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Sample records for large salamander genome

  1. LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

    PubMed Central

    Sun, Cheng; Shepard, Donald B.; Chong, Rebecca A.; López Arriaza, José; Hall, Kathryn; Castoe, Todd A.; Feschotte, Cédric; Pollock, David D.; Mueller, Rachel Lockridge

    2012-01-01

    Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders. PMID:22200636

  2. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

    PubMed Central

    Keinath, Melissa C.; Timoshevskiy, Vladimir A.; Timoshevskaya, Nataliya Y.; Tsonis, Panagiotis A.; Voss, S. Randal; Smith, Jeramiah J.

    2015-01-01

    Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes. PMID:26553646

  3. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing.

    PubMed

    Keinath, Melissa C; Timoshevskiy, Vladimir A; Timoshevskaya, Nataliya Y; Tsonis, Panagiotis A; Voss, S Randal; Smith, Jeramiah J

    2015-01-01

    Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes. PMID:26553646

  4. Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders

    PubMed Central

    Sun, Cheng; Mueller, Rachel Lockridge

    2014-01-01

    Among animals, genome sizes range from 20 Mb to 130 Gb, with 380-fold variation across vertebrates. Most of the largest vertebrate genomes are found in salamanders, an amphibian clade of 660 species. Thus, salamanders are an important system for studying causes and consequences of genomic gigantism. Previously, we showed that plethodontid salamander genomes accumulate higher levels of long terminal repeat (LTR) retrotransposons than do other vertebrates, although the evolutionary origins of such sequences remained unexplored. We also showed that some salamanders in the family Plethodontidae have relatively slow rates of DNA loss through small insertions and deletions. Here, we present new data from Cryptobranchus alleganiensis, the hellbender. Cryptobranchus and Plethodontidae span the basal phylogenetic split within salamanders; thus, analyses incorporating these taxa can shed light on the genome of the ancestral crown salamander lineage, which underwent expansion. We show that high levels of LTR retrotransposons likely characterize all crown salamanders, suggesting that disproportionate expansion of this transposable element (TE) class contributed to genomic expansion. Phylogenetic and age distribution analyses of salamander LTR retrotransposons indicate that salamanders’ high TE levels reflect persistence and diversification of ancestral TEs rather than horizontal transfer events. Finally, we show that relatively slow DNA loss rates through small indels likely characterize all crown salamanders, suggesting that a decreased DNA loss rate contributed to genomic expansion at the clade’s base. Our identification of shared genomic features across phylogenetically distant salamanders is a first step toward identifying the evolutionary processes underlying accumulation and persistence of high levels of repetitive sequence in salamander genomes. PMID:25115007

  5. Variation in salamanders: an essay on genomes, development, and evolution.

    PubMed

    Brockes, Jeremy P

    2015-01-01

    Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future. PMID:25740473

  6. Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes.

    PubMed

    Samuels, Amy K; Weisrock, David W; Smith, Jeramiah J; France, Katherine J; Walker, John A; Putta, Srikrishna; Voss, S Randal

    2005-04-11

    We report on a study that extended mitochondrial transcript information from a recent EST project to obtain complete mitochondrial genome sequence for 5 tiger salamander complex species (Ambystoma mexicanum, A. t. tigrinum, A. andersoni, A. californiense, and A. dumerilii). We describe, for the first time, aspects of mitochondrial transcription in a representative amphibian, and then use complete mitochondrial sequence data to examine salamander phylogeny at both deep and shallow levels of evolutionary divergence. The available mitochondrial ESTs for A. mexicanum (N=2481) and A. t. tigrinum (N=1205) provided 92% and 87% coverage of the mitochondrial genome, respectively. Complete mitochondrial sequences for all species were rapidly obtained by using long distance PCR and DNA sequencing. A number of genome structural characteristics (base pair length, base composition, gene number, gene boundaries, codon usage) were highly similar among all species and to other distantly related salamanders. Overall, mitochondrial transcription in Ambystoma approximated the pattern observed in other vertebrates. We inferred from the mapping of ESTs onto mtDNA that transcription occurs from both heavy and light strand promoters and continues around the entire length of the mtDNA, followed by post-transcriptional processing. However, the observation of many short transcripts corresponding to rRNA genes indicates that transcription may often terminate prematurely to bias transcription of rRNA genes; indeed an rRNA transcription termination signal sequence was observed immediately following the 16S rRNA gene. Phylogenetic analyses of salamander family relationships consistently grouped Ambystomatidae in a clade containing Cryptobranchidae and Hynobiidae, to the exclusion of Salamandridae. This robust result suggests a novel alternative hypothesis because previous studies have consistently identified Ambystomatidae and Salamandridae as closely related taxa. Phylogenetic analyses of tiger

  7. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders

    PubMed Central

    Fitzpatrick, Benjamin M; Johnson, Jarrett R; Kump, D Kevin; Shaffer, H Bradley; Smith, Jeramiah J; Voss, S Randal

    2009-01-01

    Background Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders. Results At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects. Conclusion While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain. PMID:19630983

  8. Phylogeny and genetic history of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870) inferred from complete mitochondrial genomes.

    PubMed

    Malyarchuk, Boris; Derenko, Miroslava; Denisova, Galina

    2013-05-01

    We assessed phylogeny of the Siberian salamander (Salamandrella keyserlingii, Dybowski, 1870), the most northern ectothermic, terrestrial vertebrate in Eurasia, by sequence analysis of complete mitochondrial genomes in 26 specimens from different localities (China, Khabarovsk region, Sakhalin, Yakutia, Magadan region, Chukotka, Kamchatka, Ural, European part of Russia). In addition, a complete mitochondrial genome of the Schrenck salamander, Salamandrella schrenckii, was determined for the first time. Bayesian phylogenetic analysis of the entire mtDNA genomes of S. keyserlingii demonstrates that two haplotype clades, AB and C, radiated about 1.4 million years ago (Mya). Bayesian skyline plots of population size change through time show an expansion around 250 thousand years ago (kya) and then a decline around the Last Glacial Maximum (25 kya) with subsequent restoration of population size. Climatic changes during the Quaternary period have dramatically affected the population genetic structure of the Siberian salamanders. In addition, complete mtDNA sequence analysis allowed us to recognize that the vast area of Northern Eurasia was colonized only by the Siberian salamander clade C1b during the last 150 kya. Meanwhile, we were unable to find evidence of molecular adaptation in this clade by analyzing the whole mitochondrial genomes of the Siberian salamanders. PMID:23415986

  9. Plethodontid salamander mitochondrial genomics: A parsimonyevaluation of character conflict and implications for historicalbiogeography

    SciTech Connect

    Macey, J. Robert

    2005-01-19

    A new parsimony analysis of 27 complete mitochondrial genomic sequences is conducted to investigate the phylogenetic relationships of plethodontid salamanders. This analysis focuses on the amount of character conflict between phylogenetic trees recovered from newly conducted parsimony searches and the Bayesian and maximum likelihood topology reported by Mueller et al. (2004, PNAS, 101, 13820-13825). Strong support for Hemidactylium as the sister taxon to all other plethodontids is recovered from parsimony analyses. Plotting area relationships on the most parsimonious phylogenetic tree suggests that eastern North America is the origin of the family Plethodontidae supporting the ''Out of Appalachia'' hypothesis. A new taxonomy that recognizes clades recovered from phylogenetic analyses is proposed.

  10. Cryptic sex? Estimates of genome exchange in unisexual mole salamanders (Ambystoma sp.).

    PubMed

    Gibbs, H Lisle; Denton, Robert D

    2016-06-01

    Cryptic sex has been argued to explain the exceptional longevity of certain parthenogenetic vertebrate lineages, yet direct measurements of genetic exchange between sexual and apparently parthenogenetic forms are rare. Female unisexual mole salamanders (Ambystoma sp.) are the oldest known unisexual vertebrate lineage (~5 million years), and one hypothesis for their persistence is that allopolyploid female unisexuals periodically exchange haploid genomes 'genome exchange' during gynogenetic reproduction with males from sympatric sexual species. We test this hypothesis by using genome-specific microsatellite DNA markers to estimate the rates of genome exchange between sexual males and unisexual females in two ponds in NE Ohio. We also test the prediction that levels of gene flow should be higher for 'sympatric' (sexual males present) genomes in unisexuals compared to 'allopatric' (sexual males absent) unisexual genomes. We used a model testing framework in the coalescent-based program MIGRATE-N to compare models where unidirectional gene flow is present and absent between sexual species and unisexuals. As predicted, our results show higher levels of gene flow between sexuals and sympatric unisexual genomes compared to lower (likely artefactual) levels of gene flow between sexuals and allopatric unisexual genomes. Our results provide direct evidence that genome exchange between sexual and unisexual Ambystoma occurs and demonstrate that the magnitude depends on which sexual species are present. The relatively high levels of gene flow suggest that unisexuals must be at a selective advantage over sexual forms so as to avoid extinction due to genetic swamping through genome exchange. PMID:27100619

  11. Complete nucleotide sequence of the mitochondrial genome of a salamander, Mertensiella luschani.

    PubMed

    Zardoya, Rafael; Malaga-Trillo, Edward; Veith, Michael; Meyer, Axel

    2003-10-23

    The complete nucleotide sequence (16,650 bp) of the mitochondrial genome of the salamander Mertensiella luschani (Caudata, Amphibia) was determined. This molecule conforms to the consensus vertebrate mitochondrial gene order. However, it is characterized by a long non-coding intervening sequence with two 124-bp repeats between the tRNA(Thr) and tRNA(Pro) genes. The new sequence data were used to reconstruct a phylogeny of jawed vertebrates. Phylogenetic analyses of all mitochondrial protein-coding genes at the amino acid level recovered a robust vertebrate tree in which lungfishes are the closest living relatives of tetrapods, salamanders and frogs are grouped together to the exclusion of caecilians (the Batrachia hypothesis) in a monophyletic amphibian clade, turtles show diapsid affinities and are placed as sister group of crocodiles+birds, and the marsupials are grouped together with monotremes and basal to placental mammals. The deduced phylogeny was used to characterize the molecular evolution of vertebrate mitochondrial proteins. Amino acid frequencies were analyzed across the main lineages of jawed vertebrates, and leucine and cysteine were found to be the most and least abundant amino acids in mitochondrial proteins, respectively. Patterns of amino acid replacements were conserved among vertebrates. Overall, cartilaginous fishes showed the least variation in amino acid frequencies and replacements. Constancy of rates of evolution among the main lineages of jawed vertebrates was rejected. PMID:14604788

  12. Accommodating the load: The transposable element content of very large genomes.

    PubMed

    Metcalfe, Cushla J; Casane, Didier

    2013-03-01

    Very large genomes, that is, those above 20 Gb, are rare but widely distributed throughout the eukaryotes. They are found within the diatoms, dinoflagellates, metazoans and green plants, but so far have not been found in the excavates. There is a known positive correlation between genome size and the proportion of the genome composed of transposable elements (TEs). Very large genomes may therefore be expected to be almost entirely composed of TEs. Of the large genomes examined, in the angiosperms, gymnosperms and the dinoflagellates only a small portion of the genome was identified as TEs, most of these genomes were unidentified and may be novel or diverse TEs. In the salamanders and lungfish, 25 to 47% of the genome were identifiable retrotransposons, that is, TEs that copy themselves before insertion. However, the predominant class of TEs found in the lungfish was not the same as that found in the salamanders. The little data we have at the moment suggests therefore that the diversity and abundance of TEs is variable between taxa with large genomes, similar to patterns found in taxa with smaller genomes. Based on results from the human genome, we suggest that the 'missing' portion of the lungfish and salamander genomes are old, highly divergent, and therefore inactive copies of TEs. The data available indicate that, unlike plants with large genomes, neither the lungfish nor the salamanders show an increased risk of extinction. Based on a slow rate of DNA loss in salamanders it has been suggested that the large salamander genome is the result of run-away genome expansion involving genome size increases via TE proliferation associated with reduced recombination rate. We know of no studies on DNA loss or recombination rates in lungfish genomes, however a similar scenario could describe the process of genome expansion in the lungfish. A series of waves of TE transposition and sequence decay would describe the pattern of TE content seen in both the lungfish and the

  13. [Episodes of adaptive evolution of mitochondrial genome in Asiatic salamanders (Amphibia, Caudata, Hynobiidae)].

    PubMed

    Maliarchuk, B A; Derenko, M V; Denisova, G A

    2014-02-01

    To elucidate the effect of natural selection on the evolution of mitochondrial DNA (mtDNA) in Asiatic salamanders of the family Hynobiidae, nucleotide sequences of 12 protein-coding genes were analyzed. Using a mixed effects model of evolution, it was found that, in spite of the pronounced effect of negative selection on the mtDNA evolution in Hynobiidae (which is typical for the animals in general), two phylogenetic clusters, the West Asian one, represented by the genera Ranodon and Paradactylodon, and North Eurasian one, represented by the genus Salamandrella, were formed under the influence of episodic positive selection. Analysis of protein sequences encoded by the mitochondrial genome also supported the influence of positive selection on the evolution of Hynobiidae at some stages of their cladogenesis. It is suggested that the signatures of adaptive evolution detected in the mtDNA of Hynobiidae were determined by the complex and long-lasting history of their formation, accompanied by adaptation to the changing environment. PMID:25711027

  14. Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes

    SciTech Connect

    Mueller, Rachel Lockridge; Macey, J. Robert; Jaekel, Martin; Wake, David B.; Boore, Jeffrey L.

    2004-08-01

    The evolutionary history of the largest salamander family (Plethodontidae) is characterized by extreme morphological homoplasy. Analysis of the mechanisms generating such homoplasy requires an independent, molecular phylogeny. To this end, we sequenced 24 complete mitochondrial genomes (22 plethodontids and two outgroup taxa), added data for three species from GenBank, and performed partitioned and unpartitioned Bayesian, ML, and MP phylogenetic analyses. We explored four dataset partitioning strategies to account for evolutionary process heterogeneity among genes and codon positions, all of which yielded increased model likelihoods and decreased numbers of supported nodes in the topologies (PP > 0.95) relative to the unpartitioned analysis. Our phylogenetic analyses yielded congruent trees that contrast with the traditional morphology-based taxonomy; the monophyly of three out of four major groups is rejected. Reanalysis of current hypotheses in light of these new evolutionary relationships suggests that (1) a larval life history stage re-evolved from a direct-developing ancestor multiple times, (2) there is no phylogenetic support for the ''Out of Appalachia'' hypothesis of plethodontid origins, and (3) novel scenarios must be reconstructed for the convergent evolution of projectile tongues, reduction in toe number, and specialization for defensive tail loss. Some of these novel scenarios imply morphological transformation series that proceed in the opposite direction than was previously thought. In addition, they suggest surprising evolutionary lability in traits previously interpreted to be conservative.

  15. Invasive Asian Earthworms Negatively Impact Keystone Terrestrial Salamanders.

    PubMed

    Ziemba, Julie L; Hickerson, Cari-Ann M; Anthony, Carl D

    2016-01-01

    Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp.) are invading North American forests and consuming the vital detrital layer that forest floor biota [including the keystone species Plethodon cinereus (Eastern Red-backed Salamander)], rely on for protection, food, and habitat. Plethodon cinereus population declines have been associated with leaf litter loss following the invasion of several exotic earthworm species, but there have been few studies on the specific interactions between pheretimoid earthworms and P. cinereus. Since some species of large and active pheretimoids spatially overlap with salamanders beneath natural cover objects and in detritus, they may distinctively compound the negative consequences of earthworm-mediated resource degradation by physically disturbing important salamander activities (foraging, mating, and egg brooding). We predicted that earthworms would exclude salamanders from high quality microhabitat, reduce foraging efficiency, and negatively affect salamander fitness. In laboratory trials, salamanders used lower quality microhabitat and consumed fewer flies in the presence of earthworms. In a natural field experiment, conducted on salamander populations from "non-invaded" and "pheretimoid invaded" sites in Ohio, salamanders and earthworms shared cover objects ~60% less than expected. Earthworm abundance was negatively associated with juvenile and male salamander abundance, but had no relationship with female salamander abundance. There was no effect of pheretimoid invasion on salamander body condition. Juvenile and non-resident male salamanders do not hold stable territories centered beneath cover objects such as rocks or logs, which results in reduced access to prey, greater risk of desiccation, and dispersal pressure. Habitat degradation and physical exclusion of salamanders from cover objects may hinder juvenile and male salamander performance, ultimately reducing recruitment and salamander abundance following Asian

  16. Invasive Asian Earthworms Negatively Impact Keystone Terrestrial Salamanders

    PubMed Central

    Ziemba, Julie L.

    2016-01-01

    Asian pheretimoid earthworms (e.g. Amynthas and Metaphire spp.) are invading North American forests and consuming the vital detrital layer that forest floor biota [including the keystone species Plethodon cinereus (Eastern Red-backed Salamander)], rely on for protection, food, and habitat. Plethodon cinereus population declines have been associated with leaf litter loss following the invasion of several exotic earthworm species, but there have been few studies on the specific interactions between pheretimoid earthworms and P. cinereus. Since some species of large and active pheretimoids spatially overlap with salamanders beneath natural cover objects and in detritus, they may distinctively compound the negative consequences of earthworm-mediated resource degradation by physically disturbing important salamander activities (foraging, mating, and egg brooding). We predicted that earthworms would exclude salamanders from high quality microhabitat, reduce foraging efficiency, and negatively affect salamander fitness. In laboratory trials, salamanders used lower quality microhabitat and consumed fewer flies in the presence of earthworms. In a natural field experiment, conducted on salamander populations from “non-invaded” and “pheretimoid invaded” sites in Ohio, salamanders and earthworms shared cover objects ~60% less than expected. Earthworm abundance was negatively associated with juvenile and male salamander abundance, but had no relationship with female salamander abundance. There was no effect of pheretimoid invasion on salamander body condition. Juvenile and non-resident male salamanders do not hold stable territories centered beneath cover objects such as rocks or logs, which results in reduced access to prey, greater risk of desiccation, and dispersal pressure. Habitat degradation and physical exclusion of salamanders from cover objects may hinder juvenile and male salamander performance, ultimately reducing recruitment and salamander abundance

  17. Paedomorphosis and simplification in the nervous system of salamanders.

    PubMed

    Roth, G; Nishikawa, K C; Naujoks-Manteuffel, C; Schmidt, A; Wake, D B

    1993-01-01

    Comparative neuroanatomists since Herrick [1914] have been aware of the paradox that the brain of amphibians, especially salamanders, is less complex than one would expect based on their phylogenetic position among the Tetrapoda. Many features of the brain are less differentiated in salamanders than in tetrapod outgroups, including chondrichthyans and bony fishes, and for some brain characters, the salamander brain is even more simple than that of the agnathans. Here, we perform a cladistic analysis on 23 characters of four sensory systems (visual, auditory, lateral line and olfactory) and the brain. Our taxa include myxinoids, lampreys, chondrichthyans, actinopterygians, Latimeria, Neoceratodus and the lepidosirenid lungfishes, amniotes, frogs, caecilians, salamanders and bolitoglossine salamanders. Of the 23 characters we examined, 19 are most parsimoniously interpreted as secondarily simplified in salamanders from a more complex ancestral state, two characters are equally parsimonious under both hypotheses, one character (well developed ipsilateral retinotectal projections) is more complex in bolitoglossine salamanders than in vertebrates generally, and only one character (migration of neurons in the medial pallium) is most parsimoniously interpreted as retention of the plesiomorphically simple condition. Secondary simplification of the salamander brain appears to result from paedomorphosis, or retention of juvenile or embryonic morphology into adulthood. Paedomorphosis is correlated with an increase in genome size, which in turn is positively correlated with cell size, but negatively correlated with cell proliferation and differentiation rates. Available data suggest that, although increasing genome size and paedomorphosis tend to compromise the function of the salamander brain, compensating mechanisms have evolved that may restore or even enhance brain function. PMID:8364715

  18. Salamander occupancy in headwater stream networks

    USGS Publications Warehouse

    Grant, E.H.C.; Green, L.E.; Lowe, W.H.

    2009-01-01

    1. Stream ecosystems exhibit a highly consistent dendritic geometry in which linear habitat units intersect to create a hierarchical network of connected branches. 2. Ecological and life history traits of species living in streams, such as the potential for overland movement, may interact with this architecture to shape patterns of occupancy and response to disturbance. Specifically, large-scale habitat alteration that fragments stream networks and reduces connectivity may reduce the probability a stream is occupied by sensitive species, such as stream salamanders. 3. We collected habitat occupancy data on four species of stream salamanders in first-order (i.e. headwater) streams in undeveloped and urbanised regions of the eastern U.S.A. We then used an information-theoretic approach to test alternative models of salamander occupancy based on a priori predictions of the effects of network configuration, region and salamander life history. 4. Across all four species, we found that streams connected to other first-order streams had higher occupancy than those flowing directly into larger streams and rivers. For three of the four species, occupancy was lower in the urbanised region than in the undeveloped region. 5. These results demonstrate that the spatial configuration of stream networks within protected areas affects the occurrences of stream salamander species. We strongly encourage preservation of network connections between first-order streams in conservation planning and management decisions that may affect stream species.

  19. Annotating Large Genomes With Exact Word Matches

    PubMed Central

    Healy, John; Thomas, Elizabeth E.; Schwartz, Jacob T.; Wigler, Michael

    2003-01-01

    We have developed a tool for rapidly determining the number of exact matches of any word within large, internally repetitive genomes or sets of genomes. Thus we can readily annotate any sequence, including the entire human genome, with the counts of its constituent words. We create a Burrows-Wheeler transform of the genome, which together with auxiliary data structures facilitating counting, can reside in about one gigabyte of RAM. Our original interest was motivated by oligonucleotide probe design, and we describe a general protocol for defining unique hybridization probes. But our method also has applications for the analysis of genome structure and assembly. We demonstrate the identification of chromosome-specific repeats, and outline a general procedure for finding undiscovered repeats. We also illustrate the changing contents of the human genome assemblies by comparing the annotations built from different genome freezes. PMID:12975312

  20. Effects of Red-Backed Salamanders on Ecosystem Functions

    PubMed Central

    Hocking, Daniel J.; Babbitt, Kimberly J.

    2014-01-01

    Ecosystems provide a vast array of services for human societies, but understanding how various organisms contribute to the functions that maintain these services remains an important ecological challenge. Predators can affect ecosystem functions through a combination of top-down trophic cascades and bottom-up effects on nutrient dynamics. As the most abundant vertebrate predator in many eastern US forests, woodland salamanders (Plethodon spp.) likely affect ecosystems functions. We examined the effects of red-backed salamanders (Plethodon cinereus) on a variety of forest ecosystem functions using a combined approach of large-scale salamander removals (314-m2 plots) and small-scale enclosures (2 m2) where we explicitly manipulated salamander density (0, 0.5, 1, 2, 4 m−2). In these experiments, we measured the rates of litter and wood decomposition, potential nitrogen mineralization and nitrification rates, acorn germination, and foliar insect damage on red oak seedlings. Across both experimental venues, we found no significant effect of red-backed salamanders on any of the ecosystem functions. We also found no effect of salamanders on intraguild predator abundance (carabid beetles, centipedes, spiders). Our study adds to the already conflicting evidence on effects of red-backed salamander and other amphibians on terrestrial ecosystem functions. It appears likely that the impact of terrestrial amphibians on ecosystem functions is context dependent. Future research would benefit from explicitly examining terrestrial amphibian effects on ecosystem functions under a variety of environmental conditions and in different forest types. PMID:24466269

  1. Effects of red-backed salamanders on ecosystem functions.

    PubMed

    Hocking, Daniel J; Babbitt, Kimberly J

    2014-01-01

    Ecosystems provide a vast array of services for human societies, but understanding how various organisms contribute to the functions that maintain these services remains an important ecological challenge. Predators can affect ecosystem functions through a combination of top-down trophic cascades and bottom-up effects on nutrient dynamics. As the most abundant vertebrate predator in many eastern US forests, woodland salamanders (Plethodon spp.) likely affect ecosystems functions. We examined the effects of red-backed salamanders (Plethodon cinereus) on a variety of forest ecosystem functions using a combined approach of large-scale salamander removals (314-m(2) plots) and small-scale enclosures (2 m(2)) where we explicitly manipulated salamander density (0, 0.5, 1, 2, 4 m(-2)). In these experiments, we measured the rates of litter and wood decomposition, potential nitrogen mineralization and nitrification rates, acorn germination, and foliar insect damage on red oak seedlings. Across both experimental venues, we found no significant effect of red-backed salamanders on any of the ecosystem functions. We also found no effect of salamanders on intraguild predator abundance (carabid beetles, centipedes, spiders). Our study adds to the already conflicting evidence on effects of red-backed salamander and other amphibians on terrestrial ecosystem functions. It appears likely that the impact of terrestrial amphibians on ecosystem functions is context dependent. Future research would benefit from explicitly examining terrestrial amphibian effects on ecosystem functions under a variety of environmental conditions and in different forest types. PMID:24466269

  2. Atypical regions in large genomic DNA sequences

    SciTech Connect

    Scherer, S. |; McPeek, M.S.; Speed, T.P.

    1994-07-19

    Large genomic DNA sequences contain regions with distinctive patterns of sequence organization. The authors describe a method using logarithms of probabilities based on seventh-order Markov chains to rapidly identify genomic sequences that do not resemble models of genome organization built from compilations of octanucleotide usage. Data bases have been constructed from Escherichia coli and Saccharomyces cerevisiae DNA sequences of >1000 nt and human sequences of >10,000 nt. Atypical genes and clusters of genes have been located in bacteriophage, yeast, and primate DNA sequences. The authors consider criteria for statistical significance of the results, offer possible explanations for the observed variation in genome organization, and give additional applications of these methods in DNA sequence analysis.

  3. Global Alignment System for Large Genomic Sequencing

    Energy Science and Technology Software Center (ESTSC)

    2002-03-01

    AVID is a global alignment system tailored for the alignment of large genomic sequences up to megabases in length. Features include the possibility of one sequence being in draft form, fast alignment, robustness and accuracy. The method is an anchor based alignment using maximal matches derived from suffix trees.

