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T Ryan Gregory

Publications and source records attributed to T Ryan Gregory.

18 recordsLinked to original sources
PubMed2006

Eukaryotic genome size databases.

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (www.kew.org/genomesize/homepage.html), the Animal Genome Size Database (www.genomesize.com) and the Fungal Genome Size Database (www.zbi.ee/fungal-genomesize/). In total, these databases provide freely accessible genome size data for >10,000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs.

Animals↗
PubMed2005

DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.

DNA barcoding has been successfully implemented in the identification of previously described species, and in the process has revealed several cryptic species. It has been noted that such methods could also greatly assist in the discovery and delineation of undescribed species in poorly studied groups, although to date the feasibility of such an approach has not been examined explicitly. Here, we investigate the possibility of using short mitochondrial and nuclear DNA sequences to delimit putative species in groups lacking an existing taxonomic framework. We focussed on poorly known tropical water beetles (Coleoptera: Dytiscidae, Hydrophilidae) from Madagascar and dung beetles (Scarabaeidae) in the genus Canthon from the Neotropics. Mitochondrial DNA sequence variation proved to be highly structured, with >95% of the observed variation existing between discrete sets of very closely related genotypes. Sequence variation in nuclear 28S rRNA among the same individuals was lower by at least an order of magnitude, but 16 different genotypes were found in water beetles and 12 genotypes in Canthon, differing from each other by a minimum of two base pairs. The distribution of these 28S rRNA genotypes in individuals exactly matched the distribution of mtDNA clusters, suggesting that mtDNA patterns were not misleading because of introgression. Moreover, in a few cases where sequence information was available in GenBank for morphologically defined species of Canthon, these matched some of the DNA-based clusters. These findings demonstrate that clusters of close relatives can be identified readily in the sequence variation obtained in field collected samples, and that these clusters are likely to correspond to either previously described or unknown species. The results suggest that DNA-assisted taxonomy will not require more than a short fragment of mtDNA to provide a largely accurate picture of species boundaries in these groups. Applied on a large scale, this DNA-based approach could greatly improve the rate of species discovery in the large assemblages of insects that remain undescribed.

Animals↗
PubMed2005

Preparation of samples for comparative studies of arthropod chromosomes: visualization, in situ hybridization, and genome size estimation.

The ability to obtain large amounts of genomic sequence for organisms and high throughput technology has led to a change in the thrust of research at the level of chromosomes in animals. In the past chromosomal analysis of animals was focused on gross changes such as inversions, translocations, and deletions for both genetic and evolutionary studies. The advent of in situ hybridization technology and the ability to measure genome content size changed both the precision and the scale of studies addressing chromosomal change as a tool in evolutionary biology. This chapter addresses two of the major areas of change that have occurred in chromosomal studies in the past decade -- examination of more refined and genome enabled structural changes in chromosomes and genome size measure. This chapter describes some of the chromosome structure approaches such as fluorescent in situ hybridization (FISH), comparative genomic hybridization (CGH) and other techniques. As well, advances in Genome size measurement and theory are described herein.

Animals↗
PubMed2005

Synergy between sequence and size in large-scale genomics.

Until recently the study of individual DNA sequences and of total DNA content (the C-value) sat at opposite ends of the spectrum in genome biology. For gene sequencers, the vast stretches of non-coding DNA found in eukaryotic genomes were largely considered to be an annoyance, whereas genome-size researchers attributed little relevance to specific nucleotide sequences. However, the dawn of comprehensive genome sequencing has allowed a new synergy between these fields, with sequence data providing novel insights into genome-size evolution, and with genome-size data being of both practical and theoretical significance for large-scale sequence analysis. In combination, these formerly disconnected disciplines are poised to deliver a greatly improved understanding of genome structure and evolution.

Base Sequence↗
PubMed2005

The C-value enigma in plants and animals: a review of parallels and an appeal for partnership.

AIMS: Plants and animals represent the first two kingdoms recognized, and remain the two best-studied groups in terms of nuclear DNA content variation. Unfortunately, the traditional chasm between botanists and zoologists has done much to prevent an integrated approach to resolving the C-value enigma, the long-standing puzzle surrounding the evolution of genome size. This grand division is both unnecessary and counterproductive, and the present review aims to illustrate the numerous links between the patterns and processes found in plants and animals so that a stronger unity can be developed in the future. SCOPE: This review discusses the numerous parallels that exist in genome size evolution between plants and animals, including (i) the construction of large databases, (ii) the patterns of DNA content variation among taxa, (iii) the cytological, morphological, physiological and evolutionary impacts of genome size, (iv) the mechanisms by which genomes change in size, and (v) the development of new methodologies for estimating DNA contents. CONCLUSIONS: The fundamental questions of the C-value enigma clearly transcend taxonomic boundaries, and increased communication is therefore urged among those who study genome size evolution, whether in plants, animals or other organisms.

