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Robert D. Denton

Bio: Robert D. Denton is an academic researcher from Ohio State University. The author has contributed to research in topics: Genome & Ploidy. The author has an hindex of 9, co-authored 22 publications receiving 178 citations. Previous affiliations of Robert D. Denton include University of Minnesota & University of Connecticut.
Topics: Genome, Ploidy, Polyploid, Population, Introgression

Papers
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Journal ArticleDOI
TL;DR: Comparing amphibian communities of natural wetlands to 2 types of constructed wetlands in the Daniel Boone National Forest, Kentucky underscores the need for monitoring constructed wetlands to assess ecological condition and provides suggestions to land managers who aim to construct isolated wetlands for amphibians.
Abstract: Among the many causes linked to amphibian declines, habitat loss and alteration remain the most significant. Lack of federal protection for isolated wetlands has resulted in loss of amphibian breeding habitat without subsequent mitigation. Additionally, wetlands built for mitigation often do not replicate lost natural wetlands in structure or ecological processes. The long-term role of constructed wetlands for amphibian conservation is poorly understood because monitoring is often lacking. Our objective was to compare amphibian communities of natural wetlands to 2 types of constructed wetlands in the Daniel Boone National Forest, Kentucky. We measured habitat variables including canopy closure, hydrology, upland coarse woody debris, aquatic vegetation, maximum water depth, and Ohio Wetland Rapid Assessment Score at each wetland and quantified species-specific amphibian capture per unit effort using dip-netting. Wood frogs (Lithobates sylvaticus) and marbled salamanders (Ambystoma opacum) were almost exclusively found in natural, ephemeral wetlands, whereas large frogs (L. clamitans, L. catesbeianus, L. palustris) were primarily found breeding in permanent, constructed wetlands. Permutational analysis of variance indicated significant differences in amphibian communities between constructed and natural wetland types. Redundancy analysis indicated that hydrology and canopy closure best explained the differences in community composition between natural and constructed wetlands. Regression analyses and subsequent model ranking showed that greater captures per unit effort for eastern newts (Notopthalmus viridescens) and green frogs (L. clamitans) were predicted by increasing wetland size and depth, respectively, whereas mole salamanders (Ambystoma sp.) were negatively associated with the amount of aquatic vegetation and positively associated with wetland depth. As amphibian conservation and management become increasingly important in light of recent population declines and habitat loss, the ability to construct wetlands that provide amphibian habitat and to monitor how amphibians respond will be crucial to preservation of species diversity. Our research underscores the need for monitoring constructed wetlands to assess ecological condition. We provide suggestions to land managers who aim to construct isolated wetlands for amphibians. © 2013 The Wildlife Society.

49 citations

Posted ContentDOI
24 May 2018-bioRxiv
TL;DR: This work produced a chromosome-level genome assembly for the African Bullfrog and discovered that the Bullfrog Z is surprisingly homologous to substantial portions of the human X, highlighting the consistency of sex-linked sequences despite sex determination system lability and revealing the repeated use of two major genomic sequence blocks during vertebrate sex chromosome evolution.
Abstract: Heteromorphic sex chromosomes have evolved repeatedly among vertebrate lineages despite largely deleterious reductions in gene dose. Understanding how this gene dose problem is overcome is hampered by the lack of genomic information at the base of tetrapods and comparisons across the evolutionary history of vertebrates. To address this problem, we produced a chromosome-level genome assembly for the African Bullfrog ( Pyxicephalus adspersus )--an amphibian with heteromorphic ZW sex chromosomes--and discovered that the Bullfrog Z is surprisingly homologous to substantial portions of the human X. Using this new reference genome, we identified ancestral synteny among the sex chromosomes of major vertebrate lineages, showing that non-mammalian sex chromosomes are strongly associated with a single vertebrate ancestral chromosome, while mammals are associated with another that displays increased haploinsufficiency. The sex chromosomes of the African Bullfrog however, share genomic blocks with both humans and non-mammalian vertebrates, connecting the two ancestral chromosome sequences that repeatedly characterize vertebrate sex chromosomes. Our results highlight the consistency of sex-linked sequences despite sex determination system lability and reveal the repeated use of two major genomic sequence blocks during vertebrate sex chromosome evolution.