  4. Transcriptomic Analysis of Endangered Chinese Salamander: Identification of Immune, Sex and Reproduction-Related Genes and Genetic Markers

    PubMed Central

    Che, Rongbo; Sun, Yuena; Wang, Rixin; Xu, Tianjun

    2014-01-01

    Background The Chinese salamander (Hynobius chinensis), an endangered amphibian species of salamander endemic to China, has attracted much attention because of its value of studying paleontology evolutionary history and decreasing population size. Despite increasing interest in the Hynobius chinensis genome, genomic resources for the species are still very limited. A comprehensive transcriptome of Hynobius chinensis, which will provide a resource for genome annotation, candidate genes identification and molecular marker development should be generated to supplement it. Principal Findings We performed a de novo assembly of Hynobius chinensis transcriptome by Illumina sequencing. A total of 148,510 nonredundant unigenes with an average length of approximately 580 bp were obtained. In all, 60,388 (40.66%) unigenes showed homologous matches in at least one database and 33,537 (22.58%) unigenes were annotated by all four databases. In total, 41,553 unigenes were categorized into 62 sub-categories by BLAST2GO search, and 19,468 transcripts were assigned to 140 KEGG pathways. A large number of unigenes involved in immune system, local adaptation, reproduction and sex determination were identified, as well as 31,982 simple sequence repeats (SSRs) and 460,923 putative single nucleotide polymorphisms (SNPs). Conclusion This dataset represents the first transcriptome analysis of the Chinese salamander (Hynobius chinensis), an endangered species, to be also the first time of hynobiidae. The transcriptome will provide valuable resource for further research in discovery of new genes, protection of population, adaptive evolution and survey of various pathways, as well as development of molecule markers in Chinese salamander; and reference information for closely related species. PMID:24498226

  5. Landmark learning by juvenile salamanders (Ambystoma maculatum).

    PubMed

    Heuring, Whitney L; Mathis, Alicia

    2014-10-01

    Learning to use a landmark as a beacon to locate resources is one of the simplest forms of spatial learning. We tested whether landmark learning occurs in a semifossorial salamander that migrates annually to breeding ponds as adults. Juvenile spotted salamanders (Ambystoma maculatum) were tested in square containers with a plastic feeding dish in each corner, and a piece of earthworm was placed in one randomly-chosen dish. For landmark-trained salamanders, a rock was placed beside the dish containing the prey. For control salamanders, the rock was placed beside a randomly selected feeding dish. Each salamander was trained once every 2 days for 30 days. Significantly more landmark-trained salamanders than control salamanders entered the landmark area first, and landmark-trained individuals had faster latencies to enter the landmark area and longer stay-times. These results suggest that spotted salamanders are able to locate resources by associating their positions with landmarks. PMID:25444775

  6. [Phylogenetic relationships among Asiatic salamanders of the genus Salamandrella based on variability of nuclear genes].

    PubMed

    Maliarchuk, B A; Derenko, M V; Denisova, G A

    2015-01-01

    Based on sequence variation of three nuclear genome genes (BDNF, POMC, and RAG1), the phylogenetic relationships among Asiatic salamanders of the genus Salamandrella, Siberian salamander (S. keyserlingii) and Schrenk salamander (S. schrenkii), were examined. Both species demonstrated high levels of heterozygosity determined by intraspecific polymorphism. Fixed interspecific differences were revealed at one nucleotide position of the RAG1 gene, and thus the level of interspecific divergence over the three genes constituted only 0.04%. Analysis of the RAG1 polymorphism across the whole range of S. keyserlingii showed that only one gene variant, encoding for modified RAG1 recombinase, had the highest distribution to the north of the Amur region (west and northeast of Siberia). It is possible that the changes in the RAG1 gene in Siberian salamander are of an adaptive nature. However, cases of interspecific hybridization were identified in Jewish autonomous oblast (JAO), which contains one of the range borders between the two Salamandrella species. PMID:25857197

  7. "ANEIDES AENEUS" (GREEN SALAMANDER). DISPERSAL

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aneides aeneus inhabits cliffs and rockface outcrops at elevations <1340 m in mountainous forests from southwestern Pennsylvania to extreme northeastern Mississippi (Petranka 1998. Salamanders of the United States and Canada. Smithsonian Institution Press, Washington D.C. 587pp). Populations are ...

  8. Genome comparison of Pseudomonas aeruginosa large phages.

    PubMed

    Hertveldt, Kirsten; Lavigne, Rob; Pleteneva, Elena; Sernova, Natalia; Kurochkina, Lidia; Korchevskii, Roman; Robben, Johan; Mesyanzhinov, Vadim; Krylov, Victor N; Volckaert, Guido

    2005-12-01

    Pseudomonas aeruginosa phage EL is a dsDNA phage related to the giant phiKZ-like Myoviridae. The EL genome sequence comprises 211,215 bp and has 201 predicted open reading frames (ORFs). The EL genome does not share DNA sequence homology with other viruses and micro-organisms sequenced to date. However, one-third of the predicted EL gene products (gps) shares similarity (Blast alignments of 17-55% amino acid identity) with phiKZ proteins. Comparative EL and phiKZ genomics reveals that these giant phages are an example of substantially diverged genetic mosaics. Based on the position of similar EL and phiKZ predicted gene products, five genome regions can be delineated in EL, four of which are relatively conserved between EL and phiKZ. Region IV, a 17.7 kb genome region with 28 predicted ORFs, is unique to EL. Fourteen EL ORFs have been assigned a putative function based on protein similarity. Assigned proteins are involved in DNA replication and nucleotide metabolism (NAD+-dependent DNA ligase, ribonuclease HI, helicase, thymidylate kinase), host lysis and particle structure. EL-gp146 is the first chaperonin GroEL sequence identified in a viral genome. Besides a putative transposase, EL harbours predicted mobile endonucleases related to H-N-H and LAGLIDADG homing endonucleases associated with group I intron and intein intervening sequences. PMID:16256135

  9. Precision Editing of Large Animal Genomes

    PubMed Central

    Tan, Wenfang (Spring); Carlson, Daniel F.; Walton, Mark W.; Fahrenkrug, Scott C.; Hackett, Perry B.

    2013-01-01

    Transgenic animals are an important source of protein and nutrition for most humans and will play key roles in satisfying the increasing demand for food in an ever-increasing world population. The past decade has experienced a revolution in the development of methods that permit the introduction of specific alterations to complex genomes. This precision will enhance genome-based improvement of farm animals for food production. Precision genetics also will enhance the development of therapeutic biomaterials and models of human disease as resources for the development of advanced patient therapies. PMID:23084873

  10. 'Salamander plague' on Britain's doorstep.

    PubMed

    Mills, Georgina

    2015-01-24

    Chytridiomycosis can cause mass declines in amphibians, and the chytrid fungus Batrachochytrium dendrobatidis is the classic cause of this disease. However, recently, a second strain of chytrid fungus has emerged in Europe, resulting in major declines in fire salamanders. The Zoological Society of London (ZSL) discussed this, and the implications for the UK, at a meeting in December in London. Georgina Mills reports. PMID:25614547

  11. Age-related changes in the tiger salamander retina.

    PubMed

    Townes-Anderson, E; Colantonio, A; St Jules, R S

    1998-05-01

    Tiger salamanders have been used in visual science because of the large size of their cells and the ease of preparation and maintenance of in vitro retinal preparations. We have found that salamanders over 27 cm in length show a variety of visual abnormalities. Compared to smaller animals (15-23 cm), large animals exhibited a decrease in visual responses determined by tests of the optomotor reflex. Small animals responded correctly an average of 84.5% of the time in visual testing at three light levels compared to an average of 68.4% for the large animals with the poorest visual performance at the lowest level of illumination. In addition, large animals contained (i) histological degeneration of the outer retina, in particular, loss and disruption of outer segments and abnormalities of the retinal pigmented epithelium, (ii) loss of cells, including photoreceptors, by apoptosis as evaluated with the TUNEL technique, and (iii) an increase in the number of macrophages and lymphocytes within the retina as determined by morphological examination. These histological changes were present in all large animals and all quadrants of their retinas. In contrast, small animals showed virtually no retinal degeneration, no TUNEL-positive cells, and few immune-like cells in the retina. Since large animals are also older animals. the visual changes are age-related. Loss of visual function and histological degeneration in the outer retina also typify aged human eyes. Thus, we propose that large salamanders serve as an animal model for age-related retinal degeneration. In addition to providing a source of aging retina that is readily accessible to experimental manipulation, the salamander provides a pigmented retina with a mixed (2:1, rod:cone) population of photoreceptors, similar to the degeneration-prone parafoveal region of the human eye. PMID:9631666

  12. Origin and diversification of a salamander sex pheromone system.

    PubMed

    Janssenswillen, Sunita; Vandebergh, Wim; Treer, Dag; Willaert, Bert; Maex, Margo; Van Bocxlaer, Ines; Bossuyt, Franky

    2015-02-01

    Sex pheromones form an important facet of reproductive strategies in many organisms throughout the Animal Kingdom. One of the oldest known sex pheromones in vertebrates are proteins of the Sodefrin Precursor-like Factor (SPF) system, which already had a courtship function in early salamanders. The subsequent evolution of salamanders is characterized by a diversification in courtship and reproduction, but little is known on how the SPF pheromone system diversified in relation to changing courtship strategies. Here, we combined transcriptomic, genomic, and phylogenetic analyses to investigate the evolution of the SPF pheromone system in nine salamandrid species with distinct courtship displays. First, we show that SPF originated from vertebrate three-finger proteins and diversified through multiple gene duplications in salamanders, while remaining a single copy in frogs. Next, we demonstrate that tail-fanning newts have retained a high phylogenetic diversity of SPFs, whereas loss of tail-fanning has been associated with a reduced importance or loss of SPF expression in the cloacal region. Finally, we show that the attractant decapeptide sodefrin is cleaved from larger SPF precursors that originated by a 62 bp insertion and consequent frameshift in an ancestral Cynops lineage. This led to the birth of a new decapeptide that rapidly evolved a pheromone function independently from uncleaved proteins. PMID:25415963

  13. On the analysis of large-scale genomic structures.

    PubMed

    Oiwa, Nestor Norio; Goldman, Carla

    2005-01-01

    We apply methods from statistical physics (histograms, correlation functions, fractal dimensions, and singularity spectra) to characterize large-scale structure of the distribution of nucleotides along genomic sequences. We discuss the role of the extension of noncoding segments ("junk DNA") for the genomic organization, and the connection between the coding segment distribution and the high-eukaryotic chromatin condensation. The following sequences taken from GenBank were analyzed: complete genome of Xanthomonas campestri, complete genome of yeast, chromosome V of Caenorhabditis elegans, and human chromosome XVII around gene BRCA1. The results are compared with the random and periodic sequences and those generated by simple and generalized fractal Cantor sets. PMID:15858230

  14. GDC 2: Compression of large collections of genomes.

    PubMed

    Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

    2015-01-01

    The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about. PMID:26108279

  15. GDC 2: Compression of large collections of genomes

    PubMed Central

    Deorowicz, Sebastian; Danek, Agnieszka; Niemiec, Marcin

    2015-01-01

    The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change is a necessity of storage and transfer of huge amounts of genomic data. In this paper we deal with the problem of compression of large collections of complete genomic sequences. We propose an algorithm that is able to compress the collection of 1092 human diploid genomes about 9,500 times. This result is about 4 times better than what is offered by the other existing compressors. Moreover, our algorithm is very fast as it processes the data with speed 200 MB/s on a modern workstation. In a consequence the proposed algorithm allows storing the complete genomic collections at low cost, e.g., the examined collection of 1092 human genomes needs only about 700 MB when compressed, what can be compared to about 6.7 TB of uncompressed FASTA files. The source code is available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about. PMID:26108279

  16. Thermal equilibrium and temperature differences among body regions in European plethodontid salamanders.

    PubMed

    Lunghi, Enrico; Manenti, Raoul; Canciani, Giancarlo; Scarì, Giorgio; Pennati, Roberta; Ficetola, Gentile Francesco

    2016-08-01

    Information on species thermal physiology is extremely important to understand species responses to environmental heterogeneity and changes. Thermography is an emerging technology that allows high resolution and accurate measurement of body temperature, but until now it has not been used to study thermal physiology of amphibians in the wild. Hydromantes terrestrial salamanders are strongly depending on ambient temperature for their activity and gas exchanges, but information on their body temperature is extremely limited. In this study we tested if Hydromantes salamanders are thermoconform, we assessed whether there are temperature differences among body regions, and evaluated the time required to reach the thermal equilibrium. During summers of 2014 and 2015 we analysed 56 salamanders (Hydromantes ambrosii and Hydromantes italicus) using infrared thermocamera. We photographed salamanders at the moment in which we found them and 1, 2, 3, 4, 5 and 15min after having kept them in the hands. Body temperature was equal to air temperature; salamanders attained the equilibrium with air temperature in about 8min, the time required to reach equilibrium was longer in individuals with large body size. We detected small temperature differences between body parts, the head being slightly warmer than the body and the tail (mean difference: 0.05°C). These salamanders quickly reach the equilibrium with the environment, thus microhabitat measurement allows obtaining accurate information on their tolerance limits. PMID:27503719

  17. Earliest known crown-group salamanders.

    PubMed

    Gao, Ke-Qin; Shubin, Neil H

    2003-03-27

    Salamanders are a model system for studying the rates and patterns of the evolution of new anatomical structures. Recent discoveries of abundant Late Jurassic and Early Cretaceous salamanders are helping to address these issues. Here we report the discovery of well-preserved Middle Jurassic salamanders from China, which constitutes the earliest known record of crown-group urodeles (living salamanders and their closest relatives). The new specimens are from the volcanic deposits of the Jiulongshan Formation (Bathonian), Inner Mongolia, China, and represent basal members of the Cryptobranchidae, a family that includes the endangered Asian giant salamander (Andrias) and the North American hellbender (Cryptobranchus). These fossils document a Mesozoic record of the Cryptobranchidae, predating the previous record of the group by some 100 million years. This discovery provides evidence to support the hypothesis that the divergence of the Cryptobranchidae from the Hynobiidae had taken place in Asia before the Middle Jurassic period. PMID:12660782

  18. Science Review for the Scott Bar Salamander (Plethodon asupak) and the Siskiyou Mountains Salamander (P. stormi): Biology, Taxonomy, Habitat, and Detection Probabilities/Occupancy

    USGS Publications Warehouse

    DeGross, Douglas J.; Bury, R. Bruce

    2007-01-01

    The Plethodon elongatus Complex in the Klamath-Siskiyou Ecoregion of southern Oregon and northern California includes three species: the Del Norte salamander, Plethodon elongatus; the Siskiyou Mountains salamander, P. stormi; and the Scott Bar salamander, P. asupak. This review aims to summarize the current literature and information available on select topics for P. stormi and P. asupak. These are both terrestrial salamanders belonging to the Family Plethodontidae, which contains more species and has a wider geographic distribution than any other family of salamanders (Wake 1966, 2006; Pough 1989). The genera of this family have greatly diversified ecologically across North America, Central America, northern South America, Sardinia, southeastern France and northwestern Italy, and have recently been discovered on the Korean peninsula (Min et al. 2005). The genus Plethodon is found exclusively in North America and is split into three distinct clades, based upon morphology and phylogenetics (Highton and Larson 1979): eastern small Plethodon, eastern large Plethodon, and the western Plethodon. The western Plethodon are the greatest representation of Plethodontidae in the Pacific Northwest, with 8 species. The two species with the most restricted ranges of these regional congeners are the Siskiyou Mountains and Scott Bar salamanders. These salamanders occupy the interior of the Klamath-Siskiyou Ecoregion which straddles the California and Oregon state lines, between Siskiyou County (CA) and Jackson and Josephine Counties (OR). The relatively recent discovery of P. asupak (Mead et al. 2005) and the limited range of both species have created an environment of uncertain conservation status for these species. This review will focus on four central topics of concern for land and resource managers: Biology; Taxonomy; Habitat; and Detection Probabilities/Occupancy.

  19. Identification of large-scale genomic variation in cancer genomes using in silico reference models.

    PubMed

    Killcoyne, Sarah; Del Sol, Antonio

    2016-01-01

    Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed. PMID:26264669

  20. Identification of large-scale genomic variation in cancer genomes using in silico reference models

    PubMed Central

    Killcoyne, Sarah; del Sol, Antonio

    2016-01-01

    Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed. PMID:26264669

  1. BACFinder: genomic localisation of large insert genomic clones based on restriction fingerprinting

    PubMed Central

    Crowe, Mark L.; Rana, Debashis; Fraser, Fiona; Bancroft, Ian; Trick, Martin

    2002-01-01

    We have developed software that allows the prediction of the genomic location of a bacterial artificial chromosome (BAC) clone, or other large genomic clone, based on a simple restriction digest of the BAC. The mapping is performed by comparing the experimentally derived restriction digest of the BAC DNA with a virtual restriction digest of the whole genome sequence. Our trials indicate that this program identified the genomic regions represented by BAC clones with a degree of accuracy comparable to that of end-sequencing, but at considerably less cost. Although the program has been developed principally for use with Arabidopsis BACs, it should align large insert genomic clones to any fully sequenced genome. PMID:12409477

  2. Exon capture optimization in amphibians with large genomes.

    PubMed

    McCartney-Melstad, Evan; Mount, Genevieve G; Shaffer, H Bradley

    2016-09-01

    Gathering genomic-scale data efficiently is challenging for nonmodel species with large, complex genomes. Transcriptome sequencing is accessible for organisms with large genomes, and sequence capture probes can be designed from such mRNA sequences to enrich and sequence exonic regions. Maximizing enrichment efficiency is important to reduce sequencing costs, but relatively few data exist for exon capture experiments in nonmodel organisms with large genomes. Here, we conducted a replicated factorial experiment to explore the effects of several modifications to standard protocols that might increase sequence capture efficiency for amphibians and other taxa with large, complex genomes. Increasing the amounts of c0 t-1 repetitive sequence blocker and individual input DNA used in target enrichment reactions reduced the rates of PCR duplication. This reduction led to an increase in the percentage of unique reads mapping to target sequences, essentially doubling overall efficiency of the target capture from 10.4% to nearly 19.9% and rendering target capture experiments more efficient and affordable. Our results indicate that target capture protocols can be modified to efficiently screen vertebrates with large genomes, including amphibians. PMID:27223337

  3. Large-scale structure of genomic methylation patterns.

    PubMed

    Rollins, Robert A; Haghighi, Fatemeh; Edwards, John R; Das, Rajdeep; Zhang, Michael Q; Ju, Jingyue; Bestor, Timothy H

    2006-02-01

    The mammalian genome depends on patterns of methylated cytosines for normal function, but the relationship between genomic methylation patterns and the underlying sequence is unclear. We have characterized the methylation landscape of the human genome by global analysis of patterns of CpG depletion and by direct sequencing of 3073 unmethylated domains and 2565 methylated domains from human brain DNA. The genome was found to consist of short (<4 kb) unmethylated domains embedded in a matrix of long methylated domains. Unmethylated domains were enriched in promoters, CpG islands, and first exons, while methylated domains comprised interspersed and tandem-repeated sequences, exons other than first exons, and non-annotated single-copy sequences that are depleted in the CpG dinucleotide. The enrichment of regulatory sequences in the relatively small unmethylated compartment suggests that cytosine methylation constrains the effective size of the genome through the selective exposure of regulatory sequences. This buffers regulatory networks against changes in total genome size and provides an explanation for the C value paradox, which concerns the wide variations in genome size that scale independently of gene number. This suggestion is compatible with the finding that cytosine methylation is universal among large-genome eukaryotes, while many eukaryotes with genome sizes <5 x 10(8) bp do not methylate their DNA. PMID:16365381

  4. Ambystoma maculatum (spotted salamander). Reproduction

    USGS Publications Warehouse

    Glorioso, Brad M.; Waddle, Hardin; Hefner, Jeromi

    2012-01-01

    The Spotted Salamander is a wide-ranging salamander of the eastern United States that typically breeds in winter or early spring in ephemeral pools in lowland forests. Ambystoma maculatum is known to deposit 2-4 egg masses per year, each containing 1-250 eggs. As part of ongoing research into the ecology and reproductive biology of Spotted Salamanders in the Kisatchie District of Kisatchie National Forest in Natchitoches Parish, Louisiana, USA, we have been counting the number of embryos per egg mass. We captured seven female A. maculatum in a small pool, six of which were still gravid. We took standard measurements, including SVL, and then implanted a Passive Integrated Transponder (PIT tag) into each adult female as was the protocol. About an hour after processing these animals we marked new A. maculatum egg masses found in the same small pool using PVC pin flags pushed carefully through the outer jelly. We did not have enough time to process them that evening, and it was not until a few days later that we photographed those masses. We discovered that one of the masses contained a PIT tag in the outer jelly that corresponded to one of the six gravid females that were marked that same evening. To our knowledge, this is the first report of PIT tags being the means, albeit coincidentally, by which a particular egg mass of Ambystoma maculatum has been assigned to a particular female. For our purposes, losing the PIT tag from the adult female is counter to the goals of our study of this population, and we will no longer be implanting PIT tags into gravid females.

  5. Climate change and shrinking salamanders: alternative mechanisms for changes in plethodontid salamander body size.

    PubMed

    Connette, Grant M; Crawford, John A; Peterman, William E

    2015-08-01

    An increasing number of studies have demonstrated relationships between climate trends and body size change of organisms. In many cases, climate might be expected to influence body size by altering thermoregulation, energetics or food availability. However, observed body size change can result from a variety of ecological processes (e.g. growth, selection, population dynamics) or imperfect observation of biological systems. We used two extensive datasets to evaluate alternative mechanisms for recently reported changes in the observed body size of plethodontid salamanders. We found that mean adult body size of salamanders can be highly sensitive to survey conditions, particularly rainfall. This systematic bias in the detection of larger or smaller individuals could result in a signature of body size change in relation to reported climate trends when it is simply observation error. We also identify considerable variability in body size distributions among years and find that individual growth rates can be strongly influenced by weather. Finally, our study demonstrates that measures of mean adult body size can be highly variable among surveys and that large sample sizes may be required to make reliable inferences. Identifying the effects of climate change is a critical area of research in ecology and conservation. Researchers should be aware that observed changes in certain organisms can result from multiple ecological processes or systematic bias due to nonrandom sampling of populations. PMID:25641384

  6. Late Jurassic salamanders from northern China.

    PubMed

    Gao, K Q; Shubin, N H

    2001-03-29

    With ten extant families, salamanders (urodeles) are one of the three major groups of modern amphibians (lissamphibians). Extant salamanders are often used as a model system to assess fundamental issues of developmental, morphological and biogeographical evolution. Unfortunately, our understanding of these issues has been hampered by the paucity of fossil evidence available to assess the early history of the group. Here we report the discovery of an extraordinary sample of salamander fossils, some with rare soft-tissue impressions, from the Upper Jurassic of China. With over 500 articulated specimens, this assemblage documents the morphological diversity of early urodeles and includes larvae and adults of both neotenic and metamorphosed taxa. Phylogenetic analysis confirms that these salamanders are primitive, and reveals that all basal salamander clades have Asian distributions. This is compelling evidence for an Asian origin of Recent salamanders, as well as for an extensive and early radiation of several major lineages. These discoveries show that the evolution of salamanders has involved phylogenetic and ecological diversification around a body plan that has remained fundamentally stable for over 150 million years. PMID:11279493

  7. A method to capture large DNA fragments from genomic DNA.

    PubMed

    Ball, Geneviève; Filloux, Alain; Voulhoux, Romé

    2014-01-01

    The gene capture technique is a powerful tool that allows the cloning of large DNA regions (up to 80 kb), such as entire genomic islands, without using restriction enzymes or DNA amplification. This technique takes advantage of the high recombinant capacity of the yeast. A "capture" vector containing both ends of the target DNA region must first be constructed. The target region is then captured by co-transformation and recombination in yeast between the "capture" vector and appropriate genomic DNA. The selected recombinant plasmid can be verified by sequencing and transferred in the bacteria for multiple applications. This chapter describes a protocol specifically adapted for Pseudomonas aeruginosa genomic DNA capture. PMID:24818928

  8. Stability analysis of chickpea large genomic DNA inserts in Agrobacterium.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Agrobacterium tumefaciens-mediated transformation of large DNA inserts directly into plants facilitates the transfer of gene clusters and flanking regulatory elements. It is recommended that the integrity of large genomic fragments in Agrobacterium be verified prior to plant transformation. In this ...

  9. Genome size variation affects song attractiveness in grasshoppers: evidence for sexual selection against large genomes.

    PubMed

    Schielzeth, Holger; Streitner, Corinna; Lampe, Ulrike; Franzke, Alexandra; Reinhold, Klaus

    2014-12-01

    Genome size is largely uncorrelated to organismal complexity and adaptive scenarios. Genetic drift as well as intragenomic conflict have been put forward to explain this observation. We here study the impact of genome size on sexual attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers show particularly large variation in genome size due to the high prevalence of supernumerary chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance and fitness costs if present in high numbers. We ranked male grasshoppers by song characteristics that are known to affect female preferences in this species and scored genome sizes of attractive and unattractive individuals from the extremes of this distribution. We find that attractive singers have significantly smaller genomes, demonstrating that genome size is reflected in male courtship songs and that females prefer songs of males with small genomes. Such a genome size dependent mate preference effectively selects against selfish genetic elements that tend to increase genome size. The data therefore provide a novel example of how sexual selection can reinforce natural selection and can act as an agent in an intragenomic arms race. Furthermore, our findings indicate an underappreciated route of how choosy females could gain indirect benefits. PMID:25200798

  10. Salamander growth rates increase along an experimental stream phosphorus gradient.

    PubMed

    Bumpers, Phillip M; Maerz, John C; Rosemond, Amy D; Benstead, Jonathan P

    2015-11-01

    Nutrient-driven perturbations to the resource base of food webs are predicted to attenuate with trophic distance, so it is unclear whether higher-level consumers will generally respond to anthropogenic nutrient loading. Few studies have tested whether nutrient (specifically, nitrogen [N] and phosphorus [P]) enrichment of aquatic ecosystems propagates through multiple trophic levels to affect predators, or whether N vs. P is relatively more important in driving effects on food webs. We conducted two-year whole-stream N and P additions to five streams to generate gradients in N and P concentration and N:P ratio (target N:P = 2, 8, 16, 32, 128). Larval salamanders are vertebrate predators of primary and secondary macroinvertebrate consumers in many heterotrophic headwater streams in which the basal resources are detritus and associated microorganisms. We determined the effects of N and P on the growth rates of caged and free-roaming larval Desmognathus quadramaculatus and the average body size of larval Eurycea wilderae. Growth rates and average body size increased by up to 40% and 60%, respectively, with P concentration and were negatively related to N:P ratio. These findings were consistent across both species of salamanders using different methodologies (cage vs. free-roaming) and at different temporal scales (3 months vs. 2 yr). Nitrogen concentration was not significantly related to increased growth rate or body size of the salamander species tested. Our findings suggest that salamander growth responds to the relaxation of ecosystem-level P limitation and that moderate P enrichment can have relatively large effects on vertebrate predators in detritus-based food webs. PMID:27070018

  11. Effects of hatching time for larval ambystomatid salamanders

    USGS Publications Warehouse

    Boone, M.D.; Scott, D.E.; Niewiarowski, P.H.

    2002-01-01

    In aquatic communities, the phenology of breeding may influence species interactions. In the early-breeding marbled salamander, Ambystoma opacum, timing of pond filling may determine whether interactions among larvae are competitive or predatory. The objectives of our studies were to determine how time of egg hatching affected size, larval period, and survival to metamorphosis in A. opacum, and if early-hatching in A. opacum influenced the competitive and predator-prey relationships with smaller larvae of the mole salamander, Ambystoma talpoideum. Salamander larvae were reared from hatching through metamorphosis in large, outdoor enclosures located in a natural temporary pond in Aiken County, South Carolina, in two experiments. In study 1, we reared early- and late-hatching A. opacum larvae separately from hatching through metamorphosis. In study 2, we examined how early- versus late-hatching A. opacum affected a syntopic species, A. talpoideum. In general, early-hatching A. opacum were larger and older at metamorphosis, had greater survival, and left the pond earlier than late-hatching larvae. Ambystoma talpoideum reared in the presence of early-hatching A. opacum had lower survival than in controls, suggesting that A. opacum may predate upon A. talpoideum when they gain a growth advantage over later-hatching larvae. Our studies demonstrate that time of pond filling and phenology of breeding may influence population dynamics and alter the nature of relationships that develop among species.

