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.

/pdf/genome-evolution-in-polyploids-eeag8xqgqu.pdf

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.

Restriction site mutations and trnL(UAA)-trnF(GAA) intergenic spacer length variants in the chloroplast genome were used to investigate the phylogenetic relationships among 53 Australian and New Zealand Microseris populations and to assess their position within their primarily North American genus. The study was performed to enhance understanding of evolutionary processes within this unique example of intercontinental dispersal and subsequent adaptive radiation. A southern blot method using four-base restriction enzymes and fragment separation on polyacryamide gels resulted in 55 mutations of which 30 were potentially phylogenetically informative. Most mutations were small indels of <162 bp, 80% of which were <20 bp. The small indels were useful for phylogenetic reconstruction of Australasian Microseris as judged by the high consistency indexes. The results confirmed the monophyly of the Australian and New Zealand Microseris. The occurrence of "hard" basal polytomies in the most parsimonious trees indicated that rapid radiation has occurred early in the history of the taxon. The monophyly of M. lanceolata, which includes the self-incompatible ecotypes of the Australian mainland, was confirmed. Within this species three clades were found that reflect more geographic distribution than morphological entities, suggesting that migration and possibly introgression between different ecotypes, or parallel evolution of similar adaptations, has occurred. One of the three clades was supported by a 162-bp deletion in the trnL-trnF spacer, while a subgroup of this exhibited also a tandemly repeated trnF exon. The data were inconclusive about the monophyly of the second Australasian species, M. scapigera, which comprises the New Zealand, Tasmanian, and autofertile ecotypes of Australia.

Chloroplast DNA evidence for the evolution of Microseris (Asteraceae) in Australia and New Zealand after long-distance dispersal from western North America

Die Evolutionsvorgange, die wir bisher diskutiert haben, sind exakt mesbar. Sie konnen zum grosen Teil im Labor nachvollzogen werden, und die vorher berechneten Resultate konnen mit experimentellen Ergebnissen verglichen werden. Es handelt sich dabei aber um die Evolution einzelner Gene, und es ist fraglich, ob diese Prozesse genugen, um die Evolution von Organismen zu erklaren. Das Auftreten einer melanistischen Mutante eines Schmetterlings scheint auf den ersten Blick nichts mit der Evolution der geflugelten Insekten zu tun zu haben, und was Sichelzellanamie zur Erklarung der Evolution des denkenden Menschen beitragt, ist auch keineswegs offensichtlich. Frosche mogen ein typisches Froschhamoglobin haben und Eidechsen ein Reptilienhamoglobin, aber erklart das, warum das eine Tier plump, kurz und schwanzlos ist und seine Eier nach der Ablage im Wasser befruchtet, wahrend das andere Tier einen langen Schwanz hat, geschwind uber besonnte Mauern lauft und amniotische Eier ablegt?

https://link.springer.com/content/pdf/10.1007%2F978-3-642-96343-8_26.pdf

Die Evolution der Organismen

Variation in nuclear 2C DNA content (Feulgen absorbancy) up to 25% was detected among plants from four populations of diploid Microseris bigelovii, 2n = 18. The lower DNA values were from geographically disjunct populations growing at the latitudinal extremes of the species range. These smaller genomes may have resulted from selection for low DNA content in stressful and/or time-limited environments. These data add M. bigelovii to the short list of taxa in which intraspecific variation in DNA content has been detected.

Genome size variation in diploid microseris bigelovii (asteraceae)

Nuclear DNA content varies over 20% within the diploid (2n = 18) species M. douglasEi and M. bigelovii. Two different intraspecific crosses were made between M. douglasEi biotypes which differed by about 10% in 2C nuclear DNA content. The F2 progeny of one intraspecific cross showed no striking evidence of segregation for DNA content. The mean DNA contents of F2 progeny from two sister hybrids from the second intraspecific cross were significantly different at the 1% level. An interspecific cross was made between biotypes of M. douglasEi and M. bigelovii that differed by approximately 10% in DNA amount. The 12 Fl progeny did not cluster around the parental midpoint, but instead encompassed nearly the entire range between the parental means. The five families of F2 progeny studied each had a mean DNA content corresponding to that of the particular Fl from which they were derived, indicating that the Fl plants were not of identical DNA content. The results of this study suggest that DNA sequences which account for the DNA content differences among the plants are unstable and can undergo deletion or amplification in a hybrid. The altered DNA content may be heritably stable and show little or no segregation in the F2 progeny.

Inheritance of nuclear 2c dna content variation in intraspecific and interspecific hybrids of microseris (asteraceae)

The origin of the crop species Allium fistulosum (bunching onion) and its relation to its wild relative A. altaicum were surveyed with a restriction fragment length polymorphism (RFLP) analysis of five noncoding cpDNA regions and with a random amplified polymorhic DNA (RAPD) analysis of nuclear DNA. Sixteen accessions of A. altaicum, 14 accessions of A. fistulosum, representing the morphological variability of the species, and five additional outgroup species from Allium section Cepa were included in this study. The RFLP analysis detected 14 phylogenetically informative character transformations, whereas RAPD revealed 126 polymorphic fragments. Generalized parsimony, neighbor-joining analysis of genetic distances, and a principal co-ordinate analysis were able to distinguish the two species, but only RAPD data allowed clarification of the interrelationship of the two taxa. The main results of this investigation were: (1) A. fistulosum is of monophyletic origin, and (2) A. fistulosum originated from an A. altaicum progenitor, making A. altaicum a paraphyletic species. Compared with A. altaicum the cultivated accessions of the bunching onion show less genetic variability, a phenomenon that often occurs in crop species due to the severe genetic bottleneck of domestication. Allium altaicum and A. fistulosum easily hybridize when grown together, and most garden-grown material is of recent hybrid origin.

https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.2307/2656817

Konrad Bachmann

Papers

Chloroplast DNA evidence for the evolution of Microseris (Asteraceae) in Australia and New Zealand after long-distance dispersal from western North America

Die Evolution der Organismen

Genome size variation in diploid microseris bigelovii (asteraceae)

Inheritance of nuclear 2c dna content variation in intraspecific and interspecific hybrids of microseris (asteraceae)

RAPDs and noncoding chloroplast DNA reveal a single origin of the cultivated Allium fistulosum from A. altaicum (Alliaceae).