Animals↗
PubMed2004

Insertion-deletion biases and the evolution of genome size.

Numerous theories have been proposed to account for the pronounced differences in the quantity of non-coding DNA among eukaryotic genomes, but the current repertoire remains incomplete because the only explicit mechanisms it provides involve DNA gain. It has been proposed more recently that biases in spontaneous insertions and deletions (indels) can lead to genome shrinkage by mutational mechanisms alone. The present article provides the first detailed critical discussion of this approach, and covers three different ideas related to it: (1) the general notion of DNA loss by deletion bias, (2) the "DNA loss hypothesis" which supposes that variation in genome size can be attributed to differences in DNA loss rate, and (3) the "mutational equilibrium model" which attempts to describe the long-term evolution of genome size. The mutational equilibrium model is found to be problematic, and it is noted that DNA loss by small indels is too slow in real time to determine variation in genome size above a relatively low threshold. Some alternative explanations for the observed patterns are provided, and the critique also identifies some potential problems with the current dataset. These include a failure to cite a more detailed (and somewhat contradictory) mammalian dataset, a questionable use of arithmetic means with highly skewed data, and important discrepancies among the particular DNA sequences so far analyzed. Overall, evolutionary reductions in genome size are considered important, but the specific mechanism relating to small deletion bias is far too weak to be accepted as a primary determinant of genome size variation in general.

Animals↗
PubMed2003

C-value estimates for 31 species of ladybird beetles (Coleoptera: Coccinellidae).

This study provides C-value (haploid nuclear DNA content) estimates for 31 species of ladybird beetles (representing 6 subfamilies and 8 tribes), the first such data for the family Coccinellidae. Despite their unparalleled diversity, the Coleoptera have been very poorly studied in terms of genome size variation, such that even this relatively modest sample of species makes the Coccinellidae the third best studied family of beetles, behind the Tenebrionidae and Chrysomelidae. The present study provides a comparison of patterns of genome size variation with these two relatively well-studied families. No correlation was found between genome size and body size in the ladybirds, in contrast to some other invertebrate groups but in keeping with findings for other beetle families. However, there is some indication that developmental time and/or feeding ecology is related to genome size in this group. Some phylogenetic patterns and possible associations with subgenomic features are also discussed.

Animals↗
PubMed2003

The correlation between rDNA copy number and genome size in eukaryotes.

Both rDNA gene multiplicity and genome size vary widely among eukaryotes. For some time, there has been debate regarding any possible relationship between these two parameters. The present study uses data on genome size and rDNA copy number for 162 species of plants and animals to test the association between genome size and rDNA copy number, and provides the first convincing evidence of a strong positive relationship between the two within and among these two groups of organisms. No simple explanations exist for this relationship, but it is nevertheless of clear relevance from both practical and theoretical perspectives.

Animals↗
PubMed2003

Genome size estimates for two important freshwater molluscs, the zebra mussel (Dreissena polymorpha) and the schistosomiasis vector snail (Biomphalaria glabrata).

The haploid genome sizes of two important molluscs were assessed by Feulgen image analysis densitometry. The genome size of the zebra mussel (Dreissena polymorpha), a prolific invader of North American lakes, was estimated to be 1C = 1.70 +/- 0.03 pg, and that of the freshwater snail Biomphalaria glabrata, the predominant intermediate vector of the human parasite Schistosoma mansoni, was estimated at 0.95 +/- 0.01 pg. These estimates will be important in future efforts in molluscan genomics, which at present lags far behind work being carried out with vertebrate and arthropod models. B. glabrata in particular, which has one of the smallest known gastropod genomes, is recommended as a highly suitable target for future genome sequencing.

Animals↗
PubMed2002

Genome size and developmental complexity.

Haploid genome size (C-value) is correlated positively with cell size, and negatively with cell division rate, in a variety of taxa. Because these associations are causative, genome size has the potential to impact (and in turn, be influenced by) organism-level characters affected by variation in either of these cell-level parameters. One such organismal feature is development. Developmental rate, in particular, has been associated with genome size in numerous plant, vertebrate, and invertebrate groups. However, rate is only one side of the developmental coin; the other important component is complexity. When developmental complexity is held essentially constant, as among many plants, developmental rate is the visibly relevant parameter. In this case, genome size can impose thresholds on developmental lifestyle (and vice versa), as among annual versus perennial plants. When developmental rate is constrained (as during time-limited amphibian metamorphosis), complexity becomes the notable variable. An appreciation for this rate-complexity interaction has so far been lacking, but is essential for an understanding of the relationships between genome size and development. Moreover, such an expanded view may help to explain patterns of variation in taxa as diverse as insects and fish. In each case, a hierarchical approach is necessary which recognizes the complex interaction of evolutionary processes operating at several levels of biological organization.