  12. Effect of acute low body temperature on predatory behavior and prey-capture efficiency in a plethodontid salamander.

    PubMed

    Marvin, Glenn A; Davis, Kayla; Dawson, Jacob

    2016-05-01

    The low-temperature limit for feeding in some salamander species (Desmognathus, Plethodontidae) has been inferred from field studies of seasonal variation in salamander activity and gut contents, which could not determine whether feeding is more dependent on environmental conditions influencing salamander foraging behavior or prey availability and movement. We performed two controlled laboratory experiments to examine the effect of short-term (acute) low body temperature on predatory behavior and prey-capture efficiency in a semiaquatic plethodontid salamander (Desmognathus conanti). In the first experiment, we quantified variation in the feeding responses of cold salamanders (at 1, 3, 5 and 7°C) to a video recording of a walking, warm (15°C) cricket to determine the lower thermal limit for predatory behavior, independent of any temperature effect on movement of prey. Experimental-group salamanders exhibited vigorous feeding responses at 5 and 7°C, large variation in feeding responses both among and within individuals (over time) at 3°C, and little to no feeding response at 1°C. Feeding responses at both 1 and 3°C were significantly less than at each higher temperature, whereas responses of control-group individuals at 15°C did not vary over time. In the second experiment, we quantified feeding by cold salamanders (at 3, 5, 7 and 11°C) on live, warm crickets to examine thermal effects on prey-capture ability. The mean feeding response to live crickets was significantly less at 3°C than at higher temperatures; however, 50% of salamanders captured and ingested prey with high efficiency at this temperature. We conclude that many individuals stalk and capture prey at very low temperatures (down to 3°C). Our results support a growing body of data that indicate many plethodontid salamanders feed at temperatures only a few degrees above freezing. PMID:26939728

  13. Territorial Polymers and Large Scale Genome Organization

    NASA Astrophysics Data System (ADS)

    Grosberg, Alexander

    2012-02-01

    Chromatin fiber in interphase nucleus represents effectively a very long polymer packed in a restricted volume. Although polymer models of chromatin organization were considered, most of them disregard the fact that DNA has to stay not too entangled in order to function properly. One polymer model with no entanglements is the melt of unknotted unconcatenated rings. Extensive simulations indicate that rings in the melt at large length (monomer numbers) N approach the compact state, with gyration radius scaling as N^1/3, suggesting every ring being compact and segregated from the surrounding rings. The segregation is consistent with the known phenomenon of chromosome territories. Surface exponent β (describing the number of contacts between neighboring rings scaling as N^β) appears only slightly below unity, β 0.95. This suggests that the loop factor (probability to meet for two monomers linear distance s apart) should decay as s^-γ, where γ= 2 - β is slightly above one. The later result is consistent with HiC data on real human interphase chromosomes, and does not contradict to the older FISH data. The dynamics of rings in the melt indicates that the motion of one ring remains subdiffusive on the time scale well above the stress relaxation time.

  14. Roary: rapid large-scale prokaryote pan genome analysis

    PubMed Central

    Page, Andrew J.; Cummins, Carla A.; Hunt, Martin; Wong, Vanessa K.; Reuter, Sandra; Holden, Matthew T.G.; Fookes, Maria; Falush, Daniel; Keane, Jacqueline A.; Parkhill, Julian

    2015-01-01

    Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors. Availability and implementation: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary Contact: roary@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26198102

  15. Large-scale data mining pilot project in human genome

    SciTech Connect

    Musick, R.; Fidelis, R.; Slezak, T.

    1997-05-01

    This whitepaper briefly describes a new, aggressive effort in large- scale data Livermore National Labs. The implications of `large- scale` will be clarified Section. In the short term, this effort will focus on several @ssion-critical questions of Genome project. We will adapt current data mining techniques to the Genome domain, to quantify the accuracy of inference results, and lay the groundwork for a more extensive effort in large-scale data mining. A major aspect of the approach is that we will be fully-staffed data warehousing effort in the human Genome area. The long term goal is strong applications- oriented research program in large-@e data mining. The tools, skill set gained will be directly applicable to a wide spectrum of tasks involving a for large spatial and multidimensional data. This includes applications in ensuring non-proliferation, stockpile stewardship, enabling Global Ecology (Materials Database Industrial Ecology), advancing the Biosciences (Human Genome Project), and supporting data for others (Battlefield Management, Health Care).

  16. A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians.

    PubMed

    Pyron, R Alexander; Wiens, John J

    2011-11-01

    The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (∼40% of the known extant species) from 432 genera (∼85% of the ∼500 currently recognized extant genera). Each sampled species contains up to 12,712 bp from 12 genes (three mitochondrial, nine nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups recognized in previous studies, but it also suggests non-monophyly for several currently recognized families, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomantidae). To correct these and other problems, we provide a revised classification of extant amphibians for taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several families not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontophrynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data. PMID:21723399

  17. Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources

    PubMed Central

    Smith, Jeramiah J; Putta, Srikrishna; Walker, John A; Kump, D Kevin; Samuels, Amy K; Monaghan, James R; Weisrock, David W; Staben, Chuck; Voss, S Randal

    2005-01-01

    Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1) Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2) Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3) Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4) Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5) Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6) Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at . PMID:16359543

  18. Conservation assessment for the Siskiyou Mountains salamander and Scott Bar salamander in northern California.

    SciTech Connect

    Vinikour, W. S.; LaGory, K. E.; Adduci, J. J.; Environmental Science Division

    2006-10-20

    The purpose of this conservation assessment is to summarize existing knowledge regarding the biology and ecology of the Siskiyou Mountains salamander and Scott Bar salamander, identify threats to the two species, and identify conservation considerations to aid federal management for persistence of the species. The conservation assessment will serve as the basis for a conservation strategy for the species.

  19. Optimization of AFLP for extremely large genomes over 70 Gb.

    PubMed

    Veselá, Petra; Volařík, Daniel; Mráček, Jaroslav

    2016-07-01

    Here, we present an improved amplified fragment length polymorphism (AFLP) protocol using restriction enzymes (AscI and SbfI) that recognize 8-base pair sequences to provide alternative optimization suitable for species with a genome size over 70 Gb. This cost-effective optimization massively reduces the number of amplified fragments using only +3 selective bases per primer during selective amplification. We demonstrate the effects of the number of fragments and genome size on the appearance of nonidentical comigrating fragments (size homoplasy), which has a negative impact on the informative value of AFLP genotypes. We also present various reaction conditions and their effects on reproducibility and the band intensity of the extremely large genome of Viscum album. The reproducibility of this octo-cutter protocol was calculated using several species with genome sizes ranging from 1 Gb (Carex panicea) to 76 Gb (V. album). The improved protocol also succeeded in detecting high intraspecific variability in species with large genomes (V. album, Galanthus nivalis and Pinus pumila). PMID:26849414

  20. Impacts of a gape limited Brook Trout, Salvelinus fontinalis, on larval Northwestern salamander, Ambystoma gracile, growth: A field enclosure experiment

    USGS Publications Warehouse

    Currens, C.R.; Liss, W.J.; Hoffman, R.L.

    2007-01-01

    The formation of amphibian population structure is directly affected by predation. Although aquatic predators have been shown to have direct negative effects on larval salamanders in laboratory and field experiments, the potential impacts of gape-limited fish on larval salamander growth has been largely underexplored. We designed an enclosure experiment conducted in situ to quantify the effects of gape-limited Brook Trout (Salvelinus fontinalis) on larval Northwestern Salamander (Ambystoma gracile) growth. We specifically tested whether the presence of fish too small to consume larvae had a negative effect on larval growth. The results of this study indicate that the presence of a gape-limited S. fontinalis can have a negative effect on growth of larval A. gracile salamanders. Copyright 2007 Society for the Study of Amphibians and Reptiles.

  1. Early Miocene origin and cryptic diversification of South American salamanders

    PubMed Central

    2013-01-01

    Background The currently recognized species richness of South American salamanders is surprisingly low compared to North and Central America. In part, this low richness may be due to the salamanders being a recent arrival to South America. Additionally, the number of South American salamander species may be underestimated because of cryptic diversity. The aims of our present study were to infer evolutionary relationships, lineage diversity, and timing of divergence of the South American Bolitoglossa using mitochondrial and nuclear sequence data from specimens primarily from localities in the Andes and upper Amazon Basin. We also estimated time of colonization of South America to test whether it is consistent with arrival via the Panamanian Isthmus, or land bridge connection, at its traditionally assumed age of 3 million years. Results Divergence time estimates suggest that Bolitoglossa arrived in South America from Central America by at least the Early Miocene, ca. 23.6 MYA (95% HPD 15.9-30.3 MYA), and subsequently diversified. South American salamanders of the genus Bolitoglossa show strong phylogeographic structure at fine geographic scales and deep divergences at the mitochondrial gene cytochrome b (Cytb) and high diversity at the nuclear recombination activating gene-1 (Rag1). Species often contain multiple genetically divergent lineages that are occasionally geographically overlapping. Single specimens from two southeastern localities in Ecuador are sister to the equatoriana-peruviana clade and genetically distinct from all other species investigated to date. Another single exemplar from the Andes of northwestern Ecuador is highly divergent from all other specimens and is sister to all newly studied samples. Nevertheless, all sampled species of South American Bolitoglossa are members of a single clade that is one of several constituting the subgenus Eladinea, one of seven subgenera in this large genus. Conclusions The ancestors of South American salamanders

  2. ARE SALAMANDERS USEFUL INDICATORS OF HYDROLOGIC PERMANENCE IN HEADWATER STREAMS?

    EPA Science Inventory

    Regulatory agencies need appropriate indicators of stream permanence to aid in jurisdictional determinations for headwater streams. We evaluated salamanders as permanence indicators because they are often abundant in fishless headwaters. Salamander and habitat data were collect...

  3. Kernel methods for large-scale genomic data analysis

    PubMed Central

    Xing, Eric P.; Schaid, Daniel J.

    2015-01-01

    Machine learning, particularly kernel methods, has been demonstrated as a promising new tool to tackle the challenges imposed by today’s explosive data growth in genomics. They provide a practical and principled approach to learning how a large number of genetic variants are associated with complex phenotypes, to help reveal the complexity in the relationship between the genetic markers and the outcome of interest. In this review, we highlight the potential key role it will have in modern genomic data processing, especially with regard to integration with classical methods for gene prioritizing, prediction and data fusion. PMID:25053743

  4. Genome resequencing in Populus: Revealing large-scale genome variation and implications on specialized-trait genomics

    SciTech Connect

    Muchero, Wellington; Labbe, Jessy L; Priya, Ranjan; DiFazio, Steven P; Tuskan, Gerald A

    2014-01-01

    To date, Populus ranks among a few plant species with a complete genome sequence and other highly developed genomic resources. With the first genome sequence among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable economic resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel and fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in molecular biology processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized-traits.

  5. Different season, different strategies: Feeding ecology of two syntopic forest-dwelling salamanders

    NASA Astrophysics Data System (ADS)

    Sebastiano, Salvidio; Antonio, Romano; Fabrizio, Oneto; Dario, Ottonello; Roberta, Michelon

    2012-08-01

    Trophic niche may be the most important ecological dimension for some vertebrate groups and in particular for terrestrial amphibians, that are important predators of soil invertebrates. In general, resource partitioning occurs between syntopic species with similar ecological niches, and coexistence patterns seem to be regulated by temporal resource variability. However most of the generalization on foraging strategies of terrestrial salamanders are extrapolated from studies on New World temperate species, thus we investigated the seasonal effect of resource variation in an European forest ecosystem, in which two ecologically similar but phylogenetically distinct salamander species are found. The diet of adult and juvenile cave salamanders (Speleomantes strinati), and of adult spectacled salamander (Salamandrina perspicillata) was obtained by stomach flushing, and results showed large seasonal changes both in prey availability and in salamander realised trophic niche. Values of trophic diversity were similar and niche overlaps were large among all salamander groups in spring, during high prey availability. Conversely in autumn, when a two-fold reduction in prey biomass was observed, there was a clear niche partitioning as the smaller S. perspicillata shifted from a generalist to a specialized trophic strategy. Juvenile Speleomantes strinatii, that largely overlapped in size with S. perspicillata, did not show any change in diet, suggesting that the feeding strategies were species-specific and not size-mediated. The observed patterns of variation in feeding ecology indicate that similar predators may react differently to changing prey availability to enhance niche partitioning. We also observed an increased energy intake during autumn for S perspicillata and S. strinatii juveniles, possibly related to differences in microhabitat use and activity patterns.

  6. Indexes of Large Genome Collections on a PC

    PubMed Central

    Danek, Agnieszka; Deorowicz, Sebastian; Grabowski, Szymon

    2014-01-01

    The availability of thousands of individual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key operation useful in such analyses is aligning sequencing reads against a collection of genomes, which is costly with the use of existing algorithms due to their large memory requirements. We present MuGI, Multiple Genome Index, which reports all occurrences of a given pattern, in exact and approximate matching model, against a collection of thousand(s) genomes. Its unique feature is the small index size, which is customisable. It fits in a standard computer with 16–32 GB, or even 8 GB, of RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is also fast. For example, the exact matching queries (of average length 150 bp) are handled in average time of 39 µs and with up to 3 mismatches in 373 µs on the test PC with the index size of 13.4 GB. For a smaller index, occupying 7.4 GB in memory, the respective times grow to 76 µs and 917 µs. Software is available at http://sun.aei.polsl.pl/mugi under a free license. Data S1 is available at PLOS One online. PMID:25289699

  7. Life history as a predictor of salamander recovery rate from timber harvest in southern appalachian forests, USA.

    PubMed

    Connette, Grant M; Semlitsch, Raymond D

    2013-12-01

    Forest management often represents a balance between social, economic, and ecological objectives. In the eastern United States, numerous studies have established that terrestrial salamander populations initially decline in abundance following timber harvest, yet the large-scale and long-term consequences are relatively unknown. We used count data from terrestrial survey points to examine the relation between salamander abundance and historic timber harvest while accounting for imperfect detection of individuals. Overall, stream- and terrestrial-breeding salamanders appeared to differ by magnitude of population decline, rate of population recovery, and extent of recolonization from surrounding forest. Specifically, estimated abundance of both species groups was positively associated with stand age and recovery rates were predicted to increase over time for red-legged salamanders (Plethodon shermani) and decrease in stream-breeding species. Abundance of stream-breeding salamanders was predicted to reach a peak by 100 years after timber harvest, and the population growth rate of red-legged salamanders was predicted to undergo a significant increase 100 years after harvest. Estimated abundance of stream-breeding salamanders in young forest stands was also negatively associated with the distance to adjacent forest, a result that suggests immigration has a role in the recovery of these species. Our results indicate that salamander abundance in young forest stands may be only modestly lower than in more mature forest but that full recovery from timber harvest may take a substantial amount of time and that species life history may affect patterns of recovery. Historia de Vida como un Vaticinador de la Tasa de Recuperación de una Salamandra a la Colecta de Madera en los Bosques del Sur de los Apalaches, E.U.A. PMID:24033390

  8. Data congruence, paedomorphosis and salamanders

    PubMed Central

    Struck, Torsten H

    2007-01-01

    Background The retention of ancestral juvenile characters by adult stages of descendants is called paedomorphosis. However, this process can mislead phylogenetic analyses based on morphological data, even in combination with molecular data, because the assessment if a character is primary absent or secondary lost is difficult. Thus, the detection of incongruence between morphological and molecular data is necessary to investigate the reliability of simultaneous analyses. Different methods have been proposed to detect data congruence or incongruence. Five of them (PABA, PBS, NDI, LILD, DRI) are used herein to assess incongruence between morphological and molecular data in a case study addressing salamander phylogeny, which comprises several supposedly paedomorphic taxa. Therefore, previously published data sets were compiled herein. Furthermore, two strategies ameliorating effects of paedomorphosis on phylogenetic studies were tested herein using a statistical rigor. Additionally, efficiency of the different methods to assess incongruence was analyzed using this empirical data set. Finally, a test statistic is presented for all these methods except DRI. Results The addition of morphological data to molecular data results in both different positions of three of the four paedomorphic taxa and strong incongruence, but treating the morphological data using different strategies ameliorating the negative impact of paedomorphosis revokes these changes and minimizes the conflict. Of these strategies the strategy to just exclude paedomorphic character traits seem to be most beneficial. Of the three molecular partitions analyzed herein the RAG1 partition seems to be the most suitable to resolve deep salamander phylogeny. The rRNA and mtDNA partition are either too conserved or too variable, respectively. Of the different methods to detect incongruence, the NDI and PABA approaches are more conservative in the indication of incongruence than LILD and PBS. Conclusion

  9. Abundances of northwestern salamander larvae in montane lakes with and without fish, Mount Rainier National Park, Washington

    USGS Publications Warehouse

    Larson, Gary L.; Hoffman, Robert L.

    2002-01-01

    In Mount Rainier National Park, the northwestern salamander usually inhabits relatively large and deep lakes and ponds (average size = 0.3 ha; average depth > 2 m) that contain flocculent, organic bottom sediments and abundant coarse wood. Prior to 1970, salmonids were introduced into many of the park's lakes and ponds that were typical habitat of the northwestern salamander. The objective of this study was to compare, in lakes and ponds with suitable habitat characteristics for northwestern salamanders, the observed abundances of larvae in takes and ponds with and without these introduced salmonids. Day surveys of 61 lakes were conducted between 1993 and 1999. Fish were limited to takes and ponds deeper than 2 in. For the 48 lakes and ponds deeper than 2 in (i.e., 25 fishless lakes and 23 fish lakes), the mean and median observed abundances of northwestern salamander larvae in fishless lakes and ponds was significantly greater than the mean and median observed abundances of larvae in lakes and ponds with fish. Northwestern salamander larvae were not observed in 11 fish lakes. These lakes were similar in median elevation, surface area, and maximum depth to the fishless lakes. The 12 fish lakes with observed larvae were significantly lower in median elevation, larger in median surface area, and deeper in median maximum depth than the fishless lakes. Low to null observed abundances of northwestern salamander larvae in lakes and ponds with fish were attributed to a combination of fish predation of larvae and changes in larval behavior.

  10. Evidence for Sex Chromosome Turnover in Proteid Salamanders.

    PubMed

    Sessions, Stanley K; Bizjak Mali, Lilijana; Green, David M; Trifonov, Vladimir; Ferguson-Smith, Malcolm

    2016-01-01

    A major goal of genomic and reproductive biology is to understand the evolution of sex determination and sex chromosomes. Species of the 2 genera of the Salamander family Proteidae - Necturus of eastern North America, and Proteus of Southern Europe - have similar-looking karyotypes with the same chromosome number (2n = 38), which differentiates them from all other salamanders. However, Necturus possesses strongly heteromorphic X and Y sex chromosomes that Proteus lacks. Since the heteromorphic sex chromosomes of Necturus were detectable only with C-banding, we hypothesized that we could use C-banding to find sex chromosomes in Proteus. We examined mitotic material from colchicine-treated intestinal epithelium, and meiotic material from testes in specimens of Proteus, representing 3 genetically distinct populations in Slovenia. We compared these results with those from Necturus. We performed FISH to visualize telomeric sequences in meiotic bivalents. Our results provide evidence that Proteus represents an example of sex chromosome turnover in which a Necturus-like Y-chromosome has become permanently translocated to another chromosome converting heteromorphic sex chromosomes to homomorphic sex chromosomes. These results may be key to understanding some unusual aspects of demographics and reproductive biology of Proteus, and are discussed in the context of models of the evolution of sex chromosomes in amphibians. PMID:27351721

  11. Phylogeny, evolution, and biogeography of Asiatic Salamanders (Hynobiidae)

    PubMed Central

    Zhang, Peng; Chen, Yue-Qin; Zhou, Hui; Liu, Yi-Fei; Wang, Xiu-Ling; Papenfuss, Theodore J.; Wake, David B.; Qu, Liang-Hu

    2006-01-01

    We sequenced 15 complete mitochondrial genomes and performed comprehensive molecular phylogenetic analyses to study the origin and phylogeny of the Hynobiidae, an ancient lineage of living salamanders. Our phylogenetic analyses show that the Hynobiidae is a clade with well resolved relationships, and our results contrast with a morphology-based phylogenetic hypothesis. These salamanders have low vagility and are limited in their distribution primarily by deserts, mountains, and oceans. Our analysis suggests that the relationships among living hynobiids have been shaped primarily by geography. We show that four-toed species assigned to Batrachuperus do not form a monophyletic group, and those that occur in Afghanistan and Iran are transferred to the resurrected Paradactylodon. Convergent morphological characters in different hynobiid lineages are likely produced by similar environmental selective pressures. Clock-independent molecular dating suggests that hynobiids originated in the Middle Cretaceous [≈110 million years ago (Mya)]. We propose an “out of North China” hypothesis for hynobiid origins and hypothesize an ancestral stream-adapted form. Given the particular distributional patterns and our molecular dating estimates, we hypothesize that: (i) the interior desertification from Mongolia to Western Asia began ≈50 Mya; (ii) the Tibetan plateau (at least on the eastern fringe) experienced rapid uplift ≈40 Mya and reached an altitude of at least 2,500 m; and (iii) the Ailao–Red River shear zone underwent the most intense orogenic movement ≈24 Mya. PMID:16648252

  12. Recombination-mediated genetic engineering of large genomic DNA transgenes.

    PubMed

    Ejsmont, Radoslaw Kamil; Ahlfeld, Peter; Pozniakovsky, Andrei; Stewart, A Francis; Tomancak, Pavel; Sarov, Mihail

    2011-01-01

    Faithful gene activity reporters are a useful tool for evo-devo studies enabling selective introduction of specific loci between species and assaying the activity of large gene regulatory sequences. The use of large genomic constructs such as BACs and fosmids provides an efficient platform for exploration of gene function under endogenous regulatory control. Despite their large size they can be easily engineered using in vivo homologous recombination in Escherichia coli (recombineering). We have previously demonstrated that the efficiency and fidelity of recombineering are sufficient to allow high-throughput transgene engineering in liquid culture, and have successfully applied this approach in several model systems. Here, we present a detailed protocol for recombineering of BAC/fosmid transgenes for expression of fluorescent or affinity tagged proteins in Drosophila under endogenous in vivo regulatory control. The tag coding sequence is seamlessly recombineered into the genomic region contained in the BAC/fosmid clone, which is then integrated into the fly genome using ϕC31 recombination. This protocol can be easily adapted to other recombineering projects. PMID:22065454

  13. The First Salamander Defensin Antimicrobial Peptide

    PubMed Central

    Jiang, Ke; Rong, Mingqiang; Lai, Ren

    2013-01-01

    Antimicrobial peptides have been widely identified from amphibian skins except salamanders. A novel antimicrobial peptide (CFBD) was isolated and characterized from skin secretions of the salamander, Cynops fudingensis. The cDNA encoding CFBD precursor was cloned from the skin cDNA library of C. fudingensis. The precursor was composed of three domains: signal peptide of 17 residues, mature peptide of 41 residues and intervening propeptide of 3 residues. There are six cysteines in the sequence of mature CFBD peptide, which possibly form three disulfide-bridges. CFBD showed antimicrobial activities against Staphylococcus aureus, Bacillus subtilis, Candida albicans and Escherichia coli. This peptide could be classified into family of β-defensin based on its seqeuence similarity with β-defensins from other vertebrates. Evolution analysis indicated that CFBD was close to fish β-defensin. As far as we know, CFBD is the first β-defensin antimicrobial peptide from salamanders. PMID:24386139

  14. Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions fr...

  15. Evolution of Gigantism in Amphiumid Salamanders

    PubMed Central

    Bonett, Ronald M.; Chippindale, Paul T.; Moler, Paul E.; Van Devender, R. Wayne; Wake, David B.

    2009-01-01

    The Amphiumidae contains three species of elongate, permanently aquatic salamanders with four diminutive limbs that append one, two, or three toes. Two of the species, Amphiuma means and A. tridactylum, are among the largest salamanders in the world, reaching lengths of more than one meter, whereas the third species (A. pholeter), extinct amphiumids, and closely related salamander families are relatively small. Amphiuma means and A. tridactylum are widespread species and live in a wide range of lowland aquatic habitats on the Coastal Plain of the southeastern United States, whereas A. pholeter is restricted to very specialized organic muck habitats and is syntopic with A. means. Here we present analyses of sequences of mitochondrial and nuclear loci from across the distribution of the three taxa to assess lineage diversity, relationships, and relative timing of divergence in amphiumid salamanders. In addition we analyze the evolution of gigantism in the clade. Our analyses indicate three lineages that have diverged since the late Miocene, that correspond to the three currently recognized species, but the two gigantic species are not each other's closest relatives. Given that the most closely related salamander families and fossil amphiumids from the Upper Cretaceous and Paleocene are relatively small, our results suggest at least two extreme changes in body size within the Amphuimidae. Gigantic body size either evolved once as the ancestral condition of modern amphiumas, with a subsequent strong size reduction in A. pholeter, or gigantism independently evolved twice in the modern species, A. means and A. tridactylum. These patterns are concordant with differences in habitat breadth and range size among lineages, and have implications for reproductive isolation and diversification of amphiumid salamanders. PMID:19461997

  16. Comparative Genomics of an Emerging Amphibian Virus

    PubMed Central

    Epstein, Brendan; Storfer, Andrew

    2015-01-01

    Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination. PMID:26530419

  17. Comparative Genomics of an Emerging Amphibian Virus.

    PubMed

    Epstein, Brendan; Storfer, Andrew

    2016-01-01

    Ranaviruses, a genus of the Iridoviridae, are large double-stranded DNA viruses that infect cold-blooded vertebrates worldwide. Ranaviruses have caused severe epizootics in commercial frog and fish populations, and are currently classified as notifiable pathogens in international trade. Previous work shows that a ranavirus that infects tiger salamanders throughout Western North America (Ambystoma tigrinum virus, or ATV) is in high prevalence among salamanders in the fishing bait trade. Bait ATV strains have elevated virulence and are transported long distances by humans, providing widespread opportunities for pathogen pollution. We sequenced the genomes of 15 strains of ATV collected from tiger salamanders across western North America and performed phylogenetic and population genomic analyses and tests for recombination. We find that ATV forms a monophyletic clade within the rest of the Ranaviruses and that it likely emerged within the last several thousand years, before human activities influenced its spread. We also identify several genes under strong positive selection, some of which appear to be involved in viral virulence and/or host immune evasion. In addition, we provide support for the pathogen pollution hypothesis with evidence of recombination among ATV strains, and potential bait-endemic strain recombination. PMID:26530419

  18. Effects of Timber Harvests and Silvicultural Edges on Terrestrial Salamanders

    PubMed Central

    MacNeil, Jami E.; Williams, Rod N.