26 citations

Journal ArticleDOI
TL;DR: Comparisons of gene expression levels across the three parental genomes revealed that the unisexual triploid displays a pattern of genome balance, where 72% of the genes analyzed were expressed equally among the subgenomes.
Abstract: Polyploidy is increasingly recognized as a driver of biological diversity. How and why polyploidization affects gene expression is critical to understanding the link between ploidy elevation and diversification. In polyploid plants, multiple studies have demonstrated that ploidy elevation can confer major but variable consequences for gene expression, ranging from gene-by-gene alterations to entirely silenced genomes. By contrast, animal polyploids remain largely uncharacterized. Accordingly, how animals respond to and manage polyploidy events is not understood. Here, we address this important knowledge gap by analyzing transcriptomes from a triploid hybrid animal, a unisexual Ambystoma salamander, and three sexual Ambystoma species that represent all three parental genomes in the unisexual. We used a novel bioinformatics pipeline that includes competitively mapping triploid sequences to a reference set of orthologous genes in the sexual species to evaluate subgenome expression. Our comparisons of gene expression levels across the three parental genomes revealed that the unisexual triploid displays a pattern of genome balance, where 72% of the genes analyzed were expressed equally among the subgenomes. This result is strikingly different from the genome imbalance typically observed in hybrid polyploid plants. Our analyses represent the first to address gene expression in a triploid hybrid animal and introduce a novel bioinformatic framework for analyzing transcriptomic data.

21 citations

Journal ArticleDOI
TL;DR: This study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.
Abstract: Distinct genetic markers should show similar patterns of differentiation between species reflecting their common evolutionary histories, yet there are increasing examples of differences in the biogeographic distribution of species-specific nuclear (nuDNA) and mitochondrial DNA (mtDNA) variants within and between species. Identifying the evolutionary processes that underlie these anomalous patterns of genetic differentiation is an important goal. Here, we analyse the putative mitonuclear discordance observed between sister species of mole salamanders (Ambystoma barbouri and A. texanum) in which A. barbouri-specific mtDNA is found in animals located within the range of A. texanum. We test three hypotheses for this discordance (undetected range expansion, mtDNA introgression, and hybridization) using nuDNA and mtDNA data analysed with methods that varied in the parameters estimated and the timescales measured. Results from a Bayesian clustering technique (STRUCTURE), bidirectional estimates of gene flow (MIGRATE-N and IMa2) and phylogeny-based methods (*BEAST, BUCKy) all support the conclusion that the discordance is due to geographically restricted mtDNA introgression from A. barbouri into A. texanum. Limited data on species-specific tooth morphology match this conclusion. Significant differences in environmental conditions exist between sites where A. texanum with and without A. barbouri-like mtDNA occur, suggesting a possible role for selection in the process of introgression. Overall, our study provides a general example of the value of using complimentary analyses to make inferences of the directionality, timescale, and source of mtDNA introgression in animals.

21 citations

Journal ArticleDOI
01 Aug 2016-Toxicon
TL;DR: It is found that Timber Rattlesnake (Crotalus horridus) venom inhibition by Eastern gray squirrels (Sciurus carolinensis) is higher at a site where the rattlesnakes are present, which suggests selection may maintain venom resistance in populations separated by short distances.