Amphibians↗
PubMed2002

New insights into the distribution of polyploid Daphnia: the Holarctic revisited and Argentina explored.

It has long been known that polyploid organisms are more prevalent in arctic than in temperate environments. Past explanations for this geographical trend have focused on the role of glacial cycles in generating polyploids and the influence of abiotic factors in favouring polyploidy in the north. In combination, these mechanisms probably suffice to explain the observed geographical cline in ploidy levels in members of the Daphnia pulex complex in the Holarctic. While only diploid members of the D. pulex complex are found in the temperate regions of North America and Europe, allozyme and DNA quantification analyses indicate that the southern Argentine pulex-complex fauna is dominated by polyploids. Indeed, the present study is the first to document the presence of polyploid members of the D. pulex complex in any temperate climate. The results of phylogeographic analyses suggest that this difference in polyploid distribution between the northern and southern hemispheres is based more on ecological and historical contingencies than direct selection for polyploidy. Specifically, competition with diploid relatives probably limits the lower latitudinal range of polyploids in the north, but appears not to have occurred in Argentina. Because of these differences, the present study provides important insights into the diverse factors that determine the distributions and evolutionary fates of polyploid organisms.

Animals↗
PubMed2002

A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class aves.

For half a century, variation in genome size (C-value) has been an unresolved puzzle in evolutionary biology. While the initial "C-value paradox" was solved with the discovery of noncoding DNA, a much more complex "C-value enigma" remains. The present study focuses on one aspect of this puzzle, namely the small genome sizes of birds. Significant negative correlations are reported between resting metabolic rate and both C-value and erythrocyte size. Cell size is positively correlated with both nucleus size and C-value in birds, as in other vertebrates. These findings shed light on the constraints acting on genome size in birds and illustrate the importance of interactions among various levels of the biological hierarchy, ranging from the subchromosomal to the ecological. Following from a discussion of the mechanistic bases of the correlations reported and the processes by which birds achieved and/or maintain small genomes, a pluralistic approach to the C-value enigma is recommended.

Animals↗
PubMed2002

Genome size and developmental parameters in the homeothermic vertebrates.

Although unrelated to any intuitive notions of organismal complexity, haploid genome sizes (C values) are correlated with a variety of cellular and organismal parameters in different taxa. In some cases, these relationships are universal--notably, genome size correlates positively with cell size in each of the vertebrate classes. Other relationships are apparently relevant only in particular groups. For example, although genome size is inversely correlated with metabolic rate in both mammals and birds, no such relationship is found in amphibians. More recently, it has been suggested that developmental rate and (or) longevity are related to genome size in birds. In the present study, a large dataset was used to examine possible relationships between genome size and various developmental parameters in both birds and mammals. In neither group does development appear to be of relevance to genome size evolution (except perhaps indirectly in birds through the intermediation of body size and (or) within the rodents), a situation very different from that found in amphibians. These findings make it clear that genome size evolution cannot be understood without reference to the particular biology of the organisms under study.

Animals↗
PubMed2002

From pixels to picograms: a beginners' guide to genome quantification by Feulgen image analysis densitometry.

The study of genome size variation is important from a number of practical and theoretical perspectives. For example, the long-standing "C-value enigma" relating to the more than 200,000-fold range in eukaryotic genome sizes is best studied from a broad comparative standpoint. Genome size data are also required in detailed analyses of genome structure and evolution. The choice of future genome sequencing projects will be dependent on knowledge regarding the sizes of genomes to be sequenced, and so on. To date, genome size data have been acquired primarily by Feulgen microdensitometry or flow cytometry. Each has several advantages but also important limitations. In this review, we provide a practical guide to the new technique of Feulgen image analysis densitometry. The review is designed for those interested in genome size measurements but not extensively experienced in histochemistry, densitometry, or microscopy. Therefore, relevant historical and technical background information is included. For easy reference, we provide recipes for required reagents, guidelines for cell staining, and a checklist of steps for successful image analysis. We hope that the accuracy, rapidity, and cost-effectiveness of Feulgen image analysis demonstrated here will stimulate further surveys of genome sizes in a variety of taxa.

Animals↗