    2014-01-01

    Balancing timber production and conservation in forest management requires an understanding of how timber harvests affect wildlife species. Terrestrial salamanders are useful indicators of mature forest ecosystem health due to their importance to ecosystem processes and sensitivity to environmental change. However, the effects of timber harvests on salamanders, though often researched, are still not well understood. To further this understanding, we used artificial cover objects to monitor the relative abundance of terrestrial salamanders for two seasons (fall and spring) pre-harvest and five seasons post-harvest in six forest management treatments, and for three seasons post-harvest across the edge gradients of six recent clearcuts. In total, we recorded 19,048 encounters representing nine species of salamanders. We observed declines in mean encounters of eastern red-backed salamanders (Plethodon cinereus) and northern slimy salamanders (P. glutinosus) from pre- to post-harvest in group selection cuts and in clearcuts. However, we found no evidence of salamander declines at shelterwoods and forested sites adjacent to harvests. Edge effects induced by recent clearcuts influenced salamanders for approximately 20 m into the forest, but edge influence varied by slope orientation. Temperature, soil moisture, and canopy cover were all correlated with salamander counts. Our results suggest silvicultural techniques that remove the forest canopy negatively affect salamander relative abundance on the local scale during the years immediately following harvest, and that the depth of edge influence of clearcuts on terrestrial salamanders is relatively shallow (<20 m). Small harvests (<4 ha) and techniques that leave the forest canopy intact may be compatible with maintaining terrestrial salamander populations across a forested landscape. Our results demonstrate the importance of examining species-specific responses and monitoring salamanders across multiple seasons and years

  19. Effects of timber harvests and silvicultural edges on terrestrial salamanders.

    PubMed

    MacNeil, Jami E; Williams, Rod N

    2014-01-01

    Balancing timber production and conservation in forest management requires an understanding of how timber harvests affect wildlife species. Terrestrial salamanders are useful indicators of mature forest ecosystem health due to their importance to ecosystem processes and sensitivity to environmental change. However, the effects of timber harvests on salamanders, though often researched, are still not well understood. To further this understanding, we used artificial cover objects to monitor the relative abundance of terrestrial salamanders for two seasons (fall and spring) pre-harvest and five seasons post-harvest in six forest management treatments, and for three seasons post-harvest across the edge gradients of six recent clearcuts. In total, we recorded 19,048 encounters representing nine species of salamanders. We observed declines in mean encounters of eastern red-backed salamanders (Plethodon cinereus) and northern slimy salamanders (P. glutinosus) from pre- to post-harvest in group selection cuts and in clearcuts. However, we found no evidence of salamander declines at shelterwoods and forested sites adjacent to harvests. Edge effects induced by recent clearcuts influenced salamanders for approximately 20 m into the forest, but edge influence varied by slope orientation. Temperature, soil moisture, and canopy cover were all correlated with salamander counts. Our results suggest silvicultural techniques that remove the forest canopy negatively affect salamander relative abundance on the local scale during the years immediately following harvest, and that the depth of edge influence of clearcuts on terrestrial salamanders is relatively shallow (<20 m). Small harvests (<4 ha) and techniques that leave the forest canopy intact may be compatible with maintaining terrestrial salamander populations across a forested landscape. Our results demonstrate the importance of examining species-specific responses and monitoring salamanders across multiple seasons and years

  20. Large-Scale Sequencing: The Future of Genomic Sciences Colloquium

    SciTech Connect

    Margaret Riley; Merry Buckley

    2009-01-01

    Genetic sequencing and the various molecular techniques it has enabled have revolutionized the field of microbiology. Examining and comparing the genetic sequences borne by microbes - including bacteria, archaea, viruses, and microbial eukaryotes - provides researchers insights into the processes microbes carry out, their pathogenic traits, and new ways to use microorganisms in medicine and manufacturing. Until recently, sequencing entire microbial genomes has been laborious and expensive, and the decision to sequence the genome of an organism was made on a case-by-case basis by individual researchers and funding agencies. Now, thanks to new technologies, the cost and effort of sequencing is within reach for even the smallest facilities, and the ability to sequence the genomes of a significant fraction of microbial life may be possible. The availability of numerous microbial genomes will enable unprecedented insights into microbial evolution, function, and physiology. However, the current ad hoc approach to gathering sequence data has resulted in an unbalanced and highly biased sampling of microbial diversity. A well-coordinated, large-scale effort to target the breadth and depth of microbial diversity would result in the greatest impact. The American Academy of Microbiology convened a colloquium to discuss the scientific benefits of engaging in a large-scale, taxonomically-based sequencing project. A group of individuals with expertise in microbiology, genomics, informatics, ecology, and evolution deliberated on the issues inherent in such an effort and generated a set of specific recommendations for how best to proceed. The vast majority of microbes are presently uncultured and, thus, pose significant challenges to such a taxonomically-based approach to sampling genome diversity. However, we have yet to even scratch the surface of the genomic diversity among cultured microbes. A coordinated sequencing effort of cultured organisms is an appropriate place to begin

  1. Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

    PubMed

    Iranzo, Jaime; Gómez, Manuel J; López de Saro, Francisco J; Manrubia, Susanna

    2014-06-01

    Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated. PMID:24967627

  2. SMRT® Sequencing Solutions for Large Genomes and Transcriptomes

    PubMed Central

    Chin, J.; Peluso, P.; Rank, D.; Kim, K.; Landolin, J.; Koren, S.; Phillippy, A.M.; Tseng, E.; Wang, S.; Baybayan, P.; Gu, J.

    2014-01-01

    Single Molecule, Real-Time (SMRT) Sequencing holds promise for addressing new frontiers in large genome complexities, such as long, highly repetitive, low-complexity regions and duplication events, and differentiating between transcript isoforms that are difficult to resolve with short-read technologies. We present solutions available for both reference genome improvement (100 MB) and transcriptome research to best leverage long reads that have exceeded 20 Kb in length. Benefits for these applications are further realized with consistent use of size-selection of input sample using the BluePippin™ device from Sage Science. Highlights from our genome improvement projects using the latest P5-C3 chemistry on model organisms with contig N50 exceeding 6 Mb and longest contig exceeding 12.5 Mb with an average base quality of QV50 will be shared. Additionally, the value of long, intact reads to provide a no-assembly approach to investigate transcript isoforms using our Iso-Seq protocol will be presented.

  3. Fast randomization of large genomic datasets while preserving alteration counts

    PubMed Central

    Gobbi, Andrea; Iorio, Francesco; Dawson, Kevin J.; Wedge, David C.; Tamborero, David; Alexandrov, Ludmil B.; Lopez-Bigas, Nuria; Garnett, Mathew J.; Jurman, Giuseppe; Saez-Rodriguez, Julio

    2014-01-01

    Motivation: Studying combinatorial patterns in cancer genomic datasets has recently emerged as a tool for identifying novel cancer driver networks. Approaches have been devised to quantify, for example, the tendency of a set of genes to be mutated in a ‘mutually exclusive’ manner. The significance of the proposed metrics is usually evaluated by computing P-values under appropriate null models. To this end, a Monte Carlo method (the switching-algorithm) is used to sample simulated datasets under a null model that preserves patient- and gene-wise mutation rates. In this method, a genomic dataset is represented as a bipartite network, to which Markov chain updates (switching-steps) are applied. These steps modify the network topology, and a minimal number of them must be executed to draw simulated datasets independently under the null model. This number has previously been deducted empirically to be a linear function of the total number of variants, making this process computationally expensive. Results: We present a novel approximate lower bound for the number of switching-steps, derived analytically. Additionally, we have developed the R package BiRewire, including new efficient implementations of the switching-algorithm. We illustrate the performances of BiRewire by applying it to large real cancer genomics datasets. We report vast reductions in time requirement, with respect to existing implementations/bounds and equivalent P-value computations. Thus, we propose BiRewire to study statistical properties in genomic datasets, and other data that can be modeled as bipartite networks. Availability and implementation: BiRewire is available on BioConductor at http://www.bioconductor.org/packages/2.13/bioc/html/BiRewire.html Contact: iorio@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161255

  4. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses.

    PubMed

    Iyer, Lakshminarayan M; Balaji, S; Koonin, Eugene V; Aravind, L

    2006-04-01

    A previous comparative-genomic study of large nuclear and cytoplasmic DNA viruses (NCLDVs) of eukaryotes revealed the monophyletic origin of four viral families: poxviruses, asfarviruses, iridoviruses, and phycodnaviruses [Iyer, L.M., Aravind, L., Koonin, E.V., 2001. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75 (23), 11720-11734]. Here we update this analysis by including the recently sequenced giant genome of the mimiviruses and several additional genomes of iridoviruses, phycodnaviruses, and poxviruses. The parsimonious reconstruction of the gene complement of the ancestral NCLDV shows that it was a complex virus with at least 41 genes that encoded the replication machinery, up to four RNA polymerase subunits, at least three transcription factors, capping and polyadenylation enzymes, the DNA packaging apparatus, and structural components of an icosahedral capsid and the viral membrane. The phylogeny of the NCLDVs is reconstructed by cladistic analysis of the viral gene complements, and it is shown that the two principal lineages of NCLDVs are comprised of poxviruses grouped with asfarviruses and iridoviruses grouped with phycodnaviruses-mimiviruses. The phycodna-mimivirus grouping was strongly supported by several derived shared characters, which seemed to rule out the previously suggested basal position of the mimivirus [Raoult, D., Audic, S., Robert, C., Abergel, C., Renesto, P., Ogata, H., La Scola, B., Suzan, M., Claverie, J.M. 2004. The 1.2-megabase genome sequence of Mimivirus. Science 306 (5700), 1344-1350]. These results indicate that the divergence of the major NCLDV families occurred at an early stage of evolution, prior to the divergence of the major eukaryotic lineages. It is shown that subsequent evolution of the NCLDV genomes involved lineage-specific expansion of paralogous gene families and acquisition of numerous genes via horizontal gene transfer from the eukaryotic hosts, other viruses, and bacteria

  5. The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine

    PubMed Central

    Biesecker, Leslie G.; Mullikin, James C.; Facio, Flavia M.; Turner, Clesson; Cherukuri, Praveen F.; Blakesley, Robert W.; Bouffard, Gerard G.; Chines, Peter S.; Cruz, Pedro; Hansen, Nancy F.; Teer, Jamie K.; Maskeri, Baishali; Young, Alice C.; Manolio, Teri A.; Wilson, Alexander F.; Finkel, Toren; Hwang, Paul; Arai, Andrew; Remaley, Alan T.; Sachdev, Vandana; Shamburek, Robert; Cannon, Richard O.; Green, Eric D.

    2009-01-01

    ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicine, including the exploration of issues related to the genetic architecture of disease, implementation of genomic technology, informed consent, disclosure of genetic information, and archiving, analyzing, and displaying sequence data. In the initial phase of ClinSeq, we are enrolling roughly 1000 participants; the evaluation of each includes obtaining a detailed family and medical history, as well as a clinical evaluation. The participants are being consented broadly for research on many traits and for whole-genome sequencing. Initially, Sanger-based sequencing of 300–400 genes thought to be relevant to atherosclerosis is being performed, with the resulting data analyzed for rare, high-penetrance variants associated with specific clinical traits. The participants are also being consented to allow the contact of family members for additional studies of sequence variants to explore their potential association with specific phenotypes. Here, we present the general considerations in designing ClinSeq, preliminary results based on the generation of an initial 826 Mb of sequence data, the findings for several genes that serve as positive controls for the project, and our views about the potential implications of ClinSeq. The early experiences with ClinSeq illustrate how large-scale medical sequencing can be a practical, productive, and critical component of research in genomic medicine. PMID:19602640

  6. Optimizing restriction fragment fingerprinting methods for ordering large genomic libraries

    SciTech Connect

    Branscomb, E.; Slezak, T.; Pae, R.; Carrano, A.V. ); Galas, D.; Waterman, M. )

    1990-01-01

    The authors present a statistical analysis of the problem of ordering large genomic cloned libraries through overlap detection based on restriction fingerprinting. Such ordering projects involve a large investment of effort involving many repetitious experiments. Their primary purpose here is to provide methods of maximizing the efficiency of such efforts. To this end, they adopt a statistical approach that uses the likelihood ratio as a statistic to detect overlap. The main advantages of this approach are that (1) it allows the relatively straightforward incorporation of the observed statistical properties of the data; (2) it permits the efficiency of a particular experimental method for detecting overlap to be quantitatively defined so that alternative experimental designs may be compared and optimized; and (3) it yields a direct estimate of the probability that any two library members overlap. This estimate is a critical tool for the accurate, automatic assembly of overlapping sets of fragments into islands called contigs.' These contigs must subsequently be connected by other methods to provide an ordered set of overlapping fragments covering the entire genome.

  7. Molecular mechanisms of extensive mitochondrial gene rearrangementin plethodontid salamanders

    SciTech Connect

    Mueller, Rachel Lockridge; Boore, Jeffrey L.

    2005-06-01

    Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light strand replication and the nearby tRNA genes or the regions flanking the origin of heavy strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and non-tandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mtDNAs, up to 25 percent of the total length is composed of tandem duplications of non-coding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intra-molecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.

  8. Lagged influence of North Atlantic Oscillation on population dynamics of a Mediterranean terrestrial salamander.

    PubMed

    Salvidio, Sebastiano; Oneto, Fabrizio; Ottonello, Dario; Pastorino, Mauro V

    2016-04-01

    The North Atlantic Oscillation (NAO) is a large-scale climatic pattern that strongly influences the atmospheric circulation in the northern Hemisphere and by consequence the long-term variability of marine and terrestrial ecosystem over great part of northern Europe and western Mediterranean. In the Mediterranean, the effects of the NAO on vertebrates has been studied mainly on bird populations but was rarely analysed in ectothermic animals, and in particular in amphibians. In this study, we investigated the relationships between winter, spring and summer NAO indexes and the long-term population dynamics of the plethodontid salamander Speleomantes strinatii. This terrestrial salamander was monitored inside an artificial cave in NW Italy for 24 consecutive years. The relationships between seasonal NAO indexes and the salamander dynamics were assessed by cross-correlation function (CCF) analysis, after prewhitening the time series by autoregressive moving average statistical modelling. Results of CCF analyses indicated that the salamander abundance varied in relation to the one-year ahead winter NAO (P = 0.018), while no relationships were found with spring and summer indexes. These results strengthen some previous findings that suggested a high sensitivity of temperate terrestrial amphibians to wintertime climatic conditions. PMID:26160231

  9. A survey for Batrachochytrium dendrobatidis in endangered and highly susceptible Vietnamese salamanders (Tylototriton spp.).

    PubMed

    Thien, Tao Nguyen; Martel, An; Brutyn, Melanie; Bogaerts, Sergé; Sparreboom, Max; Haesebrouck, Freddy; Fisher, Matthew C; Beukema, Wouter; Van, Tang Duong; Chiers, Koen; Pasmans, Frank

    2013-09-01

    Until now, Asian amphibians appear to have largely escaped declines driven by chytridiomycosis. Vietnamese salamanders that belong to the genus Tylototriton are rare and have a patchy distribution in mountainous areas, falling within the proposed environmental envelope of chytrid infections, surrounded by Batrachochytrium dendrobatidis infected regions. If these salamanders are susceptible to chytridiomycosis, then their populations could be highly vulnerable after the introduction of B. dendrobatidis. Examination for the presence of the chytrid fungus in skin swabs from 19 Tylototriton asperrimus and 104 Tylototriton vietnamensis by using quantitative polymerase chain reaction was performed. Susceptibility of T. asperrimus to experimental infection by using the global panzootic lineage (BdGPL) strain of B. dendrobatidis was examined. The fungus was absent in all samples from all wild salamanders examined. Inoculation with the BdGPL strain resulted in mortality of all five inoculated salamanders within 3 weeks after inoculation with infected animals that manifested severe orthokeratotic hyperkeratosis, epidermal hyperplasia, and spongiosis. Although infection by B. dendrobatidis currently appears absent in Vietnamese Tylototriton populations, the rarity of these animals, their pronounced susceptibility to chytridiomycosis, an apparently suitable environmental context and increasing likelihood of the pathogen being introduced, together suggest the need of urgent measures to avoid future scenarios of extinction as witnessed in Central America and Australia. PMID:24063090

  10. Lagged influence of North Atlantic Oscillation on population dynamics of a Mediterranean terrestrial salamander

    NASA Astrophysics Data System (ADS)

    Salvidio, Sebastiano; Oneto, Fabrizio; Ottonello, Dario; Pastorino, Mauro V.

    2016-04-01

    The North Atlantic Oscillation (NAO) is a large-scale climatic pattern that strongly influences the atmospheric circulation in the northern Hemisphere and by consequence the long-term variability of marine and terrestrial ecosystem over great part of northern Europe and western Mediterranean. In the Mediterranean, the effects of the NAO on vertebrates has been studied mainly on bird populations but was rarely analysed in ectothermic animals, and in particular in amphibians. In this study, we investigated the relationships between winter, spring and summer NAO indexes and the long-term population dynamics of the plethodontid salamander Speleomantes strinatii. This terrestrial salamander was monitored inside an artificial cave in NW Italy for 24 consecutive years. The relationships between seasonal NAO indexes and the salamander dynamics were assessed by cross-correlation function (CCF) analysis, after prewhitening the time series by autoregressive moving average statistical modelling. Results of CCF analyses indicated that the salamander abundance varied in relation to the one-year ahead winter NAO ( P = 0.018), while no relationships were found with spring and summer indexes. These results strengthen some previous findings that suggested a high sensitivity of temperate terrestrial amphibians to wintertime climatic conditions.

  11. Transcriptomic analysis of the host response to an iridovirus infection in Chinese giant salamander, Andrias davidianus.

    PubMed

    Fan, Yuding; Chang, Ming Xian; Ma, Jie; LaPatra, Scott E; Hu, Yi Wei; Huang, Lili; Nie, Pin; Zeng, Lingbing

    2015-01-01

    The emergence of an infectious viral disease caused by the Chinese giant salamander iridovirus (GSIV) has led to substantial economic losses. However, no more molecular information is available for the understanding of the mechanisms associated with virus-host interaction. In this study, de novo sequencing was used to obtain abundant high-quality ESTs and investigate differentially-expressed genes in the spleen of Chinese giant salamanders that were either infected or mock infected with GSIV. Comparative expression analysis indicated that 293 genes were down-regulated and 220 genes were up-regulated. Further enrichment analysis showed that the most enriched pathway is "complement and coagulation cascades", and significantly enriched diseases include "inherited thrombophilia", "immune system diseases", "primary immunodeficiency", "complement regulatory protein defects", and "disorders of nucleotide excision repair". Additionally, 30 678 simple sequence repeats (SSRs) from all spleen samples, 26 355 single nucleotide polymorphisms (SNPs) from the spleens of uninfected animals and 36 070 SNPs from the spleens of infected animals were detected. The large amount of variation was specific for the Chinese giant salamanders that were infected with GSIV. The results reported herein provided significant and new EST information that could contribute greatly in investigations into the molecular functions of immune genes in the Chinese giant salamander. PMID:26589400

  12. A stem batrachian from the Early Permian of Texas and the origin of frogs and salamanders.

    PubMed

    Anderson, Jason S; Reisz, Robert R; Scott, Diane; Fröbisch, Nadia B; Sumida, Stuart S

    2008-05-22

    The origin of extant amphibians (Lissamphibia: frogs, salamanders and caecilians) is one of the most controversial questions in vertebrate evolution, owing to large morphological and temporal gaps in the fossil record. Current discussions focus on three competing hypotheses: a monophyletic origin within either Temnospondyli or Lepospondyli, or a polyphyletic origin with frogs and salamanders arising among temnospondyls and caecilians among the lepospondyls. Recent molecular analyses are also controversial, with estimations for the batrachian (frog-salamander) divergence significantly older than the palaeontological evidence supports. Here we report the discovery of an amphibamid temnospondyl from the Early Permian of Texas that bridges the gap between other Palaeozoic amphibians and the earliest known salientians and caudatans from the Mesozoic. The presence of a mosaic of salientian and caudatan characters in this small fossil makes it a key taxon close to the batrachian (frog and salamander) divergence. Phylogenetic analysis suggests that the batrachian divergence occurred in the Middle Permian, rather than the late Carboniferous as recently estimated using molecular clocks, but the divergence with caecilians corresponds to the deep split between temnospondyls and lepospondyls, which is congruent with the molecular estimates. PMID:18497824

  13. Homing orientation in salamanders: A mechanism involving chemical cues

    NASA Technical Reports Server (NTRS)

    Madison, D. M.

    1972-01-01

    A detailed description is given of experiments made to determine the senses and chemical cues used by salamanders for homing orientation. Sensory impairment and cue manipulative techniques were used in the investigation. All experiments were carried out at night. Results show that sense impaired animals did not home as readily as those who were blind but retained their sensory mechanism. This fact suggests that the olfactory mechanism is necessary for homing in the salamander. It was determined that after the impaired salamander regenerated its sensory mechanism it too returned home. It was concluded that homing ability in salamanders is direction independent, distant dependent, and vision independent.

  14. Lethal effects of water quality on threatened California salamanders but not on co-occurring hybrid salamanders.

    PubMed

    Ryan, Maureen E; Johnson, Jarrett R; Fitzpatrick, Benjamin M; Lowenstine, Linda J; Picco, Angela M; Shaffer, H Bradley

    2013-02-01

    Biological invasions and habitat alteration are often detrimental to native species, but their interactions are difficult to predict. Interbreeding between native and introduced species generates novel genotypes and phenotypes, and human land use alters habitat structure and chemistry. Both invasions and habitat alteration create new biological challenges and opportunities. In the intensively farmed Salinas Valley, California (U.S.A.), threatened California tiger salamanders (Ambystoma californiense) have been replaced by hybrids between California tiger salamander and introduced barred tiger salamanders (Ambystoma tigrinum mavortium). We conducted an enclosure experiment to examine the effects habitat modification and relative frequency of hybrid and native California tiger salamanders have on recruitment of salamanders and their prey, Pacific chorus frogs (Pseudacris regilla). We tested whether recruitment differed among genetic classes of tiger salamanders (hybrid or native) and pond hydroperiod (seasonal or perennial). Roughly 6 weeks into the experiment, 70% (of 378 total) of salamander larvae died in 4 out of 6 ponds. Native salamanders survived (n = 12) in these ponds only if they had metamorphosed prior to the die-offs. During die-offs, all larvae of native salamanders died, whereas 56% of hybrid larvae died. We necropsied native and hybrid salamanders, tested water quality, and queried the California Department of Pesticide Regulation database to investigate possible causes of the die-offs. Salamander die-offs, changes in the abundance of other community members (invertebrates, algae, and cyanobacteria), shifts in salamander sex ratio, and patterns of pesticide application in adjacent fields suggest that pesticide use may have contributed to die-offs. That all survivors were hybrids suggests that environmental stress may promote rapid displacement of native genotypes. PMID:23140535

  15. Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders

    PubMed Central

    Kroll, Andrew J.; Garcia, Tiffany S.; Jones, Jay E.; Dugger, Katie; Murden, Blake; Johnson, Josh; Peerman, Summer; Brintz, Ben; Rochelle, Michael

    2015-01-01

    Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology and responses to conservation and management activities. We conducted a simulation study to evaluate the effectiveness of multi-scale and hierarchical single-scale occupancy models in the context of a Before-After Control-Impact (BACI) experimental design with multiple levels of sampling. Also, we fit the hierarchical single-scale model to empirical data collected for Oregon slender and Ensatina salamanders across two years on 66 forest stands in the Cascade Range, Oregon, USA. All models were fit within a Bayesian framework. Estimator precision in both models improved with increasing numbers of primary and secondary sampling units, underscoring the potential gains accrued when adding secondary sampling units. Both models showed evidence of estimator bias at low detection probabilities and low sample sizes; this problem was particularly acute for the multi-scale model. Our results suggested that sufficient sample sizes at both the primary and secondary sampling levels could ameliorate this issue. Empirical data indicated Oregon slender salamander occupancy was associated strongly with the amount of coarse woody debris (posterior mean = 0.74; SD = 0.24); Ensatina occupancy was not associated with amount of coarse woody debris (posterior mean = -0.01; SD = 0.29). Our simulation results indicate that either model is suitable for use in an experimental study of Plethodontid salamanders provided that sample sizes are sufficiently large. However, hierarchical single-scale and multi-scale models describe different processes and estimate different parameters. As a result, we recommend careful consideration of study questions

  16. Evaluating multi-level models to test occupancy state responses of Plethodontid salamanders

    USGS Publications Warehouse

    Kroll, Andrew J.; Garcia, Tiffany S.; Jones, Jay E.; Dugger, Catherine; Murden, Blake; Johnson, Josh; Peerman, Summer; Brintz, Ben; Rochelle, Michael

    2015-01-01

    Plethodontid salamanders are diverse and widely distributed taxa and play critical roles in ecosystem processes. Due to salamander use of structurally complex habitats, and because only a portion of a population is available for sampling, evaluation of sampling designs and estimators is critical to provide strong inference about Plethodontid ecology and responses to conservation and management activities. We conducted a simulation study to evaluate the effectiveness of multi-scale and hierarchical single-scale occupancy models in the context of a Before-After Control-Impact (BACI) experimental design with multiple levels of sampling. Also, we fit the hierarchical single-scale model to empirical data collected for Oregon slender and Ensatina salamanders across two years on 66 forest stands in the Cascade Range, Oregon, USA. All models were fit within a Bayesian framework. Estimator precision in both models improved with increasing numbers of primary and secondary sampling units, underscoring the potential gains accrued when adding secondary sampling units. Both models showed evidence of estimator bias at low detection probabilities and low sample sizes; this problem was particularly acute for the multi-scale model. Our results suggested that sufficient sample sizes at both the primary and secondary sampling levels could ameliorate this issue. Empirical data indicated Oregon slender salamander occupancy was associated strongly with the amount of coarse woody debris (posterior mean = 0.74; SD = 0.24); Ensatina occupancy was not associated with amount of coarse woody debris (posterior mean = -0.01; SD = 0.29). Our simulation results indicate that either model is suitable for use in an experimental study of Plethodontid salamanders provided that sample sizes are sufficiently large. However, hierarchical single-scale and multi-scale models describe different processes and estimate different parameters. As a result, we recommend careful consideration of study questions

  17. Kinship affects morphogenesis in cannibalistic salamanders.

    PubMed

    Pfennig, D W; Collins, J P

    1993-04-29

    Inclusive fitness theory predicts that organisms can often increase their fitness by helping relatives. Indeed, many animals modify their behaviour towards kin in a fashion consistent with theory. Morphogenesis may also be sensitive to kinship environment, especially in species that facultatively produce distinct morphs that differ in their ability to harm relatives, such as those that produce alternative cannibalistic and non-cannibalistic phenotypes. We tested this hypothesis by examining whether consanguinity affected the probability that structurally distinctive cannibal morphs would develop in larval Arizona tiger salamanders (Ambystoma tigrinum nebulosum). We report here that when tiger salamander larvae are reared in mixed-brood groups they are significantly more likely to develop the cannibal morphology and at an earlier age than siblings reared in pure-sibship groups. In general, morphogenesis may be responsive to kinship in any species that facultatively develops structures that can be used against conspecifics as weaponry. PMID:8479520

  18. CGCI Investigators Reveal Comprehensive Landscape of Diffuse Large B-Cell Lymphoma (DLBCL) Genomes | Office of Cancer Genomics

    Cancer.gov

    Researchers from British Columbia Cancer Agency used whole genome sequencing to analyze 40 DLBCL cases and 13 cell lines in order to fill in the gaps of the complex landscape of DLBCL genomes. Their analysis, “Mutational and structural analysis of diffuse large B-cell lymphoma using whole genome sequencing,” was published online in Blood on May 22. The authors are Ryan Morin, Marco Marra, and colleagues.  