19 citations


Cited by
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01 Apr 2014
TL;DR: This article reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene content and the selective pressures that preserved the surviving ancestral genes, and concluded that the gene content of Y chromosome became specialized through selection to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly expressed regulators of transcription, translation and protein stability.
Abstract: The human X and Y chromosomes evolved from an ordinary pair of autosomes, but millions of years ago genetic decay ravaged the Y chromosome, and only three per cent of its ancestral genes survived. We reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene content and the selective pressures that preserved the surviving ancestral genes. Our findings indicate that survival was nonrandom, and in two cases, convergent across placental and marsupial mammals. We conclude that the gene content of the Y chromosome became specialized through selection to maintain the ancestral dosage of homologous X–Y gene pairs that function as broadly expressed regulators of transcription, translation and protein stability. We propose that beyond its roles in testis determination and spermatogenesis, the Y chromosome is essential for male viability, and has unappreciated roles in Turner’s syndrome and in phenotypic differences between the sexes in health and disease.

439 citations

Journal ArticleDOI
01 Feb 2008-Copeia
TL;DR: This is an extraordinary book based on the experience of an impressive team of specialists on amphibian declines and conservation, primarily focused on species from the United States, and is divided into a collection of 52 essays on conservation written mainly by researchers with extensive experience in amphibian conservation.
Abstract: AMPHIBIAN DECLINES: THE CONSERVATION STATUS OF UNITED STATES SPECIES. Michael Lannoo (ed.). 2005. University of California Press, Berkeley. ISBN 0-520-235924. XXI + 1094 p. $95.00 (hard cover).—During the past decade and a half, much has been discussed and published on amphibian declines. The new information obtained created a novel field of research in herpetology. The starting point of this new field was the First World Congress of Herpetology, held in Canterbury, England, in 1989, when herpetologists found that the amphibian disappearances they had witnessed individually were not merely rare, local phenomena but rather appeared to be occurring around the globe. The relevance of amphibian declines can be measured not only by the scientific production but also by the extensive coverage by the popular press. The book ‘‘Amphibian Declines: The Conservation Status of United States Species’’ summarizes the advances of this new research field, mainly in the United States. This is an extraordinary book based on the experience of an impressive team of specialists on amphibian declines and conservation, primarily focused on species from the United States. Because North American herpetologists have accumulated detailed data on native amphibians over many years, this book is very thorough. The book is divided into two parts; part one is a collection of 52 essays on conservation written mainly by researchers with extensive experience in amphibian conservation. This first part is divided into an Introduction and chapters titled Declines, Causes, Conservation, Surveys and Monitoring, Education, and Perspective. Part two corresponds to the species accounts for Anura and Caudata. An amazing total of 215 contributors participated in the two parts of the book, producing more than a thousand pages of rich information on amphibian declines and conservation in United States. The essays vary in detail and breadth of coverage, and there is some overlap among some of them, but this is to be expected in a book written by so many scientists. In the Introduction there are five essays that provide a historical perspective on the conservation of amphibians. In the Declines chapter five essays give a historical perspective as well, but there is also specific information on the decline of cricket frogs (Acris crepitans) and a data-rich essay on the decline of the salamanders of the genus Plethodon. Together the essays address all of the relevant topics of conservation and decline in amphibians. For example, the first essay by Tim Halliday addresses the main reasons for amphibian declines, summarizing recent progress that is improving our understanding on the causal factors promoting it. He indicates habitat destruction, climate change, pollution, increased UV-B radiation, and disease as the main factors, but also calls attention to the synergistic action among some of these causes. The necessity of a more ample comprehension of the conservation status of other groups of organisms is also highlighted, given that declines may also be severe in other taxa, such as bivalves. The lack of data on distribution, population structure, and habitat of amphibians makes the task of protection more difficult. In the second essay, Martha L. Crump discusses why some species are in decline while others are not. She compares studies in different parts of the world and concludes that the patterns associated with declines in one assemblage are not necessarily repeated in other assemblages. She did not find a clear pattern of differences (in phylogeny, distribution, habitat, activity, diet, body size, skin characteristics, and life history traits) between declining and non-declining species. She concludes that some species are less able to cope with anthropogenic environmental changes. In Causes, 12 essays adequately cover the main causes that have been proposed or demonstrated to be involved in amphibian declines. Global warming, UV radiation, chemical pollution, parasites and malformations, habitat destruction or alteration, and commercial trade of amphibians are among the treated topics. However, in this chapter some essays are not related to the causes of decline per se, such as the essay on the Lucké renal adenocarcinoma in Northern Leopard Frogs (Lithobates pipiens). In this case there is no evidence that the carcinoma is a factor in frog population decline. In Conservation, 18 essays treat different aspects of amphibian conservation. There are essays on the conservation of specific taxa, such as one on the endangered Houston Toad (Anaxyrus houstonensis) that includes information on the major causes of decline and the politics that play an important role in conservation. The essay on fluctuations in the size of tiger salamander populations provides useful information for understanding the related natural and anthropogenic factors that affect this amphibian. The essay on the Texas spring and cave salamanders (Eurycea) shows that most species have restricted distributions and are threatened by human activities. The essay on the Southwestern desert bufonids indicates that, although these toads escaped the declines experienced by many anurans, some species are being eliminated from some areas as a result of habitat alteration. Two essays raise questions on taxonomic and systematic problems and the conservation status of the amphibians. They call attention to the necessity of clear and workable systems of classification to describe biodiversity, the importance of phylogenetic taxonomies, and the importance of conservation systematics in management and politics. The essay by Karen R. Lips and Maureen A. Donnelly is an exception in the book in that it aims to describe the nature, extent, and possible causes of amphibian declines in the tropics and not in United States. The limitation of this essay is the lack of data on tropical amphibian, which is not the authors’ fault (see below). Other essays in this chapter are on amphibian decline and management, landscape ecology, ecotoxicology, importance of museum collections in amphibian conservation, reserve network, population manipulations of imperiled species, exotic invading species of fish and amphibians and their impacts on the natural systems, and the importance of natural history in the conservation of amphibians. In the Surveys and Monitoring chapter, nine essays cover general and specific aspects, including methodological proposals. Some essays treat the distribution, decline, and monitoring of amphibians from specific places in the United States or from a general program, the North American

