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 These new estimates are either scattered in a wide range of scientific journals or, in many cases, unpublished; so they are not readily accessible.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.

Nuclear DNA Amounts in Angiosperms

Preface. Part I: Molecules and genomes in plant systematics. Chloroplast DNA and the study of plant phylogeny: present status and future prospects - M T Clegg and G Zurawski Use of chloroplast DNA rearrangements in reconstructing plant phylogeny - S R Downie and J D Palmer Mitochondrial DNA in plant systematics: applications and limitations - J D Palmer Ribosomal RNA as a phylogenetic tool in plant systematics - R K Hamby and E A Zimmer Evolution of the NOR and 5S DNA loci in the Triticeae - R Appels and B Baum Part II: Molecular approaches to plant evolution Intraspecific chloroplast DNA variation: systematic and phylogenetic implications - D E Soltis, P S Soltis and B G Milligan Molecular data and polyploid evolution in plants - P S Soltis, J J Doyle and D E Soltis Molecular systematics and crop evolution - J Deobley Part III: Model studies of phylogenetic relationships Contributions of molecular data to polyploid evolution in plants - P S Soltis, J J Doyle and D E Soltis Molecular systematics and crop evolution - J Deobley Contributions of molecular data to papilionoid legume systematics - J J Doyle, M Levin and A Bruneau Chloroplast DNA variation in the asteraceae: phylogenetic and evolutionary implications - R K Jansen, H J Michaels, R S Wallace, K-J Kim, S C Keeley, L E Watson and J D Palmer Chloroplast DNA restriction site variation and the evolution of the annual habit in North American Coreopsis (Asteraceae) - D J Crawford, J D Palmer and M Kobayashi Molecular systematics of onagraceae: examples from Clarkia and Fuschia - K J Systema and J E Smith Floral morphology and chromosome number in the subtribe oncidiinae (Orchidaceae): evolutionary insights from a phylogenetic analysis of the chloroplast DNA restriction site variation - M W Chase and J D Palmer Part IV: Theoretical perspectives The suitability of molecular and morphological evidence in reconstructing plant phylogeny -M J Donaghue and M J Sanderson Character-site weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA - V A Albert, B D Mishler and M W Chase Polymorphism, hybridization and variable evolutionary rate in molecular phylogenies - K Ritland and J E Eckenwalder Index.

Molecular Systematics of Plants

For nearly a century, biologists, and botanists in particular, have been interested in the determination and documentation of chromosome numbers for extant taxa (reviewed in Goldblatt & Lowry, 2011) as well as extinct ones (Laane & Hoiland, 1986; Masterson, 1994). These data have beenwidely used to evaluate the evolutionary pattern of chromosome number change and to estimate the base chromosome number of clades of interest. Chromosome numbers have also been extensively utilized as an important phylogenetic character in the context of cytotaxonomy (Chatterjee & Kumar Sharma, 1969; Schlarbaum & Tsuchiya, 1984; Guerra, 2012). Perhaps the most influential use of chromosome number data has been in the inference of major genomic events such aswhole genomeduplications (polyploidy), as well as changes in single chromosome numbers (e.g. dysploidy). Early researchers analyzed the distribution of chromosome numbers within a group of interest and employed various threshold techniques to estimate ploidy levels for the analyzed taxa (Stebbins, 1938; Grant, 1963; Goldblatt, 1980).More recently, phylogenetic information was incorporated into the analyses, allowing researchers to infer transitions in chromosome numbers along branches of the tree using either the maximum parsimony principle (Schultheis, 2001; Hansen et al., 2006; Ohi-Toma et al., 2006; Wood et al., 2009) or by using a probabilistic evolutionary model within the likelihood paradigm (Mayrose et al., 2010; Cusimano et al., 2012; Glick & Mayrose, 2014). Due to their significance and the relative ease by which chromosome numbers can be obtained, it is not surprising that chromosome number is the most extensively and consistently recorded cytological property in most plant families and genera (Guerra, 2008). These data have been documented along the years in an array of journal manuscripts, printed books (L€ove & L€ove, 1948; Darlington & Wylie, 1955; Fedorov, 1969) and, more recently, in the form of online databases (Goldblatt & Johnson, 1979; Watanabe, 2002; Bennett & Leitch, 2011). To date, the most comprehensive data source is the Index to PlantChromosome Numbers (IPCN; Goldblatt & Johnson, 1979), which provides reference point to original chromosome counts reported in the literature. IPCN was initially established at the University of California Berkeley in the 1950s and was later maintained by Canada Department of Agriculture, Missouri Botanical Garden, and currently by the International Association for Plant Taxonomy (IAPT). A large portion of the counts referenced during 1979– 2006, the years that IPCN has been housed in the Missouri Botanical Garden, can be accessed and searched online. Counts reported in more recent years are currently published under IAPT/ IOPBChromosomeData series (Marhold, 2006) but are not stored within a central, easily searched, database. In addition to IPCN, several other online data sources are available, most of which are dedicated to either a specific geographical region (Slovakia – Marhold et al., 2007; Poland –G oralski et al., 2009 onwards) or to a certain taxonomic group (e.g. Hieracium – Schuhwerk, 1996; Asteraceae –Watanabe, 2002). The amount of chromosome counts that exist to date is extensive, and searching the large number of resources that contain such information is a daunting task, particularly when a large number of taxa is examined. Consequently, many researchers search for chromosome number information only through the largest online database(s), while smaller but nonetheless valuable sources are ignored.This usually results inmissing data for someof the species in question, which may lead to erroneous conclusions drawn from the analysis. Obviously, a large accessible database that unifies all currently known databases, including both printed and online sources, would be of great value to the botanical community and wouldmake the task of data collectionmuch easier. In addition, such a central resource would enable researchers to add new counts as soon as they are being reported, facilitating the task of data sharing. Here, we present the Chromosome Counts Database (CCDB), as a community resource of plant chromosome numbers. The database incorporates data from dozens of sources, more than doubling the amount of data available within any single resource. The online database additionally enables researchers to add new counts or to comment on existing data entries, thereby facilitating data sharing. The extensive amount of data currently available in CCDB further allowed us to analyze the patterns of chromosome number distribution among major plant groups. We estimate the percentage of plant species exhibiting intraspecific variation in chromosome numbers as well as in their ploidy levels.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.13191