  19. Stream salamanders as indicators of stream quality in Maryland, USA

    USGS Publications Warehouse

    Southerland, M.T.; Jung, R.E.; Baxter, D.P.; Chellman, I.C.; Mercurio, G.; Volstad, J.H.

    2004-01-01

    Biological indicators are critical to the protection of small, headwater streams and the ecological values they provide. Maryland and other state monitoring programs have determined that fish indicators are ineffective in small streams, where stream salamanders may replace fish as top predators. Because of their life history, physiology, abundance, and ubiquity, stream salamanders are likely representative of biological integrity in these streams. The goal of this study was to determine whether stream salamanders are effective indicators of ecological conditions across biogeographic regions and gradients of human disturbance. During the summers of 2001 and 2002, we intensively surveyed for stream salamanders at 76 stream sites located west of the Maryland Coastal Plain, sites also monitored by the Maryland Biological Stream Survey (MBSS) and City of Gaithersburg. We found 1,584 stream salamanders, including all eight species known in Maryland, using two 15 ? 2 m transects and two 4 m2 quadrats that spanned both stream bank and channel. We performed removal sampling on transects to estimate salamander species detection probabilities, which ranged from 0.67-0.85. Stepwise regressions identified 15 of 52 non-salamander variables, representing water quality, physical habitat, land use, and biological conditions, which best predicted salamander metrics. Indicator development involved (1) identifying reference (non-degraded) and degraded sites (using percent forest, shading, riparian buffer width, aesthetic rating, and benthic macroinvertebrate and fish indices of biotic integrity); (2) testing 12 candidate salamander metrics (representing species richness and composition, abundance, species tolerance, and reproductive function) for their ability to distinguish reference from degraded sites; and (3) combining metrics into an index that effectively discriminated sites according to known stream conditions. Final indices for Highlands, Piedmont, and Non-Coastal Plain

  20. Comparing population size estimators for plethodontid salamanders

    USGS Publications Warehouse

    Bailey, L.L.; Simons, T.R.; Pollock, K.H.

    2004-01-01

    Despite concern over amphibian declines, few studies estimate absolute abundances because of logistic and economic constraints and previously poor estimator performance. Two estimation approaches recommended for amphibian studies are mark-recapture and depletion (or removal) sampling. We compared abundance estimation via various mark-recapture and depletion methods, using data from a three-year study of terrestrial salamanders in Great Smoky Mountains National Park. Our results indicate that short-term closed-population, robust design, and depletion methods estimate surface population of salamanders (i.e., those near the surface and available for capture during a given sampling occasion). In longer duration studies, temporary emigration violates assumptions of both open- and closed-population mark-recapture estimation models. However, if the temporary emigration is completely random, these models should yield unbiased estimates of the total population (superpopulation) of salamanders in the sampled area. We recommend using Pollock's robust design in mark-recapture studies because of its flexibility to incorporate variation in capture probabilities and to estimate temporary emigration probabilities.

  1. Volume visualization of multiple alignment of large genomicDNA

    SciTech Connect

    Shah, Nameeta; Dillard, Scott E.; Weber, Gunther H.; Hamann, Bernd

    2005-07-25

    Genomes of hundreds of species have been sequenced to date, and many more are being sequenced. As more and more sequence data sets become available, and as the challenge of comparing these massive ''billion basepair DNA sequences'' becomes substantial, so does the need for more powerful tools supporting the exploration of these data sets. Similarity score data used to compare aligned DNA sequences is inherently one-dimensional. One-dimensional (1D) representations of these data sets do not effectively utilize screen real estate. As a result, tools using 1D representations are incapable of providing informatory overview for extremely large data sets. We present a technique to arrange 1D data in 3D space to allow us to apply state-of-the-art interactive volume visualization techniques for data exploration. We demonstrate our technique using multi-millions-basepair-long aligned DNA sequence data and compare it with traditional 1D line plots. The results show that our technique is superior in providing an overview of entire data sets. Our technique, coupled with 1D line plots, results in effective multi-resolution visualization of very large aligned sequence data sets.

  2. Genomic analysis of regulatory network dynamics reveals large topological changes

    NASA Astrophysics Data System (ADS)

    Luscombe, Nicholas M.; Madan Babu, M.; Yu, Haiyuan; Snyder, Michael; Teichmann, Sarah A.; Gerstein, Mark

    2004-09-01

    Network analysis has been applied widely, providing a unifying language to describe disparate systems ranging from social interactions to power grids. It has recently been used in molecular biology, but so far the resulting networks have only been analysed statically. Here we present the dynamics of a biological network on a genomic scale, by integrating transcriptional regulatory information and gene-expression data for multiple conditions in Saccharomyces cerevisiae. We develop an approach for the statistical analysis of network dynamics, called SANDY, combining well-known global topological measures, local motifs and newly derived statistics. We uncover large changes in underlying network architecture that are unexpected given current viewpoints and random simulations. In response to diverse stimuli, transcription factors alter their interactions to varying degrees, thereby rewiring the network. A few transcription factors serve as permanent hubs, but most act transiently only during certain conditions. By studying sub-network structures, we show that environmental responses facilitate fast signal propagation (for example, with short regulatory cascades), whereas the cell cycle and sporulation direct temporal progression through multiple stages (for example, with highly inter-connected transcription factors). Indeed, to drive the latter processes forward, phase-specific transcription factors inter-regulate serially, and ubiquitously active transcription factors layer above them in a two-tiered hierarchy. We anticipate that many of the concepts presented here-particularly the large-scale topological changes and hub transience-will apply to other biological networks, including complex sub-systems in higher eukaryotes.

  3. Intron-genome size relationship on a large evolutionary scale.

    PubMed

    Vinogradov, A E

    1999-09-01

    The intron-genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general trend. In baker's yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition (dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron size due to its putative link to chromatin structure (and constraints of the splicing machinery). PMID:10473779

  4. Bromeliad selection by two salamander species in a harsh environment.

    PubMed

    Ruano-Fajardo, Gustavo; Rovito, Sean M; Ladle, Richard J

    2014-01-01

    Bromeliad phytotelmata are frequently used by several Neotropical amphibian taxa, possibly due to their high humidity, microclimatic stability, and role as a refuge from predators. Indeed, the ability of phytotelmata to buffer against adverse environmental conditions may be instrumental in allowing some amphibian species to survive during periods of environmental change or to colonize sub-optimal habitats. Association between bromeliad traits and salamanders has not been studied at a fine scale, despite the intimate association of many salamander species with bromeliads. Here, we identify microhabitat characteristics of epiphytic bromeliads used by two species of the Bolitoglossa morio group (B. morio and B. pacaya) in forest disturbed by volcanic activity in Guatemala. Specifically, we measured multiple variables for bromeliads (height and position in tree, phytotelma water temperature and pH, canopy cover, phytotelma size, leaf size, and tree diameter at breast height), as well as salamander size. We employed a DNA barcoding approach to identify salamanders. We found that B. morio and B. pacaya occurred in microsympatry in bromeliads and that phytotelmata size and temperature of bromeliad microhabitat were the most important factors associated with the presence of salamanders. Moreover, phytotelmata with higher pH contained larger salamanders, suggesting that larger salamanders or aggregated individuals might modify pH. These results show that bromeliad selection is nonrandom with respect to microhabitat characteristics, and provide insight into the relationship between salamanders and this unique arboreal environment. PMID:24892414

  5. Bromeliad Selection by Two Salamander Species in a Harsh Environment

    PubMed Central

    Ruano-Fajardo, Gustavo; Rovito, Sean M.; Ladle, Richard J.

    2014-01-01

    Bromeliad phytotelmata are frequently used by several Neotropical amphibian taxa, possibly due to their high humidity, microclimatic stability, and role as a refuge from predators. Indeed, the ability of phytotelmata to buffer against adverse environmental conditions may be instrumental in allowing some amphibian species to survive during periods of environmental change or to colonize sub-optimal habitats. Association between bromeliad traits and salamanders has not been studied at a fine scale, despite the intimate association of many salamander species with bromeliads. Here, we identify microhabitat characteristics of epiphytic bromeliads used by two species of the Bolitoglossa morio group (B. morio and B. pacaya) in forest disturbed by volcanic activity in Guatemala. Specifically, we measured multiple variables for bromeliads (height and position in tree, phytotelma water temperature and pH, canopy cover, phytotelma size, leaf size, and tree diameter at breast height), as well as salamander size. We employed a DNA barcoding approach to identify salamanders. We found that B. morio and B. pacaya occurred in microsympatry in bromeliads and that phytotelmata size and temperature of bromeliad microhabitat were the most important factors associated with the presence of salamanders. Moreover, phytotelmata with higher pH contained larger salamanders, suggesting that larger salamanders or aggregated individuals might modify pH. These results show that bromeliad selection is nonrandom with respect to microhabitat characteristics, and provide insight into the relationship between salamanders and this unique arboreal environment. PMID:24892414

  6. Evaluation of Target Preparation Methods for Single Feature Polymorphism Detection in Large Complex Plant Genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For those genomes low in repetitive DNA, hybridizing total genomic DNA to high-density expression arrays offers an effective strategy for scoring single feature polymorphisms (SFPs). Of the ~2.5 Gb that constitute the maize genome (Zea mays L.), only 10-20% are genic sequences, with large amounts o...

  7. Combining p-values in large-scale genomics experiments.

    PubMed

    Zaykin, Dmitri V; Zhivotovsky, Lev A; Czika, Wendy; Shao, Susan; Wolfinger, Russell D

    2007-01-01

    In large-scale genomics experiments involving thousands of statistical tests, such as association scans and microarray expression experiments, a key question is: Which of the L tests represent true associations (TAs)? The traditional way to control false findings is via individual adjustments. In the presence of multiple TAs, p-value combination methods offer certain advantages. Both Fisher's and Lancaster's combination methods use an inverse gamma transformation. We identify the relation of the shape parameter of that distribution to the implicit threshold value; p-values below that threshold are favored by the inverse gamma method (GM). We explore this feature to improve power over Fisher's method when L is large and the number of TAs is moderate. However, the improvement in power provided by combination methods is at the expense of a weaker claim made upon rejection of the null hypothesis - that there are some TAs among the L tests. Thus, GM remains a global test. To allow a stronger claim about a subset of p-values that is smaller than L, we investigate two methods with an explicit truncation: the rank truncated product method (RTP) that combines the first K-ordered p-values, and the truncated product method (TPM) that combines p-values that are smaller than a specified threshold. We conclude that TPM allows claims to be made about subsets of p-values, while the claim of the RTP is, like GM, more appropriately about all L tests. GM gives somewhat higher power than TPM, RTP, Fisher, and Simes methods across a range of simulations. PMID:17879330

  8. Combining p-values in large scale genomics experiments

    PubMed Central

    Zaykin, Dmitri V.; Zhivotovsky, Lev A.; Czika, Wendy; Shao, Susan; Wolfinger, Russell D.

    2008-01-01

    Summary In large-scale genomics experiments involving thousands of statistical tests, such as association scans and microarray expression experiments, a key question is: Which of the L tests represent true associations (TAs)? The traditional way to control false findings is via individual adjustments. In the presence of multiple TAs, p-value combination methods offer certain advantages. Both Fisher’s and Lancaster’s combination methods use an inverse gamma transformation. We identify the relation of the shape parameter of that distribution to the implicit threshold value; p-values below that threshold are favored by the inverse gamma method (GM). We explore this feature to improve power over Fisher’s method when L is large and the number of TAs is moderate. However, the improvement in power provided by combination methods is at the expense of a weaker claim made upon rejection of the null hypothesis – that there are some TAs among the L tests. Thus, GM remains a global test. To allow a stronger claim about a subset of p-values that is smaller than L, we investigate two methods with an explicit truncation: the rank truncated product method (RTP) that combines the first K ordered p-values, and the truncated product method (TPM) that combines p-values that are smaller than a specified threshold. We conclude that TPM allows claims to be made about subsets of p-values, while the claim of the RTP is, like GM, more appropriately about all L tests. GM gives somewhat higher power than TPM, RTP, Fisher, and Simes methods across a range of simulations. PMID:17879330

  9. Northwestern salamanders Ambystoma gracile in mountain lakes: record oviposition depths among salamanders

    USGS Publications Warehouse

    Hoffman, R., Jr.; Pearl, C.A.; Larson, G.L.; Samora, B.

    2012-01-01

    Oviposition timing, behaviors, and microhabitats of ambystomatid salamanders vary considerably (Egan and Paton 2004; Figiel and Semlitsch 1995; Howard and Wallace 1985; Mac-Cracken 2007). Regardless of species, however, females typically oviposit using sites conducive to embryo development and survival. For example, the results of an experiment by Figiel and Semlitsch (1995) on Ambystoma opacum (Marbled Salamander) oviposition indicated that females actively selected sites that were under grass clumps in wet versus dry treatments, and surmised that environmental conditions such as humidity, moisture, and temperature contributed to their results. Other factors associated with ambystomatid oviposition and embryo survival include water temperature (Anderson 1972; Brown 1976), dissolved oxygen concentration (Petranka et al. 1982; Sacerdote and King 2009), oviposition depth (Dougherty et al. 2005; Egan and Paton 2004), and oviposition attachment structures such as woody vegetation (McCracken 2007; Nussbaum et al. 1983). Resetarits (1996), in creating a model of oviposition site selection for anuran amphibians, hypothesized that oviparous organisms were also capable of modifying oviposition behavior and site selection to accommodate varying habitat conditions and to minimize potential negative effects of environmental stressors. Kats and Sih (1992), investigating the oviposition of Ambystoma barbouri (Streamside Salamander) in pools of a Kentucky stream, found that females preferred pools without predatory Lepomis cyanellus (Green Sunfish), and that the number of egg masses present in a pool historically containing fish increased significantly the year after fish had been extirpated from the pool. Palen et al. (2005) determined that Ambystoma gracile (Northwestern Salamander) and Ambystoma macrodactylum (Longtoed Salamander) eggs were deposited either at increased depth or in full shaded habitats, respectively, as water transperancy to UV-B radiation increased.

  10. Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water.

    PubMed

    Deagle, Bruce E; Faux, Cassandra; Kawaguchi, So; Meyer, Bettina; Jarman, Simon N

    2015-10-01

    Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist. PMID:26340718

  11. Locomotion and visually guided behavior in salamander: a neuromechanical study

    NASA Astrophysics Data System (ADS)

    Ijspeert, Auke J.; Arbib, Michael A.

    2000-10-01

    This article investigates the neural mechanisms underlying locomotion and visually-guided behavior in a lower vertebrate: the salamander. We develop connectionist models of the salamander's locomotor circuitry and visual system, and analyze their functioning by embedding them into a biomechanical simulation of the salamander's body. This work is therefore an experiment in computational neuroethology which aims at investigating how behavior results from the coupling of a central nervous system (CNS) and a body, and from the interactions of the CNS-body pair with the environment. We believe that understanding these mechanisms is not only relevant for neurobiology but also for potential applications in robotics.

  12. Could we also be regenerative superheroes, like salamanders?

    PubMed

    Dall'Agnese, Alessandra; Puri, Pier Lorenzo

    2016-09-01

    Development of methods to reawaken the semi-dormant regenerative potential that lies within adult human tissues would hold promise for the restoration of diseased or damaged organs and tissues. While most of the regeneration potential is suppressed in many vertebrates, including humans, during adult life, urodele amphibians (salamanders) retain their regenerative ability throughout adulthood. Studies in newts and axolotls, two salamander models, have provided significant knowledge about adult limb regeneration. In this review, we present a comparative analysis of salamander and mammalian regeneration and discuss how evolutionarily altered properties of the regenerative environment can be exploited to restore full regenerative potential in the human body. PMID:27338874

  13. Biodiversity of Costa Rican salamanders: Implications of high levels of genetic differentiation and phylogeographic structure for species formation

    PubMed Central

    García-París, Mario; Good, David A.; Parra-Olea, Gabriela; Wake, David B.

    2000-01-01

    Although salamanders are characteristic amphibians in Holarctic temperate habitats, in tropical regions they have diversified evolutionarily only in tropical America. An adaptive radiation centered in Middle America occurred late in the history of a single clade, the supergenus Bolitoglossa (Plethodontidae), and large numbers of species now occur in diverse habitats. Sublineages within this clade decrease in number from the northern to southern parts of Middle America, and in Costa Rica, there are but three. Despite this phylogenetic constraint, Costa Rica has many species; the number of salamander species on one local elevational transect in the Cordillera de Talamanca may be the largest for any such transect in the world. Extraordinary variation in sequences of the mitochondrial gene cytochrome b within a clade of the genus Bolitoglossa in Costa Rica reveals strong phylogeographic structure within a single species, Bolitoglossa pesrubra. Allozymic variation in 19 proteins reveals a pattern largely concordant with the mitochondrial DNA phylogeography. More species exist than are currently recognized. Diversification occurs in restricted geographic areas and involves sharp geographic and elevational differentiation and zonation. In their degree of genetic differentiation at a local scale, these species of the deep tropics exceed the known variation of extratropical salamanders, which also differ in being less restricted in elevational range. Salamanders display “tropicality” in that although speciose, they are usually local in distribution and rare. They display strong ecological and physiological differentiation that may contribute importantly to morphological divergence and species formation. PMID:10677512

  14. Identifying Recent Adaptations in Large-scale Genomic Data

    PubMed Central

    Grossman, Sharon R.; Andersen, Kristian G.; Shlyakhter, Ilya; Tabrizi, Shervin; Winnicki, Sarah; Yen, Angela; Park, Daniel J.; Griesemer, Dustin; Karlsson, Elinor K.; Wong, Sunny H.; Cabili, Moran; Adegbola, Richard A.; Bamezai, Rameshwar N. K.; Hill, Adrian V. S.; Vannberg, Fredrik O.; Rinn, John L.; Lander, Eric S.; Schaffner, Stephen F.; Sabeti, Pardis C.

    2013-01-01

    SUMMARY While several hundred regions of the human genome harbor signals of positive natural selection, few of the relevant adaptive traits and variants have been elucidated. Using full-genome sequence variation from the 1000 Genomes Project (1000G) and the Composite of Multiple Signals (CMS) test, we investigated 412 candidate signals and leveraged functional annotation, protein structure modeling, epigenetics, and association studies to identify and extensively annotate candidate causal variants. The resulting catalog provides a tractable list for experimental follow-up; it includes thirty-five high-scoring non-synonymous variants, fifty-nine variants associated with expression levels of a nearby coding gene or lincRNA, and numerous variants associated with susceptibility to infectious disease and other phenotypes. We experimentally characterized one candidate non-synonymous variant in TLR5, and show that it leads to altered NF-κB signaling in response to bacterial flagellin. PMID:23415221

  15. SURGICAL IMPLANTATION OF COELOMIC RADIOTRANSMITTERS AND POSTOPERATIVE SURVIVAL OF CHINESE GIANT SALAMANDERS (ANDRIAS DAVIDIANUS) FOLLOWING REINTRODUCTION.

    PubMed

    Marcec, Ruth; Kouba, Andrew; Zhang, Lu; Zhang, Hongxing; Wang, Qijun; Zhao, Hu; Jiang, Wei; Willard, Scott

    2016-03-01

    Worldwide, there are only a handful of reintroduction programs for threatened salamander species, and very few have conducted postrelease studies to examine survival, habitat selection, and dispersal. Limitations in postrelease monitoring are primarily due to size constraints of amphibians and to dimensions of the radiotransmitters available for implantation. However, due to the large size of the critically endangered Chinese giant salamander (Andrias davidianus), these animals make optimal candidates for surgical implantation of radiotransmitters prior to reintroduction or translocation. The objective of this study was to develop an anesthetic protocol using tricane methanesulfonate (MS-222) and test a surgical procedure for coelomic implantation of radiotransmitters for this species. A total of 32 Chinese giant salamanders from two age groups (Group A: 4.7 yr old, n = 16; Group B: 2.7 yr old, n = 16) were implanted with 4-g radiotransmitters designed for underwater monitoring of fish. Group A was held 16 wk before release while Group B was held 6 wk before release, and the salamanders' survival and postoperative complications recorded for the first month postrelease. Group A animals took longer to reach a surgical plane of anesthesia than did Group B animals, and this was directly correlated to mass of the animals. Postsurgery, one animal from Group B died of dehiscence before release while 83.9% animals survived after the first month in the wild. All of the animals that died postrelease were from Group B; three animals experienced dehiscence of the suture site and died while another two animals expired from trauma and fungal infection, respectively. Improvements for future studies include use of alternative suture material for closure after implantation and additional healing time of the incision. PMID:27010279

  16. Targeted Large-Scale Deletion of Bacterial Genomes Using CRISPR-Nickases

    PubMed Central

    2015-01-01

    Programmable CRISPR-Cas systems have augmented our ability to produce precise genome manipulations. Here we demonstrate and characterize the ability of CRISPR-Cas derived nickases to direct targeted recombination of both small and large genomic regions flanked by repetitive elements in Escherichia coli. While CRISPR directed double-stranded DNA breaks are highly lethal in many bacteria, we show that CRISPR-guided nickase systems can be programmed to make precise, nonlethal, single-stranded incisions in targeted genomic regions. This induces recombination events and leads to targeted deletion. We demonstrate that dual-targeted nicking enables deletion of 36 and 97 Kb of the genome. Furthermore, multiplex targeting enables deletion of 133 Kb, accounting for approximately 3% of the entire E. coli genome. This technology provides a framework for methods to manipulate bacterial genomes using CRISPR-nickase systems. We envision this system working synergistically with preexisting bacterial genome engineering methods. PMID:26451892

  17. Habitat requirements of New Mexico’s endangered salamanders

    USGS Publications Warehouse

    Ramotnik, Cindy A.; Scott, N.J.

    1988-01-01

    We measured habitat components for two state-listed endangered salamanders in New Mexico in 1986 and 1987. Both species are restricted to mesic environments within high-elevation, mixed coniferous forests. Steep slope and high elevation were the most useful variables for predicting the occurrence of Jemez Mountains salamanders and Sacramento Mountain salamanders, respectively. Although the discriminant models show some predictive value in detecting salamanders based on habitat variables, we believe that the best survey technique is ground-truth surveys in wet weather. A better fit of the discriminant models might be obtained by including variables not measured e.g., fire and logging history, and soil characteristics. We offer interim management guidelines as a result of our analysis.

  18. Salamander-like development in a seymouriamorph revealed by palaeohistology.

    PubMed

    Sanchez, Sophie; Klembara, Jozef; Castanet, Jacques; Steyer, J Sébastien

    2008-08-23

    The amniotes generally lay eggs on land and are thereby differentiated from lissamphibians (salamanders, frogs and caecilians) by their developmental pattern. Although a number of 330-300-Myr old fossils are regarded as early tetrapods placed close to amniotes on the basis of anatomical data, we still do not know whether their developmental pattern was more similar to those of lissamphibians or amniotes. Here we report palaeohistological and skeletochronological evidence supporting a salamander-like development in the seymouriamorph Discosauriscus. Its long-bone growth pattern, slow diaphyseal growth rate and delayed sexual maturity (at more than 10 years old) are more comparable with growth features of extant salamanders rather than extant amniotes, even though they are mostly hypothesized to be phylogenetically closer to living amniotes than salamanders. PMID:18460423

  19. Variation in Salamander Tail Regeneration Is Associated with Genetic Factors That Determine Tail Morphology

    PubMed Central

    Voss, Gareth J.; Kump, D. Kevin; Walker, John A.; Voss, S. Randal

    2013-01-01

    Very little is known about the factors that cause variation in regenerative potential within and between species. Here, we used a genetic approach to identify heritable genetic factors that explain variation in tail regenerative outgrowth. A hybrid ambystomatid salamander (Ambystoma mexicanum x A. andersoni) was crossed to an A. mexicanum and 217 offspring were induced to undergo metamorphosis and attain terrestrial adult morphology using thyroid hormone. Following metamorphosis, each salamander’s tail tip was amputated and allowed to regenerate, and then amputated a second time and allowed to regenerate. Also, DNA was isolated from all individuals and genotypes were determined for 187 molecular markers distributed throughout the genome. The area of tissue that regenerated after the first and second amputations was highly positively correlated across males and females. Males presented wider tails and regenerated more tail tissue during both episodes of regeneration. Approximately 66–68% of the variation in regenerative outgrowth was explained by tail width, while tail length and genetic sex did not explain a significant amount of variation. A small effect QTL was identified as having a sex-independent effect on tail regeneration, but this QTL was only identified for the first episode of regeneration. Several molecular markers significantly affected regenerative outgrowth during both episodes of regeneration, but the effect sizes were small (<4%) and correlated with tail width. The results show that ambysex and minor effect QTL explain variation in adult tail morphology and importantly, tail width. In turn, tail width at the amputation plane largely determines the rate of regenerative outgrowth. Because amputations in this study were made at approximately the same position of the tail, our results resolve an outstanding question in regenerative biology: regenerative outgrowth positively co-varies as a function of tail width at the amputation site. PMID:23843997

  20. The influence of large scale genomics and the changing role of ex situ collections

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of large scale genomics resources in non-model organisms promises to have a fundamental impact on the utilization of genetic resources. Technical innovation in high through-put sequencing has reduced the cost to a point where genome-wide SNP development is feasible across a range of ...

  1. Mutational and structural analysis of diffuse large B-cell lymphoma using whole genome sequencing | Office of Cancer Genomics

    Cancer.gov

    Abstract: Diffuse large B-cell lymphoma (DLBCL) is a genetically heterogeneous cancer comprising at least two molecular subtypes that differ in gene expression and distribution of mutations. Recently, application of genome/exome sequencing and RNA-seq to DLBCL has revealed numerous genes that are recurrent targets of somatic point mutation in this disease.