432 citations

Dissertation
01 Jan 1995
TL;DR: A potent and structurally novel antimicrobial peptide was isolated and characterized from the stomach tissue of Bufo bufo gargarizans, an Asian toad.
Abstract: A potent and structurally novel antimicrobial peptide was isolated and characterized from the stomach tissue of Bufo bufo gargarizans, an Asian toad. The 39-amino acid peptide, named buforin I, was purified to homogeneity by heparin-affinity column and reverse-phase HPLC. The amino acid sequence of buforin I was identical in 37 of 39 amino-terminal residues of Xenopus histone H2A. The buforin I showed strong antimicrobial activities in vitro against a broad-spectrum of microorganisms and was found to be more potent than magainin 2. In addition, a 21-amino acid peptide, named buforin II, which was derived from buforin I, showed more potent antimicrobial activities than buforin I.

250 citations

Journal ArticleDOI
TL;DR: This review will make a foray into the world of animal venoms, discuss synergies and complementarities of the different approaches used in their study, and identify current bottlenecks that prevent inferring the evolutionary mechanisms and ecological constraints that molded snake venoms to their present-day variability landscape.
Abstract: Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection. Reconstructing the natural history of venoms, particularly those of snakes, which will be dealt with in more detail in this review, requires the integration of different levels of knowledge into a meaningful and comprehensive evolutionary framework for separating stochastic changes from adaptive evolution. The application of omics technologies and other disciplines have contributed to a qualitative and quantitative advance in the road map towards this goal. In this review we will make a foray into the world of animal venoms, discuss synergies and complementarities of the different approaches used in their study, and identify current bottlenecks that prevent inferring the evolutionary mechanisms and ecological constraints that molded snake venoms to their present-day variability landscape.

129 citations