The Chromosome Counts Database (CCDB) – a community resource of plant chromosome numbers

Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs Yet numerous experimental studies have not detected widespread costs Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits to the evolution of plasticity and of generalists vs specialists We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity Some forms of plasticity, such as learning, may be inherently costly In addition, we examine opportunities to offset costs of phenotypes through ontogeny, amelioration of phenotypic costs across environments, and the condition-dependent hypothesis We propose avenues of further inquiry in the limits of plasticity using new and classic methods of ecological parameterization, phylogenetics and omics in the context of answering questions on the constraints of plasticity Given plasticity's key role in coping with environmental change, approaches spanning the spectrum from applied to basic will greatly enrich our understanding of the evolution of plasticity and resolve our understanding of limits

https://digitalcommons.wcupa.edu/cgi/viewcontent.cgi?article=1032&context=bio_facpub

Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity

The advent of fast, relatively inexpensive (thus, widely available) microcomputers is transforming the way we analyze data in ecological and evolutionary research. Even more profound, however, are the associated changes in questions asked, empirical methods used, studies conducted, and interpretations offered. Now that an array of computation-intensive statistical methods is newly available for general use, it seems particularly important to assess their advantages and limitations, to note how they are currently being used, and then to consider implications for the future. I focus in this review on four related techniques known in the statistical and biological literature as randomization (or permutation) tests, Monte Carlo methods, bootstrapping, and the jackknife. I refer to them collectively as resampling methods, because each involves taking several-to-many samples from the original data set (randomization, bootstrap, jackknife) or from a stochastic process like the one believed to have generated the data set (Monte Carlo). Each of these methods is actually an extensive family of techniques and specific applications that cannot be thoroughly examined here; instead, I briefly characterize the focal methods and then survey the recent literature in ecology and evolution to identify the issues most frequently associated with these techniques. It emerges that resampling methods are well represented in

Resampling methods for computation-intensive data analysis in ecology and evolution

Reports of 150 original chromosome counts are recorded, including reports of 22 genera and 57 species and subspecific taxa in tribe Lactuceae. Also included are first reports for 12 specific or subspecific taxa. x = 9 appears to be the ancestral base of the tribe. Chromosome numbers are known for over 85% of the genera of the tribe and the frequency of polyploidy is ca. 23%, which is about one-half that of the angiosperms.

Chromosome numbers in the compositae.

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)

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.

Kenton L. Chambers

Papers

Chromosome numbers in the compositae.

Detection of Intraspecific Variation in Nuclear DNA Content in Microseris douglasii

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

Genome size variation in diploid microseris bigelovii (asteraceae)

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