  2. GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis.

    PubMed

    Gonzalez, Michael A; Lebrigio, Rafael F Acosta; Van Booven, Derek; Ulloa, Rick H; Powell, Eric; Speziani, Fiorella; Tekin, Mustafa; Schüle, Rebecca; Züchner, Stephan

    2013-06-01

    Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges, we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ∼1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 sec across ∼1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease. PMID:23463597

  3. BactoGeNIE: a large-scale comparative genome visualization for big displays

    PubMed Central

    2015-01-01

    Background The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. Results In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. Conclusions BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics. PMID:26329021

  4. BactoGeNIE: A large-scale comparative genome visualization for big displays

    DOE PAGESBeta

    Aurisano, Jillian; Reda, Khairi; Johnson, Andrew; Marai, Elisabeta G.; Leigh, Jason

    2015-08-13

    The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

  5. BactoGeNIE: A large-scale comparative genome visualization for big displays

    SciTech Connect

    Aurisano, Jillian; Reda, Khairi; Johnson, Andrew; Marai, Elisabeta G.; Leigh, Jason

    2015-08-13

    The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.

  6. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.

    PubMed

    Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F

    2015-01-01

    The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. PMID:25919952

  7. Large-scale genomic comparison using two-dimensional DNA gels

    SciTech Connect

    Sidman, C.L.; Shaffer, D.J.

    1994-09-01

    Two-dimensional electrophoresis (2DE) of DNA fragments, in which separation occurs first by size and then by sequence variation, is a method enabling large-scale comparison of complex genomes. Combining 2DE with probing for various classes of repetitive genomic elements allows rapid and efficient comparison of thousands of fragments and millions of basepairs of DNA distributed across most genomic regions. This approach is demonstrated here by analyzing the extent of genomic relatedness of different inbred strains of mice. Such strains are shown to differ from each other by approximately 0.2-1% of their nucleotides, above which level reproductive speciation occurs. The 2DE method of assessing the overall relationship between two genomes represents an appropriate tool for analyzing members of a single species, but is too sensitive for use in interspecies comparisons. 51 refs., 4 figs., 1 tab.

  8. Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an e...

  9. Are Salamanders Useful Indicators of Hydrologic Permanence in Headwater Streams?

    NASA Astrophysics Data System (ADS)

    Johnson, B.; Fritz, K.

    2005-05-01

    Regulatory agencies need appropriate indicators of stream permanence to aid in jurisdictional determinations for headwater streams. We evaluated salamanders as permanence indicators because they are often abundant in fishless headwaters. Salamander and habitat data were collected in spring and summer 2003 from 59 sites located longitudinally along 17 forested streams in KY, IN, and OH. Larval Eurycea bislineata/cirrigera dominated all forests, and their abundances were highly correlated with drainage areas and channel dimensions. Appalachian streams were more diverse and had intermittent sites with more Desmognathus and Gyrinophilus spp. Of 22 sites where larvae were collected in spring, 9 sites subsequently dried in summer, suggesting salamanders either emigrated or died. We therefore only used taxa with multi-year larval stages as indicators of perennial water. Salamander larvae >1 yr old were collected from each locality in drainage areas <0.17 km2. However, these older larvae were often found in isolated pools that serve as refugia during dry periods. Findings suggest salamanders with multi-year larval periods can indicate perennial waters and that their use is more effective in Appalachia where abundance and diversity are high. Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy.

  10. Large-scale profiling of microRNAs for The Cancer Genome Atlas.

    PubMed

    Chu, Andy; Robertson, Gordon; Brooks, Denise; Mungall, Andrew J; Birol, Inanc; Coope, Robin; Ma, Yussanne; Jones, Steven; Marra, Marco A

    2016-01-01

    The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts. PMID:26271990

  11. Large-scale profiling of microRNAs for The Cancer Genome Atlas

    PubMed Central

    Chu, Andy; Robertson, Gordon; Brooks, Denise; Mungall, Andrew J.; Birol, Inanc; Coope, Robin; Ma, Yussanne; Jones, Steven; Marra, Marco A.

    2016-01-01

    The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ∼11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts. PMID:26271990

  12. The draft genome of the large yellow croaker reveals well-developed innate immunity.

    PubMed

    Wu, Changwen; Zhang, Di; Kan, Mengyuan; Lv, Zhengmin; Zhu, Aiyi; Su, Yongquan; Zhou, Daizhan; Zhang, Jianshe; Zhang, Zhou; Xu, Meiying; Jiang, Lihua; Guo, Baoying; Wang, Ting; Chi, Changfeng; Mao, Yong; Zhou, Jiajian; Yu, Xinxiu; Wang, Hailing; Weng, Xiaoling; Jin, Jason Gang; Ye, Junyi; He, Lin; Liu, Yun

    2014-01-01

    The large yellow croaker, Larimichthys crocea, is one of the most economically important marine fish species endemic to China. Its wild stocks have severely suffered from overfishing, and the aquacultured species are vulnerable to various marine pathogens. Here we report the creation of a draft genome of a wild large yellow croaker using a whole-genome sequencing strategy. We estimate the genome size to be 728 Mb with 19,362 protein-coding genes. Phylogenetic analysis shows that the stickleback is most closely related to the large yellow croaker. Rapidly evolving genes under positive selection are significantly enriched in pathways related to innate immunity. We also confirm the existence of several genes and identify the expansion of gene families that are important for innate immunity. Our results may reflect a well-developed innate immune system in the large yellow croaker, which could aid in the development of wild resource preservation and mariculture strategies. PMID:25407894

  13. A tadpole-induced polyphenism in the salamander Hynobius retardatus.

    PubMed

    Michimae, Hirofumi; Wakahara, Masami

    2002-10-01

    Larvae of the salamander Hynobius retardatus have two distinct morphs: normal and broad-headed, cannibal morphs. We performed three experiments to differentiate among the following hypotheses: The broad-headed morph is induced to allow: (1) feeding on nutritious conspecifics; (2) exclusion of strong competitors for food or space; or (3) feeding on large, tough prey when smaller prey items are unavailable. When newly hatched larvae were reared with a heterospecific, Rana pirica (an anuran amphibian) tadpoles, the broad-headed morph was induced more frequently compared with those reared with conspecifics. The phenotype expressed depended on the size of the tadpoles: The broad-headed morph occurred more frequently with small and the normal morph with large tadpoles. Metamorphosis occurred sooner in larvae fed conspecifics compared with those fed heterospecific tadpoles, and the mean growth rate of larvae fed conspecifics was significantly faster than that of those fed tadpoles, suggesting that the heterospecific tadpoles were less nutritive than the conspecifics. These results do not support the hypotheses that the broad-headed morph evolved for consuming conspecifics because of their better balance of nutrients or for excluding strong competitors for food or space. We tentatively conclude that the morph evolved to eat large, tough prey, including both conspecifics and heterospecific tadpoles. Because H. retardatus usually spawns very early in the spring in small ponds partially covered with ice and snow, newly hatched larvae may starve from the lack of proper food owing to extremely low water temperatures. Thus, the broad-headed morph of H. retardatus may represent a cold-habitat adaptation to overcome the severe circumstance when the only food items available are relatively large conspecifics or heterospecific tadpoles. PMID:12449490

  14. Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials

    PubMed Central

    Meric-Bernstam, Funda; Brusco, Lauren; Shaw, Kenna; Horombe, Chacha; Kopetz, Scott; Davies, Michael A.; Routbort, Mark; Piha-Paul, Sarina A.; Janku, Filip; Ueno, Naoto; Hong, David; De Groot, John; Ravi, Vinod; Li, Yisheng; Luthra, Raja; Patel, Keyur; Broaddus, Russell; Mendelsohn, John; Mills, Gordon B.

    2015-01-01

    Purpose We report the experience with 2,000 consecutive patients with advanced cancer who underwent testing on a genomic testing protocol, including the frequency of actionable alterations across tumor types, subsequent enrollment onto clinical trials, and the challenges for trial enrollment. Patients and Methods Standardized hotspot mutation analysis was performed in 2,000 patients, using either an 11-gene (251 patients) or a 46- or 50-gene (1,749 patients) multiplex platform. Thirty-five genes were considered potentially actionable based on their potential to be targeted with approved or investigational therapies. Results Seven hundred eighty-nine patients (39%) had at least one mutation in potentially actionable genes. Eighty-three patients (11%) with potentially actionable mutations went on genotype-matched trials targeting these alterations. Of 230 patients with PIK3CA/AKT1/PTEN/BRAF mutations that returned for therapy, 116 (50%) received a genotype-matched drug. Forty patients (17%) were treated on a genotype-selected trial requiring a mutation for eligibility, 16 (7%) were treated on a genotype-relevant trial targeting a genomic alteration without biomarker selection, and 40 (17%) received a genotype-relevant drug off trial. Challenges to trial accrual included patient preference of noninvestigational treatment or local treatment, poor performance status or other reasons for trial ineligibility, lack of trials/slots, and insurance denial. Conclusion Broad implementation of multiplex hotspot testing is feasible; however, only a small portion of patients with actionable alterations were actually enrolled onto genotype-matched trials. Increased awareness of therapeutic implications and access to novel therapeutics are needed to optimally leverage results from broad-based genomic testing. PMID:26014291

  15. Small effective population size in the long-toed salamander.

    PubMed

    Funk, W C; Tallmon, D A; Allendorf, F W

    1999-10-01

    The effective population sizes (Ne) of six populations of the long-toed salamander (Ambystoma macrodactylum) from Montana and Idaho, USA were estimated from allozyme data from samples collected in 1978, 1996 and 1997 using the temporal allele frequency method. Five of the six estimates ranged from 23 to 207 (mean = 123 +/- 79); one estimate was indistinguishable from infinity. In order to infer the actual Ne of salamander populations, we compared the frequency distribution of our observed Ne estimates with distributions obtained from simulated populations of known Ne. Our observed Ne estimate distribution was consistent with distributions from simulated populations with Ne values of 10, 25, and 50, suggesting an actual Ne for each of the six salamander populations of less than 100. This Ne estimate agrees with most other Ne estimates for amphibians. We conclude by discussing the conservation implications of small Ne values in amphibians in the context of increasing isolation of populations due to habitat fragmentation. PMID:10583827

  16. Duration of immobility in salamanders, genus Plethodon (Caudata: Plethodontidae)

    USGS Publications Warehouse

    Dodd, C. Kenneth, Jr.

    1989-01-01

    Immobility is a potentially important antipredator behavior in salamanders, especially for those posessing noxious skin secretions. The duration of immobility in 15 species of terrestrial salamanders (Plethodon) varied among species. Most salamanders (78.8%) became immobile when initially contacted under field conditions, and remained immobile from 1-180 s. Immobility duration was inversely correlated with substrate temperature and covaried with air temperature, but snout-vent level (SVL) had no effect on duration. Only immobility times of Plethodon shenandoah were significantly different from any other species. Substrate temperature, air temperature, SVL, and species accounted for only a small percentage of the variance (r2=0.09). The degree of disturbance received during a predator-prey encounter is probably more important than the subtle effects of temperature and SVL in determining immobility duration.

  17. Heterochrony repolarized: a phylogenetic analysis of developmental timing in plethodontid salamanders

    PubMed Central

    2014-01-01

    Background Disentangling evolutionary shifts in developmental timing (heterochony) is dependent upon accurate estimates of ancestral patterns. However, many classic assessments of heterochronic patterns predate robust phylogenetic hypotheses and methods for trait reconstruction, and therefore may have been polarized with untested ‘primitive’ conditions. Here we revisit the heterochronic modes of development that underlie the evolution of metamorphosis, maturation, and paedomorphosis in plethodontid salamanders. We focus on the tribe Spelerpini, which is a diverse clade that exhibits tremendous variation in timing of metamorphosis and maturation, as well as multiple independent instances of larval form paedomorphosis. Based on morphology and biogeography, early investigators concluded that the most recent common ancestors of plethodontids, and also spelerpines, were large salamanders, with very long larval periods and late maturation times. This prevailing assumption influenced subsequent heterochronic assessments, which concluded that most modern spelerpines (with shorter larval periods) were derived through multiple independent accelerations in larval development. It was also concluded that most occurrences of larval form paedomorphosis in this clade resulted from progenesis (acceleration of gonadal development relative to metamorphosis). Results By reconstructing the time to metamorphosis on a molecular-based phylogeny of plethodontids, we find that ancestral spelerpines likely had relatively shorter larval periods than previously proposed. Taken together with the credibility interval from our ancestral state estimation we show that very long larval periods are likely derived decelerations, only a few lineages have undergone appreciable accelerations in metamorphic timing, and the remaining taxa have lower probabilities of being different than the ancestral condition (possibly due to stasis). Reconstructing maturation age across nodes concomitant with the

  18. Ecological implications of metabolic compensation at low temperatures in salamanders

    PubMed Central

    2016-01-01

    Global warming is influencing the biology of the world’s biota. Temperature increases are occurring at a faster pace than that experienced by organisms in their evolutionary histories, limiting the organisms’ response to new conditions. Mechanistic models that include physiological traits can help predict species’ responses to warming. Changes in metabolism at high temperatures are often examined; yet many species are behaviorally shielded from high temperatures. Salamanders generally favor cold temperatures and are one of few groups of metazoans to be most species-rich in temperate regions. I examined variation in body temperature, behavioral activity, and temperature dependence of resting heart rate, used as a proxy for standard metabolic rate, in fire salamanders (Salamandra salamandra). Over 26 years, I found that salamanders are behaviorally active at temperatures as low as 1 °C, and aestivate at temperatures above 16 °C. Infrared thermography indicates limited thermoregulation opportunities for these nocturnal amphibians. Temperature affects resting heart rate, causing metabolic depression above 11 °C, and metabolic compensation below 8 °C: heart rate at 3 °C is 224% the expected heart rate. Thus, salamanders operating at low temperatures during periods of peak behavioral activity are able to maintain a higher metabolic rate than the rate expected in absence of compensation. This compensatory mechanism has important ecological implications, because it increases estimated seasonal heart rates. Increased heart rate, and thus metabolism, will require higher caloric intake for field-active salamanders. Thus, it is important to consider a species performance breadth over the entire temperature range, and particularly low temperatures that are ecologically relevant for cold tolerant species such as salamanders. PMID:27257549

  19. Ecological implications of metabolic compensation at low temperatures in salamanders.

    PubMed

    Catenazzi, Alessandro

    2016-01-01

    Global warming is influencing the biology of the world's biota. Temperature increases are occurring at a faster pace than that experienced by organisms in their evolutionary histories, limiting the organisms' response to new conditions. Mechanistic models that include physiological traits can help predict species' responses to warming. Changes in metabolism at high temperatures are often examined; yet many species are behaviorally shielded from high temperatures. Salamanders generally favor cold temperatures and are one of few groups of metazoans to be most species-rich in temperate regions. I examined variation in body temperature, behavioral activity, and temperature dependence of resting heart rate, used as a proxy for standard metabolic rate, in fire salamanders (Salamandra salamandra). Over 26 years, I found that salamanders are behaviorally active at temperatures as low as 1 °C, and aestivate at temperatures above 16 °C. Infrared thermography indicates limited thermoregulation opportunities for these nocturnal amphibians. Temperature affects resting heart rate, causing metabolic depression above 11 °C, and metabolic compensation below 8 °C: heart rate at 3 °C is 224% the expected heart rate. Thus, salamanders operating at low temperatures during periods of peak behavioral activity are able to maintain a higher metabolic rate than the rate expected in absence of compensation. This compensatory mechanism has important ecological implications, because it increases estimated seasonal heart rates. Increased heart rate, and thus metabolism, will require higher caloric intake for field-active salamanders. Thus, it is important to consider a species performance breadth over the entire temperature range, and particularly low temperatures that are ecologically relevant for cold tolerant species such as salamanders. PMID:27257549

  20. Ontogenetic evidence for the Paleozoic ancestry of salamanders.

    PubMed

    Schoch, Rainer R; Carroll, Robert L

    2003-01-01

    The phylogenetic positions of frogs, salamanders, and caecilians have been difficult to establish. Data matrices based primarily on Paleozoic taxa support a monophyletic origin of all Lissamphibia but have resulted in widely divergent hypotheses of the nature of their common ancestor. Analysis that concentrates on the character states of the stem taxa of the extant orders, in contrast, suggests a polyphyletic origin from divergent Paleozoic clades. Comparison of patterns of larval development in Paleozoic and modern amphibians provides a means to test previous phylogenies based primarily on adult characteristics. This proves to be highly informative in the case of the origin of salamanders. Putative ancestors of salamanders are recognized from the Permo-Carboniferous boundary of Germany on the basis of ontogenetic changes observed in fossil remains of larval growth series. The entire developmental sequence from hatching to metamorphosis is revealed in an assemblage of over 600 specimens from a single locality, all belonging to the genus Apateon. Apateon forms the most speciose genus of the neotenic temnospondyl family Branchiosauridae. The sequence of ossification of individual bones and the changing configuration of the skull closely parallel those observed in the development of primitive living salamanders. These fossils provide a model of how derived features of the salamander skull may have evolved in the context of feeding specializations that appeared in early larval stages of members of the Branchiosauridae. Larvae of Apateon share many unique derived characters with salamanders of the families Hynobiidae, Salamandridae, and Ambystomatidae, which have not been recognized in any other group of Paleozoic amphibians. PMID:12752770

  1. The Psychiatric Genomics Consortium Posttraumatic Stress Disorder Workgroup: Posttraumatic Stress Disorder Enters the Age of Large-Scale Genomic Collaboration

    PubMed Central

    Logue, Mark W; Amstadter, Ananda B; Baker, Dewleen G; Duncan, Laramie; Koenen, Karestan C; Liberzon, Israel; Miller, Mark W; Morey, Rajendra A; Nievergelt, Caroline M; Ressler, Kerry J; Smith, Alicia K; Smoller, Jordan W; Stein, Murray B; Sumner, Jennifer A; Uddin, Monica

    2015-01-01

    The development of posttraumatic stress disorder (PTSD) is influenced by genetic factors. Although there have been some replicated candidates, the identification of risk variants for PTSD has lagged behind genetic research of other psychiatric disorders such as schizophrenia, autism, and bipolar disorder. Psychiatric genetics has moved beyond examination of specific candidate genes in favor of the genome-wide association study (GWAS) strategy of very large numbers of samples, which allows for the discovery of previously unsuspected genes and molecular pathways. The successes of genetic studies of schizophrenia and bipolar disorder have been aided by the formation of a large-scale GWAS consortium: the Psychiatric Genomics Consortium (PGC). In contrast, only a handful of GWAS of PTSD have appeared in the literature to date. Here we describe the formation of a group dedicated to large-scale study of PTSD genetics: the PGC-PTSD. The PGC-PTSD faces challenges related to the contingency on trauma exposure and the large degree of ancestral genetic diversity within and across participating studies. Using the PGC analysis pipeline supplemented by analyses tailored to address these challenges, we anticipate that our first large-scale GWAS of PTSD will comprise over 10 000 cases and 30 000 trauma-exposed controls. Following in the footsteps of our PGC forerunners, this collaboration—of a scope that is unprecedented in the field of traumatic stress—will lead the search for replicable genetic associations and new insights into the biological underpinnings of PTSD. PMID:25904361

  2. Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration

    PubMed Central

    Zhu, Wei; Kuo, Dwight; Nathanson, Jason; Satoh, Akira; Pao, Gerald M.; Yeo, Gene W.; Bryant, Susan V.; Voss, S. Randal; Gardiner, David M.; Hunter, Tony

    2012-01-01

    Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mammals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of salamander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. In addition, higher genomic LINE-1 content was also detected in the limb regenerate when compared to that before amputation indicating that LINE-1 retrotransposition is indeed active during regeneration. Active LINE-1 retrotransposition has been suggested to have a potentially deleterious impact on genomic integrity. Silencing of activated LINE-1 by small RNAs has been reported to be part of the machinery aiming to maintain genomic integrity. Indeed, we were able to identify putative LINE-1-related piRNAs in the limb blastema. Transposable element-related piRNAs have been identified frequently in the germline in other organisms. Thus, we present here a scenario in which a unique germline-like state is established during axolotl limb regeneration, and the re-activation of LINE-1 may serve as a marker for cellular dedifferentiation in the early-stage of limb regeneration. PMID:22913491

  3. Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects

    PubMed Central

    Göker, Markus; Klenk, Hans-Peter

    2013-01-01

    Despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. Phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. Here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. The scoring itself, as well as pre- and post-processing of the data, is illustrated using two real-world examples in which the method has already been applied for selecting targets for genome sequencing. These projects are the JGI CSP Genomic Encyclopedia of Bacteria and Archaea phase I, targeting 1,000 type strains, and, on a smaller-scale, the phylogenomics of the Roseobacter clade. Potential artifacts of the method are discussed and compared to a selection approach based on the taxonomic classification. PMID:23991265

  4. Estimating site occupancy and species detection probability parameters for terrestrial salamanders

    USGS Publications Warehouse

    Bailey, L.L.; Simons, T.R.; Pollock, K.H.

    2004-01-01

    Recent, worldwide amphibian declines have highlighted a need for more extensive and rigorous monitoring programs to document species occurrence and detect population change. Abundance estimation methods, such as mark-recapture, are often expensive and impractical for large-scale or long-term amphibian monitoring. We apply a new method to estimate proportion of area occupied using detection/nondetection data from a terrestrial salamander system in Great Smoky Mountains National Park. Estimated species-specific detection probabilities were all <1 and varied among seven species and four sampling methods. Time (i.e., sampling occasion) and four large-scale habitat characteristics (previous disturbance history, vegetation type, elevation, and stream presence) were important covariates in estimates of both proportion of area occupied and detection probability. All sampling methods were consistent in their ability to identify important covariates for each salamander species. We believe proportion of area occupied represents a useful state variable for large-scale monitoring programs. However, our results emphasize the importance of estimating detection and occupancy probabilities rather than using an unadjusted proportion of sites where species are observed where actual occupancy probabilities are confounded with detection probabilities. Estimated detection probabilities accommodate variations in sampling effort; thus comparisons of occupancy probabilities are possible among studies with different sampling protocols.

  5. Large-Scale Development of Gene-Associated Single-Nucleotide Polymorphism Markers for Molluscan Population Genomic, Comparative Genomic, and Genome-Wide Association Studies

    PubMed Central

    Jiao, Wenqian; Fu, Xiaoteng; Li, Jinqin; Li, Ling; Feng, Liying; Lv, Jia; Zhang, Lu; Wang, Xiaojian; Li, Yangping; Hou, Rui; Zhang, Lingling; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

    2014-01-01

    Mollusca is the second most diverse group of animals in the world. Despite their perceived importance, omics-level studies have seldom been applied to this group of animals largely due to a paucity of genomic resources. Here, we report the first large-scale gene-associated marker development and evaluation for a bivalve mollusc, Chlamys farreri. More than 21,000 putative single-nucleotide polymorphisms (SNPs) were identified from the C. farreri transcriptome. Primers and probes were designed and synthesized for 4500 SNPs, and 1492 polymorphic markers were successfully developed using a high-resolution melting genotyping platform. These markers are particularly suitable for population genomic analysis due to high polymorphism within and across populations, a low frequency of null alleles, and conformation to neutral expectations. Unexpectedly, high cross-species transferability was observed, suggesting that the transferable SNPs may largely represent ancestral genetic variations that have been preserved differentially among subfamilies of Pectinidae. Gene annotations were available for 73% of the markers, and 65% could be anchored to the recently released Pacific oyster genome. Large-scale association analysis revealed key candidate genes responsible for scallop growth regulation, and provided markers for further genetic improvement of C. farreri in breeding programmes. PMID:24277739

  6. Using counts to simultaneously estimate abundance and detection probabilities in a salamander community

    USGS Publications Warehouse

    Dodd, C.K., Jr.; Dorazio, R.M.

    2004-01-01

    A critical variable in both ecological and conservation field studies is determining how many individuals of a species are present within a defined sampling area. Labor intensive techniques such as capture-mark-recapture and removal sampling may provide estimates of abundance, but there are many logistical constraints to their widespread application. Many studies on terrestrial and aquatic salamanders use counts as an index of abundance, assuming that detection remains constant while sampling. If this constancy is violated, determination of detection probabilities is critical to the accurate estimation of abundance. Recently, a model was developed that provides a statistical approach that allows abundance and detection to be estimated simultaneously from spatially and temporally replicated counts. We adapted this model to estimate these parameters for salamanders sampled over a six vear period in area-constrained plots in Great Smoky Mountains National Park. Estimates of salamander abundance varied among years, but annual changes in abundance did not vary uniformly among species. Except for one species, abundance estimates were not correlated with site covariates (elevation/soil and water pH, conductivity, air and water temperature). The uncertainty in the estimates was so large as to make correlations ineffectual in predicting which covariates might influence abundance. Detection probabilities also varied among species and sometimes among years for the six species examined. We found such a high degree of variation in our counts and in estimates of detection among species, sites, and years as to cast doubt upon the appropriateness of using count data to monitor population trends using a small number of area-constrained survey plots. Still, the model provided reasonable estimates of abundance that could make it useful in estimating population size from count surveys.

  7. Core-SINE blocks comprise a large fraction of monotreme genomes; implications for vertebrate chromosome evolution.

    PubMed

    Kirby, Patrick J; Greaves, Ian K; Koina, Edda; Waters, Paul D; Marshall Graves, Jennifer A

    2007-01-01

    The genomes of the egg-laying platypus and echidna are of particular interest because monotremes are the most basal mammal group. The chromosomal distribution of an ancient family of short interspersed repeats (SINEs), the core-SINEs, was investigated to better understand monotreme genome organization and evolution. Previous studies have identified the core-SINE as the predominant SINE in the platypus genome, and in this study we quantified, characterized and localized subfamilies. Dot blot analysis suggested that a very large fraction (32% of the platypus and 16% of the echidna genome) is composed of Mon core-SINEs. Core-SINE-specific primers were used to amplify PCR products from platypus and echidna genomic DNA. Sequence analysis suggests a common consensus sequence Mon 1-B, shared by platypus and echidna, as well as platypus-specific Mon 1-C and echidna specific Mon 1-D consensus sequences. FISH mapping of the Mon core-SINE products to platypus metaphase spreads demonstrates that the Mon-1C subfamily is responsible for the striking Mon core-SINE accumulation in the distal regions of the six large autosomal pairs and the largest X chromosome. This unusual distribution highlights the dichotomy between the seven large chromosome pairs and the 19 smaller pairs in the monotreme karyotype, which has some similarity to the macro- and micro-chromosomes of birds and reptiles, and suggests that accumulation of repetitive sequences may have enlarged small chromosomes in an ancestral vertebrate. In the forthcoming sequence of the platypus genome there are still large gaps, and the extensive Mon core-SINE accumulation on the distal regions of the six large autosomal pairs may provide one explanation for this missing sequence. PMID:18185983

  8. Bleached pigment activates transduction in salamander cones

    PubMed Central

    1995-01-01

    We have used suction electrode recording together with rapid steps into 0.5 mM IBMX solution to investigate changes in guanylyl cyclase velocity produced by pigment bleaching in isolated cones of the salamander Ambystoma tigrinum. Both backgrounds and bleaches accelerate the time course of current increase during steps into IBMX. We interpret this as evidence that the velocity of the guanylyl cyclase is increased in background light or after bleaching. Our results indicate that cyclase velocity increases nearly linearly with increasing percent pigment bleached but nonlinearly (and may saturate) with increasing back-ground intensity. In cones (as previously demonstrated for rods), light-activated pigment and bleached pigment appear to have somewhat different effects on the transduction cascade. The effect of bleaching on cyclase rate is maintained for at least 15-20 min after the light is removed, much longer than is required after a bleach for circulating current and sensitivity to stabilize in an isolated cone. The effect on the cyclase rate can be completely reversed by treatment with liposomes containing 11-cis retinal. The effects of bleaching can also be partially reversed by beta-ionone, an analogue of the chromophore 11- cis-retinal which does not form a covalent attachment to opsin. Perfusion of a bleached cone with beta-ionone produces a rapid increase in circulating current and sensitivity, which rapidly reverses when the beta-ionone is removed. Perfusion with beta-ionone also causes a partial reversal of the bleach-induced acceleration of cyclase velocity. We conclude that bleaching produces an "equivalent background" excitation of the transduction cascade in cones, perhaps by a mechanism similar to that in rods. PMID:8786347

  9. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity

    PubMed Central

    Nikolaev, L.G; Akopov, S.B; Didych, D.A; Sverdlov, E.D

    2009-01-01

    The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s). PMID:20119526

  10. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity.

