Coelogyninae. Whereas Coelogyninae are monophyletic, Coelogyne is polyphyletic, with species falling into at least two well-supported clades. The utility of morphological characters used in previous classifications was explored by reconstructing character state evolution on one of the four molecular trees. Lip base and petal shape were homoplasious, whereas ovary indumentum and flower number were congruent with well-supported groups. The implications of our results for the classification of Coelogyne are discussed, and a reorganization of the genus by including Neogyna and Pholidota and removing several species is proposed.

https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.2307/3558367

Molecular phylogeny of Coelogyne (Epidendroideae; Orchidaceae) based on plastid RFLPS, matK, and nuclear ribosomal ITS sequences: evidence for polyphyly

A precise technique to measure DNA content in Microseris douglasii is reported. Relative absorbancy (560 nm) of Feulgen-stained spherical nuclei, arrested at the 2C DNA level, was measured microspectrophotometrically. Relative DNA contents were determined by placing epidermis of an inbred line on the same slide with epidermis from the unknown sample prior to hydrolysis and staining. The DNA values were adjusted to the internal standard; direct comparisons were made of values collected from different slides and staining batches. Differences among individual plant specimens in the 2.5%-5% range are detectable with this procedure. Intraspecific variation up to 20% in DNA content was apparent

Detection of Intraspecific Variation in Nuclear DNA Content in Microseris douglasii

We measured nuclear 2C DNA content (Feulgen absorbancy) of 222 plants of Microseris douglasii representing 24 geographically, ecologically, and morphologically diverse populations in California. The DNA content among plants varied more than 20% and was not correlated with morphological traits. Mean DNA contents of populations varied about 14%. For most populations, the DNA content was relatively uniform, even when the biotypes were morphologically diverse. Populations with higher DNA contents were restricted to the more mesic sites, generally with well-developed soil. A correlation between the amount of precipitation and DNA content was temporally observed within a single population near Jolon, California, over a 15-yr interim. Natural selection may be responsible, at least in part, for the observed distributional pattern of DNA content.

Geographic and Ecological Distribution of Genomic DNA Content Variation in Microseris douglasii (Asteraceae)

A B S T R A C T Relative 2C nuclear DNA contents were microphotometrically determined from nuclei isolated from eight species of Microseris, four species of Agoseris, and Phalacroseris Bolanderi. The thirteen species are diploid (2n = 18) western North American members of the subtribe Microseridinae, tribe Cichorieae, of the family Compositae. A 7.7-fold variation in DNA content was detected. Phalacroseris has the highest DNA content and Agoseris heterophylla has the lowest. Within the genera Microseris and Agoseris, a 2.8- and 3.1-fold range in DNA content was detected. The higher values were from perennial species, and the lower values were from annual inbreeding species. Both evolutionary increases and decreases in nuclear DNA content have apparently occurred during the differentiation of the subtribe. DNA CONTENT per nucleus and per chromosome varies over 100-fold among vascular plants (Rees, 1972; Rees and Jones, 1972; Sparrow, Price, and Underbrink, 1972; Price, Sparrow, and Nauman, in press). Although polyploidy is responsible for some of the variation in nuclear DNA content, an approximate 65-fold range is found among diploid

Dna content and evolution in the microseridinae

There are good reasons why the importance of developmental biology for an understanding of evolution had to be rediscovered recently (Gould, 1977; Lovtrup, 1981; Bonner, 1982). The Synthetic Theory of Evolution had been built up on the demonstration that natural populations contain an immense amount of genetic variation that could fully account for the morphological variation studied by naturalists (Mayr and Provine, 1980). This central achievement of the Synthetic Theory had to be defended against a false picture of genetic evolution due to rare mutations with major, often deleterious effects. The creative force in evolution undoubtedly is not mutation pressure, but selection. To support this statement, the store of genetic variation in natural populations had to be characterized, and it had to be shown that steady selection pressure could slowly and gradually alter characters by accumulating small additive effects of many genes.

Konrad Bachmann

Papers

Molecular phylogeny of Coelogyne (Epidendroideae; Orchidaceae) based on plastid RFLPS, matK, and nuclear ribosomal ITS sequences: evidence for polyphyly

Detection of Intraspecific Variation in Nuclear DNA Content in Microseris douglasii

Geographic and Ecological Distribution of Genomic DNA Content Variation in Microseris douglasii (Asteraceae)

Dna content and evolution in the microseridinae

Evolutionary Genetics and the Genetic Control of Morphogenesis in Flowering Plants