    PubMed

    Nikolaev, L G; Akopov, S B; Didych, D A; Sverdlov, E D

    2009-08-01

    The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s). PMID:20119526

  11. The PRRS Host Genomic Consortium (PHGC) Database: Management of large data sets.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In any consortium project where large amounts of phenotypic and genotypic data are collected across several research labs, issues arise with maintenance and analysis of datasets. The PRRS Host Genomic Consortium (PHGC) Database was developed to meet this need for the PRRS research community. The sch...

  12. Software engineering the mixed model for genome-wide association studies on large samples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample siz...

  13. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

    PubMed Central

    2012-01-01

    Background Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. Results Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH

  14. Captured segment exchange: a strategy for custom engineering large genomic regions in Drosophila melanogaster.

    PubMed

    Bateman, Jack R; Palopoli, Michael F; Dale, Sarah T; Stauffer, Jennifer E; Shah, Anita L; Johnson, Justine E; Walsh, Conor W; Flaten, Hanna; Parsons, Christine M

    2013-02-01

    Site-specific recombinases (SSRs) are valuable tools for manipulating genomes. In Drosophila, thousands of transgenic insertions carrying SSR recognition sites have been distributed throughout the genome by several large-scale projects. Here we describe a method with the potential to use these insertions to make custom alterations to the Drosophila genome in vivo. Specifically, by employing recombineering techniques and a dual recombinase-mediated cassette exchange strategy based on the phiC31 integrase and FLP recombinase, we show that a large genomic segment that lies between two SSR recognition-site insertions can be "captured" as a target cassette and exchanged for a sequence that was engineered in bacterial cells. We demonstrate this approach by targeting a 50-kb segment spanning the tsh gene, replacing the existing segment with corresponding recombineered sequences through simple and efficient manipulations. Given the high density of SSR recognition-site insertions in Drosophila, our method affords a straightforward and highly efficient approach to explore gene function in situ for a substantial portion of the Drosophila genome. PMID:23150604

  15. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity

    PubMed Central

    Pope, Welkin H; Bowman, Charles A; Russell, Daniel A; Jacobs-Sera, Deborah; Asai, David J; Cresawn, Steven G; Jacobs, William R; Hendrix, Roger W; Lawrence, Jeffrey G; Hatfull, Graham F; Abbazia, Patrick; Ababio, Amma; Adam, Naazneen

    2015-01-01

    The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001 PMID:25919952

  16. Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli

    PubMed Central

    Lee, Heewook; Doak, Thomas G.; Popodi, Ellen; Foster, Patricia L.; Tang, Haixu

    2016-01-01

    A majority of large-scale bacterial genome rearrangements involve mobile genetic elements such as insertion sequence (IS) elements. Here we report novel insertions and excisions of IS elements and recombination between homologous IS elements identified in a large collection of Escherichia coli mutation accumulation lines by analysis of whole genome shotgun sequencing data. Based on 857 identified events (758 IS insertions, 98 recombinations and 1 excision), we estimate that the rate of IS insertion is 3.5 × 10−4 insertions per genome per generation and the rate of IS homologous recombination is 4.5 × 10−5 recombinations per genome per generation. These events are mostly contributed by the IS elements IS1, IS2, IS5 and IS186. Spatial analysis of new insertions suggest that transposition is biased to proximal insertions, and the length spectrum of IS-caused deletions is largely explained by local hopping. For any of the ISs studied there is no region of the circular genome that is favored or disfavored for new insertions but there are notable hotspots for deletions. Some elements have preferences for non-coding sequence or for the beginning and end of coding regions, largely explained by target site motifs. Interestingly, transposition and deletion rates remain constant across the wild-type and 12 mutant E. coli lines, each deficient in a distinct DNA repair pathway. Finally, we characterized the target sites of four IS families, confirming previous results and characterizing a highly specific pattern at IS186 target-sites, 5′-GGGG(N6/N7)CCCC-3′. We also detected 48 long deletions not involving IS elements. PMID:27431326

  17. FVGWAS: Fast voxelwise genome wide association analysis of large-scale imaging genetic data.

    PubMed

    Huang, Meiyan; Nichols, Thomas; Huang, Chao; Yu, Yang; Lu, Zhaohua; Knickmeyer, Rebecca C; Feng, Qianjin; Zhu, Hongtu

    2015-09-01

    More and more large-scale imaging genetic studies are being widely conducted to collect a rich set of imaging, genetic, and clinical data to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. Several major big-data challenges arise from testing genome-wide (NC>12 million known variants) associations with signals at millions of locations (NV~10(6)) in the brain from thousands of subjects (n~10(3)). The aim of this paper is to develop a Fast Voxelwise Genome Wide Association analysiS (FVGWAS) framework to efficiently carry out whole-genome analyses of whole-brain data. FVGWAS consists of three components including a heteroscedastic linear model, a global sure independence screening (GSIS) procedure, and a detection procedure based on wild bootstrap methods. Specifically, for standard linear association, the computational complexity is O (nNVNC) for voxelwise genome wide association analysis (VGWAS) method compared with O ((NC+NV)n(2)) for FVGWAS. Simulation studies show that FVGWAS is an efficient method of searching sparse signals in an extremely large search space, while controlling for the family-wise error rate. Finally, we have successfully applied FVGWAS to a large-scale imaging genetic data analysis of ADNI data with 708 subjects, 193,275voxels in RAVENS maps, and 501,584 SNPs, and the total processing time was 203,645s for a single CPU. Our FVGWAS may be a valuable statistical toolbox for large-scale imaging genetic analysis as the field is rapidly advancing with ultra-high-resolution imaging and whole-genome sequencing. PMID:26025292

  18. Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond

    SciTech Connect

    Oehmen, Christopher S.; Sofia, Heidi J.; Baxter, Douglas; Szeto, Ernest; Hugenholtz, Philip; Kyrpides, Nikos; Markowitz, Victor; Straatsma, Tjerk P.

    2007-06-01

    Genome sequence comparisons of exponentially growing data sets form the foundation for the comparative analysis tools provided by community biological data resources such as the Integrated Microbial Genome (IMG) system at the Joint Genome Institute (JGI). We present an example of how ScalaBLAST, a high-throughput sequence analysis program harnesses increasingly critical high-performance computing to perform sequence analysis which is a critical component of maintaining a state-of-the-art sequence data repository. The Integrated Microbial Genomes (IMG) system1 is a data management and analysis platform for microbial genomes hosted at the JGI. IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for interactive analysis of genomes, genes and functions, individually or in a comparative context. Most of these tools are based on pre-computed pairwise sequence similarities involving millions of genes. These computations are becoming prohibitively time consuming with the rapid increase in the number of newly sequenced genomes incorporated into IMG and the need to refresh regularly the content of IMG in order to reflect changes in the annotations of existing genomes. Thus, building IMG 2.0 (released on December 1st 2006) entailed reloading from NCBI's RefSeq all the genomes in the previous version of IMG (IMG 1.6, as of September 1st, 2006) together with 1,541 new public microbial,viral and eukaryal genomes, bringing the total of IMG genomes to 2,301. A critical part of building IMG 2.0 involved using PNNL ScalaBLAST software for computing pairwise similarities for over 2.2 million genes in under 26 hours on 1,000 processors, thus illustrating the impact that new generation bioinformatics tools are poised to make in biology. The BLAST algorithm2, 3 is a familiar bioinformatics application for computing sequence similarity, and has become a workhorse in large

  19. Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076

    SciTech Connect

    Challacombe, Jean F; Eichorst, Stephanie A; Hauser, Loren John; Land, Miriam L; Xie, Gary; Kuske, Cheryl R

    2011-01-01

    Members of the bacterial phylum Acidobacteria are widespread in soils and sediments worldwide, and are abundant in many soils. Acidobacteria are challenging to culture in vitro, and many basic features of their biology and functional roles in the soil have not been determined. Candidatus Solibacter usitatus strain Ellin6076 has a 9.9 Mb genome that is approximately 2 5 times as large as the other sequenced Acidobacteria genomes. Bacterial genome sizes typically range from 0.5 to 10 Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Our comparative genome analyses indicate that the Ellin6076 large genome has arisen by horizontal gene transfer via ancient bacteriophage and/or plasmid-mediated transduction, and widespread small-scale gene duplications, resulting in an increased number of paralogs. Low amino acid sequence identities among functional group members, and lack of conserved gene order and orientation in regions containing similar groups of paralogs, suggest that most of the paralogs are not the result of recent duplication events. The genome sizes of additional cultured Acidobacteria strains were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 3 had larger genomes than those of subdivision 1, but none were as large as the Ellin6076 genome. The large genome of Ellin6076 may not be typical of the phylum, and encodes traits that could provide a selective metabolic, defensive and regulatory advantage in the soil environment.

  20. Final report. Human artificial episomal chromosome (HAEC) for building large genomic libraries

    SciTech Connect

    Jean-Michael H. Vos

    1999-12-09

    Collections of human DNA fragments are maintained for research purposes as clones in bacterial host cells. However for unknown reasons, some regions of the human genome appear to be unclonable or unstable in bacteria. Their team has developed a system using episomes (extrachromosomal, autonomously replication DNA) that maintains large DNA fragments in human cells. This human artificial episomal chromosomal (HAEC) system may prove useful for coverage of these especially difficult regions. In the broader biomedical community, the HAEC system also shows promise for use in functional genomics and gene therapy. Recent improvements to the HAEC system and its application to mapping, sequencing, and functionally studying human and mouse DNA are summarized. Mapping and sequencing the human genome and model organisms are only the first steps in determining the function of various genetic units critical for gene regulation, DNA replication, chromatin packaging, chromosomal stability, and chromatid segregation. Such studies will require the ability to transfer and manipulate entire functional units into mammalian cells.

  1. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    ScienceCinema

    Shih, Patrick [Kerfeld Lab, UC Berkeley and JGI

    2013-01-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  2. CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

    SciTech Connect

    Shih, Patrick

    2012-03-22

    Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

  3. 3D Bite Modeling and Feeding Mechanics of the Largest Living Amphibian, the Chinese Giant Salamander Andrias davidianus (Amphibia:Urodela)

    PubMed Central

    Fortuny, Josep; Marcé-Nogué, Jordi; Heiss, Egon; Sanchez, Montserrat; Gil, Lluis; Galobart, Àngel

    2015-01-01

    Biting is an integral feature of the feeding mechanism for aquatic and terrestrial salamanders to capture, fix or immobilize elusive or struggling prey. However, little information is available on how it works and the functional implications of this biting system in amphibians although such approaches might be essential to understand feeding systems performed by early tetrapods. Herein, the skull biomechanics of the Chinese giant salamander, Andrias davidianus is investigated using 3D finite element analysis. The results reveal that the prey contact position is crucial for the structural performance of the skull, which is probably related to the lack of a bony bridge between the posterior end of the maxilla and the anterior quadrato-squamosal region. Giant salamanders perform asymmetrical strikes. These strikes are unusual and specialized behavior but might indeed be beneficial in such sit-and-wait or ambush-predators to capture laterally approaching prey. However, once captured by an asymmetrical strike, large, elusive and struggling prey have to be brought to the anterior jaw region to be subdued by a strong bite. Given their basal position within extant salamanders and their “conservative” morphology, cryptobranchids may be useful models to reconstruct the feeding ecology and biomechanics of different members of early tetrapods and amphibians, with similar osteological and myological constraints. PMID:25853557

  4. Computer-assisted photo identification outperforms visible implant elastomers in an endangered salamander, Eurycea tonkawae.

    PubMed

    Bendik, Nathan F; Morrison, Thomas A; Gluesenkamp, Andrew G; Sanders, Mark S; O'Donnell, Lisa J

    2013-01-01

    Despite recognition that nearly one-third of the 6300 amphibian species are threatened with extinction, our understanding of the general ecology and population status of many amphibians is relatively poor. A widely-used method for monitoring amphibians involves injecting captured individuals with unique combinations of colored visible implant elastomer (VIE). We compared VIE identification to a less-invasive method - computer-assisted photographic identification (photoID) - in endangered Jollyville Plateau salamanders (Eurycea tonkawae), a species with a known range limited to eight stream drainages in central Texas. We based photoID on the unique pigmentation patterns on the dorsal head region of 1215 individual salamanders using identification software Wild-ID. We compared the performance of photoID methods to VIEs using both 'high-quality' and 'low-quality' images, which were taken using two different camera types and technologies. For high-quality images, the photoID method had a false rejection rate of 0.76% compared to 1.90% for VIEs. Using a comparable dataset of lower-quality images, the false rejection rate was much higher (15.9%). Photo matching scores were negatively correlated with time between captures, suggesting that evolving natural marks could increase misidentification rates in longer term capture-recapture studies. Our study demonstrates the utility of large-scale capture-recapture using photo identification methods for Eurycea and other species with stable natural marks that can be reliably photographed. PMID:23555669

  5. Side-by-side secretion of Late Palaeozoic diverged courtship pheromones in an aquatic salamander.

    PubMed

    Van Bocxlaer, Ines; Treer, Dag; Maex, Margo; Vandebergh, Wim; Janssenswillen, Sunita; Stegen, Gwij; Kok, Philippe; Willaert, Bert; Matthijs, Severine; Martens, Erik; Mortier, Anneleen; de Greve, Henri; Proost, Paul; Bossuyt, Franky

    2015-03-22

    Males of the advanced salamanders (Salamandroidea) attain internal fertilization without a copulatory organ by depositing a spermatophore on the substrate in the environment, which females subsequently take up with their cloaca. The aquatically reproducing modern Eurasian newts (Salamandridae) have taken this to extremes, because most species do not display close physical contact during courtship, but instead largely rely on females following the male track at spermatophore deposition. Although pheromones have been widely assumed to represent an important aspect of male courtship, molecules able to induce the female following behaviour that is the prelude for successful insemination have not yet been identified. Here, we show that uncleaved sodefrin precursor-like factor (SPF) protein pheromones are sufficient to elicit such behaviour in female palmate newts (Lissotriton helveticus). Combined transcriptomic and proteomic evidence shows that males simultaneously tail-fan multiple ca 20 kDa glycosylated SPF proteins during courtship. Notably, molecular dating estimates show that the diversification of these proteins already started in the late Palaeozoic, about 300 million years ago. Our study thus not only extends the use of uncleaved SPF proteins outside terrestrially reproducing plethodontid salamanders, but also reveals one of the oldest vertebrate pheromone systems. PMID:25694622

  6. Computer-Assisted Photo Identification Outperforms Visible Implant Elastomers in an Endangered Salamander, Eurycea tonkawae

    PubMed Central

    Bendik, Nathan F.; Morrison, Thomas A.; Gluesenkamp, Andrew G.; Sanders, Mark S.; O’Donnell, Lisa J.

    2013-01-01

    Despite recognition that nearly one-third of the 6300 amphibian species are threatened with extinction, our understanding of the general ecology and population status of many amphibians is relatively poor. A widely-used method for monitoring amphibians involves injecting captured individuals with unique combinations of colored visible implant elastomer (VIE). We compared VIE identification to a less-invasive method – computer-assisted photographic identification (photoID) – in endangered Jollyville Plateau salamanders (Eurycea tonkawae), a species with a known range limited to eight stream drainages in central Texas. We based photoID on the unique pigmentation patterns on the dorsal head region of 1215 individual salamanders using identification software Wild-ID. We compared the performance of photoID methods to VIEs using both ‘high-quality’ and ‘low-quality’ images, which were taken using two different camera types and technologies. For high-quality images, the photoID method had a false rejection rate of 0.76% compared to 1.90% for VIEs. Using a comparable dataset of lower-quality images, the false rejection rate was much higher (15.9%). Photo matching scores were negatively correlated with time between captures, suggesting that evolving natural marks could increase misidentification rates in longer term capture-recapture studies. Our study demonstrates the utility of large-scale capture-recapture using photo identification methods for Eurycea and other species with stable natural marks that can be reliably photographed. PMID:23555669

  7. Tuataras and salamanders show that walking and running mechanics are ancient features of tetrapod locomotion

    PubMed Central

    Reilly, Stephen M; McElroy, Eric J; Andrew Odum, R; Hornyak, Valerie A

    2006-01-01

    The lumbering locomotor behaviours of tuataras and salamanders are the best examples of quadrupedal locomotion of early terrestrial vertebrates. We show they use the same walking (out-of-phase) and running (in-phase) patterns of external mechanical energy fluctuations of the centre-of-mass known in fast moving (cursorial) animals. Thus, walking and running centre-of-mass mechanics have been a feature of tetrapods since quadrupedal locomotion emerged over 400 million years ago. When walking, these sprawling animals save external mechanical energy with the same pendular effectiveness observed in cursorial animals. However, unlike cursorial animals (that change footfall patterns and mechanics with speed), tuataras and salamanders use only diagonal couplet gaits and indifferently change from walking to running mechanics with no significant change in total mechanical energy. Thus, the change from walking to running is not related to speed and the advantage of walking versus running is unclear. Furthermore, lumbering mechanics in primitive tetrapods is reflected in having total mechanical energy driven by potential energy (rather than kinetic energy as in cursorial animals) and relative centre-of-mass displacements an order of magnitude greater than cursorial animals. Thus, large vertical displacements associated with lumbering locomotion in primitive tetrapods may preclude their ability to increase speed. PMID:16777753

  8. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    SciTech Connect

    Smith, David R.; Lee, Robert W.; Cushman, John C.; Magnuson, Jon K.; Tran, Duc; Polle, Juergen E.

    2010-05-07

    Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions: These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable

  9. Hyper-expansion of large DNA segments in the genome of kuruma shrimp, Marsupenaeus japonicus

    PubMed Central

    2010-01-01

    Background Higher crustaceans (class Malacostraca) represent the most species-rich and morphologically diverse group of non-insect arthropods and many of its members are commercially important. Although the crustacean DNA sequence information is growing exponentially, little is known about the genome organization of Malacostraca. Here, we constructed a bacterial artificial chromosome (BAC) library and performed BAC-end sequencing to provide genomic information for kuruma shrimp (Marsupenaeus japonicus), one of the most widely cultured species among crustaceans, and found the presence of a redundant sequence in the BAC library. We examined the BAC clone that includes the redundant sequence to further analyze its length, copy number and location in the kuruma shrimp genome. Results Mj024A04 BAC clone, which includes one redundant sequence, contained 27 putative genes and seemed to display a normal genomic DNA structure. Notably, of the putative genes, 3 genes encode homologous proteins to the inhibitor of apoptosis protein and 7 genes encode homologous proteins to white spot syndrome virus, a virulent pathogen known to affect crustaceans. Colony hybridization and PCR analysis of 381 BAC clones showed that almost half of the BAC clones maintain DNA segments whose sequences are homologous to the representative BAC clone Mj024A04. The Mj024A04 partial sequence was detected multiple times in the kuruma shrimp nuclear genome with a calculated copy number of at least 100. Microsatellites based BAC genotyping clearly showed that Mj024A04 homologous sequences were cloned from at least 48 different chromosomal loci. The absence of micro-syntenic relationships with the available genomic sequences of Daphnia and Drosophila suggests the uniqueness of these fragments in kuruma shrimp from current arthropod genome sequences. Conclusions Our results demonstrate that hyper-expansion of large DNA segments took place in the kuruma shrimp genome. Although we analyzed only a part of the

  10. Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

    PubMed Central

    Salipante, Stephen J.; Roach, David J.; Kitzman, Jacob O.; Snyder, Matthew W.; Stackhouse, Bethany; Butler-Wu, Susan M.; Lee, Choli; Cookson, Brad T.

    2015-01-01

    Large-scale bacterial genome sequencing efforts to date have provided limited information on the most prevalent category of disease: sporadically acquired infections caused by common pathogenic bacteria. Here, we performed whole-genome sequencing and de novo assembly of 312 blood- or urine-derived isolates of extraintestinal pathogenic (ExPEC) Escherichia coli, a common agent of sepsis and community-acquired urinary tract infections, obtained during the course of routine clinical care at a single institution. We find that ExPEC E. coli are highly genomically heterogeneous, consistent with pan-genome analyses encompassing the larger species. Investigation of differential virulence factor content and antibiotic resistance phenotypes reveals markedly different profiles among lineages and among strains infecting different body sites. We use high-resolution molecular epidemiology to explore the dynamics of infections at the level of individual patients, including identification of possible person-to-person transmission. Notably, a limited number of discrete lineages caused the majority of bloodstream infections, including one subclone (ST131-H30) responsible for 28% of bacteremic E. coli infections over a 3-yr period. We additionally use a microbial genome-wide-association study (GWAS) approach to identify individual genes responsible for antibiotic resistance, successfully recovering known genes but notably not identifying any novel factors. We anticipate that in the near future, whole-genome sequencing of microorganisms associated with clinical disease will become routine. Our study reveals what kind of information can be obtained from sequencing clinical isolates on a large scale, even well-characterized organisms such as E. coli, and provides insight into how this information might be utilized in a healthcare setting. PMID:25373147

  11. Native Salamanders and Introduced Fish: Changing the Nature of Mountain Lakes and Ponds

    USGS Publications Warehouse

    Larson, Gary L.; Hoffman, Robert L.

    2003-01-01

    During the last century, many fishless mountain lakes and ponds in the Pacific Northwest were stocked with non-native fish, such as brook trout, for recreational purposes. These introduced fish replaced long-toed and northwestern salamander larvae as the top aquatic vertebrate predator by preying on salamander larvae. This predatory interaction has been shown to reduce the abundances of larval salamander populations. We conducted studies in two national parks to assess the abundances of salamander larvae in lakes with and without introduced fish. These studies suggest that the two salamander species were affected quite differently by the presence of introduced fish because of different life-history traits and different distributions of salamanders and fish within each park.

  12. Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments

    PubMed Central

    Richter, Michael; de Beer, Dirk; Preisler, André; Jørgensen, Bo B; Huntemann, Marcel; Glöckner, Frank Oliver; Amann, Rudolf; Koopman, Werner J. H; Lasken, Roger S; Janto, Benjamin; Hogg, Justin; Stoodley, Paul; Boissy, Robert; Ehrlich, Garth D

    2007-01-01

    Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments. PMID:17760503

  13. Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

    PubMed Central

    Heath, Allison P; Greenway, Matthew; Powell, Raymond; Spring, Jonathan; Suarez, Rafael; Hanley, David; Bandlamudi, Chai; McNerney, Megan E; White, Kevin P; Grossman, Robert L

    2014-01-01

    Background As large genomics and phenotypic datasets are becoming more common, it is increasingly difficult for most researchers to access, manage, and analyze them. One possible approach is to provide the research community with several petabyte-scale cloud-based computing platforms containing these data, along with tools and resources to analyze it. Methods Bionimbus is an open source cloud-computing platform that is based primarily upon OpenStack, which manages on-demand virtual machines that provide the required computational resources, and GlusterFS, which is a high-performance clustered file system. Bionimbus also includes Tukey, which is a portal, and associated middleware that provides a single entry point and a single sign on for the various Bionimbus resources; and Yates, which automates the installation, configuration, and maintenance of the software infrastructure required. Results Bionimbus is used by a variety of projects to process genomics and phenotypic data. For example, it is used by an acute myeloid leukemia resequencing project at the University of Chicago. The project requires several computational pipelines, including pipelines for quality control, alignment, variant calling, and annotation. For each sample, the alignment step requires eight CPUs for about 12 h. BAM file sizes ranged from 5 GB to 10 GB for each sample. Conclusions Most members of the research community have difficulty downloading large genomics datasets and obtaining sufficient storage and computer resources to manage and analyze the data. Cloud computing platforms, such as Bionimbus, with data commons that contain large genomics datasets, are one choice for broadening access to research data in genomics. PMID:24464852

  14. An improved method for oriT-directed cloning and functionalization of large bacterial genomic regions.

    PubMed

    Kvitko, Brian H; McMillan, Ian A; Schweizer, Herbert P

    2013-08-01

    We have made significant improvements to a broad-host-range system for the cloning and manipulation of large bacterial genomic regions based on site-specific recombination between directly repeated oriT sites during conjugation. Using two suicide capture vectors carrying flanking homology regions, oriT sites are recombined on either side of the target region. Using a broad-host-range conjugation helper plasmid, the region between the oriT sites is conjugated into an Escherichia coli recipient strain, where it is circularized and maintained as a chimeric mini-F vector. The cloned target region is functionalized in multiple ways to accommodate downstream manipulation. The target region is flanked with Gateway attB sites for recombination into other vectors and by rare 18-bp I-SceI restriction sites for subcloning. The Tn7-functionalized target can also be inserted at a naturally occurring chromosomal attTn7 site(s) or maintained as a broad-host-range plasmid for complementation or heterologous expression studies. We have used the oriTn7 capture technique to clone and complement Burkholderia pseudomallei genomic regions up to 140 kb in size and have created isogenic Burkholderia strains with various combinations of genomic islands. We believe this system will greatly aid the cloning and genetic analysis of genomic islands, biosynthetic gene clusters, and large open reading frames. PMID:23747708

  15. An Improved Method for oriT-Directed Cloning and Functionalization of Large Bacterial Genomic Regions

    PubMed Central

    Kvitko, Brian H.; McMillan, Ian A.

    2013-01-01

    We have made significant improvements to a broad-host-range system for the cloning and manipulation of large bacterial genomic regions based on site-specific recombination between directly repeated oriT sites during conjugation. Using two suicide capture vectors carrying flanking homology regions, oriT sites are recombined on either side of the target region. Using a broad-host-range conjugation helper plasmid, the region between the oriT sites is conjugated into an Escherichia coli recipient strain, where it is circularized and maintained as a chimeric mini-F vector. The cloned target region is functionalized in multiple ways to accommodate downstream manipulation. The target region is flanked with Gateway attB sites for recombination into other vectors and by rare 18-bp I-SceI restriction sites for subcloning. The Tn7-functionalized target can also be inserted at a naturally occurring chromosomal attTn7 site(s) or maintained as a broad-host-range plasmid for complementation or heterologous expression studies. We have used the oriTn7 capture technique to clone and complement Burkholderia pseudomallei genomic regions up to 140 kb in size and have created isogenic Burkholderia strains with various combinations of genomic islands. We believe this system will greatly aid the cloning and genetic analysis of genomic islands, biosynthetic gene clusters, and large open reading frames. PMID:23747708

  16. Impact of valley fills on streamside salamanders in southern West Virginia

    USGS Publications Warehouse

    Wood, Petra Bohall; Williams, Jennifer M.

    2013-01-01

    Valley fills associated with mountaintop-removal mining bury stream headwaters and affect water quality and ecological function of reaches below fills. We quantified relative abundance of streamside salamanders in southern West Virginia during 2002 in three streams below valley fills (VFS) and in three reference streams (RS). We surveyed 36 10- × 2-m stream transects, once in summer and fall, paired by order and structure. Of 2,343 salamanders captured, 66.7% were from RS. Total salamanders (adults plus larvae) were more abundant in RS than VFS for first-order and second-order reaches. Adult salamanders had greater abundance in first-order reaches of RS than VFS. Larval salamanders were more abundant in second-order reaches of RS than VFS. No stream width or mesohabitat variables differed between VFS and RS. Only two cover variables differed. Silt cover, greater in VFS than RS first-order reaches, is a likely contributor to reduced abundance of salamanders in VFS. Second-order RS had more boulder cover than second-order VFS, which may have contributed to the higher total and larval salamander abundance in RS. Water chemistry assessments of our VFS and RS reported elevated levels of metal and ion concentrations in VFS, which can depress macroinvertebrate populations and likely affect salamander abundance. Valley fills appear to have significant negative effects on stream salamander abundance due to alterations in habitat structure, water quality and chemistry, and macroinvertebrate communities in streams below fills.

  17. Whole-genome mapping reveals a large chromosomal inversion on Iberian Brucella suis biovar 2 strains.

    PubMed

    Ferreira, Ana Cristina; Dias, Ricardo; de Sá, Maria Inácia Corrêa; Tenreiro, Rogério

    2016-08-30

    Optical mapping is a technology able to quickly generate high resolution ordered whole-genome restriction maps of bacteria, being a proven approach to search for diversity among bacterial isolates. In this work, optical whole-genome maps were used to compare closely-related Brucella suis biovar 2 strains. This biovar is the unique isolated in domestic pigs and wild boars in Portugal and Spain and most of the strains share specific molecular characteristics establishing an Iberian clonal lineage that can be differentiated from another lineage mainly isolated in several Central European countries. We performed the BamHI whole-genome optical maps of five B. suis biovar 2 field strains, isolated from wild boars in Portugal and Spain (three from the Iberian lineage and two from the Central European one) as well as of the reference strain B. suis biovar 2 ATCC 23445 (Central European lineage, Denmark). Each strain showed a distinct, highly individual configuration of 228-231 BamHI fragments. Nevertheless, a low divergence was globally observed in chromosome II (1.6%) relatively to chromosome I (2.4%). Optical mapping also disclosed genomic events associated with B. suis strains in chromosome I, namely one indel (3.5kb) and one large inversion (944kb). By using targeted-PCR in a set of 176 B. suis strains, including all biovars and haplotypes, the indel was found to be specific of the reference strain ATCC 23445 and the large inversion was shown to be an exclusive genomic marker of the Iberian clonal lineage of biovar 2. PMID:27527786

  18. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.

    PubMed

    Gao, Song; Bertrand, Denis; Chia, Burton K H; Nagarajan, Niranjan

    2016-01-01

    The assembly of large, repeat-rich eukaryotic genomes represents a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be expensive for larger genomes. OPERA-LG is a scalable, exact algorithm for the scaffold assembly of large, repeat-rich genomes, out-performing state-of-the-art programs for scaffold correctness and contiguity. It provides a rigorous framework for scaffolding of repetitive sequences and a systematic approach for combining data from different second-generation and third-generation sequencing technologies. OPERA-LG provides an avenue for systematic augmentation and improvement of thousands of existing draft eukaryotic genome assemblies. PMID:27169502

  19. Apparent predation by Gray Jays, Perisoreus canadensis, on Long-toed Salamanders, Ambystoma macrodactylum, in the Oregon Cascade Range

    USGS Publications Warehouse

    Murray, M.P.; Pearl, C.A.; Bury, R.B.

    2005-01-01

    We report observations of Gray Jays (Perisoreus canadensis) appearing to consume larval Long-toed Salamanders (Ambystoma macrodactylum) in a drying subalpine pond in Oregon, USA. Corvids are known to prey upon a variety of anuran amphibians, but to our knowledge, this is the first report of predation by any corvid on aquatic salamanders. Long-toed Salamanders appear palatable to Gray Jays, and may provide a food resource to Gray Jays when salamander larvae are concentrated in drying temporary ponds.

  20. Extreme morphological and ecological homoplasy in tropical salamanders

    PubMed Central

    Parra-Olea, Gabriela; Wake, David B.

    2001-01-01

    Fossorial salamanders typically have elongate and attenuated heads and bodies, diminutive limbs, hands and feet, and extremely elongate tails. Batrachoseps from California, Lineatriton from eastern México, and Oedipina from southern México to Ecuador, all members of the family Plethodontidae, tribe Bolitoglossini, resemble one another in external morphology, which has evolved independently. Whereas Oedipina and Batrachoseps are elongate because there are more trunk vertebrae, a widespread homoplasy (parallelism) in salamanders, the genus Lineatriton is unique in having evolved convergently by an alternate “giraffe-neck” developmental program. Lineatriton has the same number of trunk vertebrae as related, nonelongated taxa, but individual trunk vertebrae are elongated. A robust phylogenetic hypothesis, based on sequences of three mtDNA genes, finds Lineatriton to be deeply nested within a clade characterized by generalized ecology and morphology. Lineatriton lineolus, the only currently recognized taxon in the genus, shows unanticipated genetic diversity. Surprisingly, geographically separated populations of L. lineolus are not monophyletic, but are sister taxa of different species of the morphologically generalized genus Pseudoeurycea. Lineatriton, long thought to be a unique monospecific lineage, is polyphyletic. Accordingly, the specialized morphology of Lineatriton displays homoplasy at two hierarchical levels: (i) with respect to other elongate lineages in the family (convergence), and (ii) within what is currently recognized as a single taxon (parallelism). These evolutionary events are of adaptive significance because to invade the lowland tropics salamanders must be either arboreal or fossorial; the repeated evolution of elongation and attenuation has led to multiple lowland invasions. PMID:11427707

  1. Better than fish on land? Hearing across metamorphosis in salamanders.

    PubMed

    Christensen, Christian Bech; Lauridsen, Henrik; Christensen-Dalsgaard, Jakob; Pedersen, Michael; Madsen, Peter Teglberg

    2015-03-01

    Early tetrapods faced an auditory challenge from the impedance mismatch between air and tissue in the transition from aquatic to terrestrial lifestyles during the Early Carboniferous (350 Ma). Consequently, tetrapods may have been deaf to airborne sounds for up to 100 Myr until tympanic middle ears evolved during the Triassic. The middle ear morphology of recent urodeles is similar to that of early 'lepospondyl' microsaur tetrapods, and experimental studies on their hearing capabilities are therefore useful to understand the evolutionary and functional drivers behind the shift from aquatic to aerial hearing in early tetrapods. Here, we combine imaging techniques with neurophysiological measurements to resolve how the change from aquatic larvae to terrestrial adult affects the ear morphology and sensory capabilities of salamanders. We show that air-induced pressure detection enhances underwater hearing sensitivity of salamanders at frequencies above 120 Hz, and that both terrestrial adults and fully aquatic juvenile salamanders can detect airborne sound. Collectively, these findings suggest that early atympanic tetrapods may have been pre-equipped to aerial hearing and are able to hear airborne sound better than fish on land. When selected for, this rudimentary hearing could have led to the evolution of tympanic middle ears. PMID:25652830

  2. Mechanisms underlying vertebrate limb regeneration: lessons from the salamander.

    PubMed

    Brockes, Jeremy P; Gates, Phillip B

    2014-06-01

    Limb regeneration in adult salamanders proceeds by formation of a mound of progenitor cells called the limb blastema. It provides several pointers for regenerative medicine. These include the role of differentiated cells in the origin of the blastema, the role of regenerating axons of peripheral nerves and the importance of cell specification in conferring morphogenetic autonomy on the blastema. One aspect of regeneration that has received less attention is the ability to undergo multiple episodes without detectable change in the outcome, and with minimal effect of aging. We suggest that, although such pointers are valuable, it is important to understand why salamanders are the only adult tetrapod vertebrates able to regenerate their limbs. Although this remains a controversial issue, the existence of salamander-specific genes that play a significant role in the mechanism of regeneration provides evidence for the importance of local evolution, rather than a purely ancestral mechanism. The three-finger protein called Prod1 is discussed in the present article as an exemplar of this approach. PMID:24849229

  3. Evolutionary history of a complex adaptation: tetrodotoxin resistance in salamanders.

    PubMed

    Hanifin, Charles T; Gilly, William F

    2015-01-01

    Understanding the processes that generate novel adaptive phenotypes is central to evolutionary biology. We used comparative analyses to reveal the history of tetrodotoxin (TTX) resistance in TTX-bearing salamanders. Resistance to TTX is a critical component of the ability to use TTX defensively but the origin of the TTX-bearing phenotype is unclear. Skeletal muscle of TTX-bearing salamanders (modern newts, family: Salamandridae) is unaffected by TTX at doses far in excess of those that block action potentials in muscle and nerve of other vertebrates. Skeletal muscle of non-TTX-bearing salamandrids is also resistant to TTX but at lower levels. Skeletal muscle TTX resistance in the Salamandridae results from the expression of TTX-resistant variants of the voltage-gated sodium channel NaV 1.4 (SCN4a). We identified four substitutions in the coding region of salSCN4a that are likely responsible for the TTX resistance measured in TTX-bearing salamanders and variation at one of these sites likely explains variation in TTX resistance among other lineages. Our results suggest that exaptation has played a role in the evolution of the TTX-bearing phenotype and provide empirical evidence that complex physiological adaptations can arise through the accumulation of beneficial mutations in the coding region of conserved proteins. PMID:25346116

  4. Better than fish on land? Hearing across metamorphosis in salamanders

    PubMed Central

    Christensen, Christian Bech; Lauridsen, Henrik; Christensen-Dalsgaard, Jakob; Pedersen, Michael; Madsen, Peter Teglberg

    2015-01-01

    Early tetrapods faced an auditory challenge from the impedance mismatch between air and tissue in the transition from aquatic to terrestrial lifestyles during the Early Carboniferous (350 Ma). Consequently, tetrapods may have been deaf to airborne sounds for up to 100 Myr until tympanic middle ears evolved during the Triassic. The middle ear morphology of recent urodeles is similar to that of early ‘lepospondyl’ microsaur tetrapods, and experimental studies on their hearing capabilities are therefore useful to understand the evolutionary and functional drivers behind the shift from aquatic to aerial hearing in early tetrapods. Here, we combine imaging techniques with neurophysiological measurements to resolve how the change from aquatic larvae to terrestrial adult affects the ear morphology and sensory capabilities of salamanders. We show that air-induced pressure detection enhances underwater hearing sensitivity of salamanders at frequencies above 120 Hz, and that both terrestrial adults and fully aquatic juvenile salamanders can detect airborne sound. Collectively, these findings suggest that early atympanic tetrapods may have been pre-equipped to aerial hearing and are able to hear airborne sound better than fish on land. When selected for, this rudimentary hearing could have led to the evolution of tympanic middle ears. PMID:25652830

  5. Cannibalistic-morph Tiger Salamanders in unexpected ecological contexts

    USGS Publications Warehouse

    McLean, Kyle I.; Stockwell, Craig A.; Mushet, David M.

    2016-01-01

    Barred tiger salamanders [Ambystoma mavortium (Baird, 1850)] exhibit two trophic morphologies; a typical and a cannibalistic morph. Cannibalistic morphs, distinguished by enlarged vomerine teeth, wide heads, slender bodies, and cannibalistic tendencies, are often found where conspecifics occur at high density. During 2012 and 2013, 162 North Dakota wetlands and lakes were sampled for salamanders. Fifty-one contained A. mavortium populations; four of these contained cannibalistic morph individuals. Two populations with cannibalistic morphs occurred at sites with high abundances of conspecifics. However, the other two populations occurred at sites with unexpectedly low conspecific but high fathead minnow [Pimephales promelas (Rafinesque, 1820)] abundances. Further, no typical morphs were observed in either of these later two populations, contrasting with earlier research suggesting cannibalistic morphs only occur at low frequencies in salamander populations. Another anomaly of all four populations was the occurrence of cannibalistic morphs in permanent water sites, suggesting their presence was due to factors other than faster growth allowing them to occupy ephemeral habitats. Therefore, our findings suggest environmental factors inducing the cannibalistic morphism may be more complex than previously thought.

  6. Detection of an enigmatic plethodontid Salamander using Environmental DNA

    USGS Publications Warehouse

    Pierson, Todd W.; Mckee, Anna; Spear, Stephen F.; Maerz, John C.; Camp, Carlos D.; Glenn, Travis C.

    2016-01-01

    The isolation and identification of environmental DNA (eDNA) offers a non-invasive and efficient method for the detection of rare and secretive aquatic wildlife, and it is being widely integrated into inventory and monitoring efforts. The Patch-Nosed Salamander (Urspelerpes brucei) is a tiny, recently discovered species of plethodontid salamander known only from headwater streams in a small region of Georgia and South Carolina. Here, we present results of a quantitative PCR-based eDNA assay capable of detecting Urspelerpes in more than 75% of 33 samples from five confirmed streams. We deployed the method at 31 additional streams and located three previously undocumented populations of Urspelerpes. We compare the results of our eDNA assay with our attempt to use aquatic leaf litterbags for the rapid detection of Urspelerpes and demonstrate the relative efficacy of the eDNA assay. We suggest that eDNA offers great potential for use in detecting other aquatic and semi-aquatic plethodontid salamanders.

  7. Distilling Artificial Recombinants from Large Sets of Complete mtDNA Genomes

    PubMed Central

    Kong, Qing-Peng; Salas, Antonio; Sun, Chang; Fuku, Noriyuki; Tanaka, Masashi; Zhong, Li; Wang, Cheng-Ye; Yao, Yong-Gang; Bandelt, Hans-Jürgen

    2008-01-01

    Background Large-scale genome sequencing poses enormous problems to the logistics of laboratory work and data handling. When numerous fragments of different genomes are PCR amplified and sequenced in a laboratory, there is a high immanent risk of sample confusion. For genetic markers, such as mitochondrial DNA (mtDNA), which are free of natural recombination, single instances of sample mix-up involving different branches of the mtDNA phylogeny would give rise to reticulate patterns and should therefore be detectable. Methodology/Principal Findings We have developed a strategy for comparing new complete mtDNA genomes, one by one, to a current skeleton of the worldwide mtDNA phylogeny. The mutations distinguishing the reference sequence from a putative recombinant sequence can then be allocated to two or more different branches of this phylogenetic skeleton. Thus, one would search for two (or three) near-matches in the total mtDNA database that together best explain the variation seen in the recombinants. The evolutionary pathway from the mtDNA tree connecting this pair together with the recombinant then generate a grid-like median network, from which one can read off the exchanged segments. Conclusions We have applied this procedure to a large collection of complete human mtDNA sequences, where several recombinants could be distilled by our method. All these recombinant sequences were subsequently corrected by de novo experiments – fully concordant with the predictions from our data-analytical approach. PMID:18714389

  8. Genome-scale phylogenetic function annotation of large and diverse protein families

    PubMed Central

    Engelhardt, Barbara E.; Jordan, Michael I.; Srouji, John R.; Brenner, Steven E.

    2011-01-01

    The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. Here we present a revised approach (SIFTER version 2.0) that enables annotations on a genomic scale. SIFTER 2.0 produces equivalently precise predictions compared to the earlier version on a carefully studied family and on a collection of 100 protein families. We have added an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0%, and 5.7% of these proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available at http://sifter.berkeley.edu. PMID:21784873

  9. Biological consequences of ancient gene acquisition and duplication in the large genome soil bacterium, ""solibacter usitatus"" strain Ellin6076

    SciTech Connect

    Challacombe, Jean F; Eichorst, Stephanie A; Xie, Gary; Kuske, Cheryl R; Hauser, Loren; Land, Miriam

    2009-01-01

    Bacterial genome sizes range from ca. 0.5 to 10Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Sequenced genomes of strains in the phylum Acidobacteria revealed that 'Solibacter usistatus' strain Ellin6076 harbors a 9.9 Mb genome. This large genome appears to have arisen by horizontal gene transfer via ancient bacteriophage and plasmid-mediated transduction, as well as widespread small-scale gene duplications. This has resulted in an increased number of paralogs that are potentially ecologically important (ecoparalogs). Low amino acid sequence identities among functional group members and lack of conserved gene order and orientation in the regions containing similar groups of paralogs suggest that most of the paralogs were not the result of recent duplication events. The genome sizes of cultured subdivision 1 and 3 strains in the phylum Acidobacteria were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 1 were estimated to have smaller genome sizes ranging from ca. 2.0 to 4.8 Mb, whereas members of subdivision 3 had slightly larger genomes, from ca. 5.8 to 9.9 Mb. It is hypothesized that the large genome of strain Ellin6076 encodes traits that provide a selective metabolic, defensive and regulatory advantage in the variable soil environment.

  10. A Roadmap for Natural Product Discovery Based on Large-Scale Genomics and Metabolomics

    PubMed Central

    Doroghazi, James R.; Albright, Jessica C.; Goering, Anthony W.; Ju, Kou-San; Haines, Robert R.; Tchalukov, Konstantin A.; Labeda, David P.; Kelleher, Neil L.; Metcalf, William W.

    2014-01-01

    Actinobacteria encode a wealth of natural product biosynthetic gene clusters (NPGCs), whose systematic study is complicated by numerous repetitive motifs. By combining several metrics we developed a method for global classification of these gene clusters into families (GCFs) and analyzed the biosynthetic capacity of Actinobacteria in 830 genome sequences, including 344 obtained for this project. The GCF network, comprised of 11,422 gene clusters grouped into 4,122 GCFs, was validated in hundreds of strains by correlating confident mass spectrometric detection of known small molecules with the presence/absence of their established biosynthetic gene clusters. The method also linked previously unassigned GCFs to known natural products, an approach that will enable de novo, bioassay-free discovery of novel natural products using large data sets. Extrapolation from the 830-genome dataset reveals that Actinobacteria encode hundreds of thousands of future drug leads, while the strong correlation between phylogeny and GCFs frames a roadmap to efficiently access them. PMID:25262415

  11. Phylogeography and evolution of the Red Salamander (Pseudotriton ruber).

    PubMed

    Folt, Brian; Garrison, Nicole; Guyer, Craig; Rodriguez, Juanita; Bond, Jason E

    2016-05-01

    Phylogeographic studies frequently result in the elevation of subspecific taxa to species given monophyly, or the synonymy of subspecies that are not monophyletic. However, given limited or incongruent datasets, retention of subspecies can be useful to describe hypothesized incipient species or to illustrate interesting biological phenomena driving morphological diversity. Four subspecific taxa have been used to describe largely allopatric geographic variation within the species Pseudotriton ruber, a plethodontid salamander occupying stream and spring habitats across eastern North America: P. r. vioscai occurs in lowland Coastal Plain habitats, while P. r. ruber, P. r. nitidus, and P. r. schencki occupy upland regions in and around the Appalachian Mountains. Pseudotriton ruber co-occurs through its distribution with the aposematic newt Notophthalmus viridescens, and both species are hypothesized to be part of a Müllerian mimicry complex. In this study, we sequenced regions of two mitochondrial (cytochrome b, NADH dehydrogenase subunit 2) and one single copy nuclear protein-coding gene (pro-opiomelanocortin) from individuals sampled across much of the distribution of P. ruber and then used maximum-likelihood and Bayesian phylogenetic inference to test the monophyly of subspecies, reconstruct biogeographic history, and make inferences about morphological evolution. Phylogeographic hypotheses from mitochondrial and nuclear datasets described structure among populations of P. ruber which separated Coastal Plain and upland Appalachian populations, but subspecies were not monophyletic. Biogeographic reconstruction estimated the ancestor of all populations to have occupied and initially diverged in the Coastal Plain during the Pliocene (∼3.6mya), before one lineage subsequently invaded upland areas of Appalachia. Bold bright coloration of high elevation subspecies P. r. nitidus and P. r. schencki appears to have evolved twice. We hypothesize that the Müllerian mimicry

  12. Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?

    PubMed

    Schiffer, Philipp H; Gravemeyer, Jan; Rauscher, Martina; Wiehe, Thomas

    2016-01-01

    Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR)-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome. We were interested to see whether such a tight clustering is characteristic for ultra large gene families. Our data reconfirm that most gene family inflations are lineage-specific, but we can only identify very few gene clusters. Based on our observations we hypothesise that, beyond a certain size threshold, ultra large gene families continue to proliferate in a mechanism we term "run-away evolution". This process might ultimately lead to the failure of genomic integrity and drive species to extinction. PMID:27509525

  13. Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions

    PubMed Central

    2009-01-01

    Background The highly compacted 2.9-Mb genome of Encephalitozoon cuniculi placed the microsporidia in the spotlight, encoding a mere 2,000 proteins and a highly reduced suite of biochemical pathways. This extreme level of reduction is not universal across the microsporidia, with genomes known to vary up to sixfold in size, suggesting that some genomes may harbor a gene content that is not as reduced as that of Enc. cuniculi. In this study, we present an in-depth survey of the large genome of Octosporea bayeri, a pathogen of Daphnia magna, with an estimated genome size of 24 Mb, in order to shed light on the organization and content of a large microsporidian genome. Results Using Illumina sequencing, 898 Mb of O. bayeri genome sequence was generated, resulting in 13.3 Mb of unique sequence. We annotated a total of 2,174 genes, of which 893 encodes proteins with assigned function. The gene density of the O. bayeri genome is very low on average, but also highly uneven, so gene-dense regions also occur. The data presented here suggest that the O. bayeri proteome is well represented in this analysis and is more complex that that of Enc. cuniculi. Functional annotation of O. bayeri proteins suggests that this species might be less biochemically dependent on its host for its metabolism than its more reduced relatives. Conclusions The combination of the data presented here, together with the imminent annotated genome of Daphnia magna, will provide a wealth of genetic and genomic tools to study host-parasite interactions in an interesting model for pathogenesis. PMID:19807911

  14. Habitat relationships of eastern red-backed salamanders (Plethodon cinereus) in Appalachian grazing systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Altered microclimates and vegetation structure after timber harvest can result in longterm population declines of some Appalachian salamanders. If changes in forest structure following harvest alter woodland salamander habitat quality, conversion of forests to pastures or meadows is believed to resu...

  15. Gene lineages and eastern North American palaeodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex.

    PubMed

    Kozak, Kenneth H; Blaine, Russell A; Larson, Allan

    2006-01-01

    Contemporary North American drainage basins are composites of formerly isolated drainages, suggesting that fragmentation and fusion of palaeodrainage systems may have been an important factor generating current patterns of genetic and species diversity in stream-associated organisms. Here, we combine traditional molecular-phylogenetic, multiple-regression, nested clade, and molecular-demographic analyses to investigate the relationship between phylogeographic variation and the hydrogeological history of eastern North American drainage basins in semiaquatic plethodontid salamanders of the Eurycea bislineata species complex. Four hundred forty-two sequences representing 1108 aligned bases from the mitochondrial genome are reported for the five formally recognized species of the E. bislineata complex and three outgroup taxa. Within the in-group, 270 haplotypes are recovered from 144 sampling locations. Geographic patterns of mtDNA-haplotype coalescence identify 13 putatively independent population-level lineages, suggesting that the current taxonomy of the group underestimates species-level diversity. Spatial and temporal patterns of phylogeographic divergence are strongly associated with historical rather than modern drainage connections, indicating that shifts in major drainage patterns played a pivotal role in the allopatric fragmentation of populations and build-up of lineage diversity in these stream-associated salamanders. More generally, our molecular genetic results corroborate geological and faunistic evidence suggesting that palaeodrainage connections altered by glacial advances and headwater erosion occurring between the mid-Miocene and Pleistocene epochs explain regional patterns of biodiversity in eastern North American streams. PMID:16367840

  16. Reverse engineering and analysis of large genome-scale gene networks

    PubMed Central

    Aluru, Maneesha; Zola, Jaroslaw; Nettleton, Dan; Aluru, Srinivas

    2013-01-01

    Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. To enable fast and accurate reconstruction of large networks, we developed Tool for Inferring Network of Genes (TINGe), a parallel mutual information (MI)-based program. The novel features of our approach include: (i) B-spline-based formulation for linear-time computation of MI, (ii) a novel algorithm for direct permutation testing and (iii) development of parallel algorithms to reduce run-time and facilitate construction of large networks. We assess the quality of our method by comparison with ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and GeneNet and demonstrate its unique capability by reverse engineering the whole-genome network of Arabidopsis thaliana from 3137 Affymetrix ATH1 GeneChips in just 9 min on a 1024-core cluster. We further report on the development of a new software Gene Network Analyzer (GeNA) for extracting context-specific subnetworks from a given set of seed genes. Using TINGe and GeNA, we performed analysis of 241 Arabidopsis AraCyc 8.0 pathways, and the results are made available through the web. PMID:23042249

  17. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection

    PubMed Central

    Xie, Weibo; Wang, Gongwei; Yuan, Meng; Yao, Wen; Lyu, Kai; Zhao, Hu; Yang, Meng; Li, Pingbo; Zhang, Xing; Yuan, Jing; Wang, Quanxiu; Liu, Fang; Dong, Huaxia; Zhang, Lejing; Li, Xinglei; Meng, Xiangzhou; Zhang, Wan; Xiong, Lizhong; He, Yuqing; Wang, Shiping; Yu, Sibin; Xu, Caiguo; Luo, Jie; Li, Xianghua; Xiao, Jinghua; Lian, Xingming; Zhang, Qifa

    2015-01-01

    Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement. PMID:26358652

  18. Evolution of the Australian lungfish (Neoceratodus forsteri) genome: a major role for CR1 and L2 LINE elements.

    PubMed

    Metcalfe, Cushla J; Filée, Jonathan; Germon, Isabelle; Joss, Jean; Casane, Didier

    2012-11-01

    Haploid genomes greater than 25,000 Mb are rare, within the animals only the lungfish and some of the salamanders and crustaceans are known to have genomes this large. There is very little data on the structure of genomes this size. It is known, however, that for animal genomes up to 3,000 Mb, there is in general a good correlation between genome size and the percent of the genome composed of repetitive sequence and that this repetitive component is highly dynamic. In this study, we sampled the Australian lungfish genome using three mini-genomic libraries and found that with very little sequence, the results converged on an estimate of 40% of the genome being composed of recognizable transposable elements (TEs), chiefly from the CR1 and L2 long interspersed nuclear element clades. We further characterized the CR1 and L2 elements in the lungfish genome and show that although most CR1 elements probably represent recent amplifications, the L2 elements are more diverse and are more likely the result of a series of amplifications. We suggest that our sampling method has probably underestimated the recognizable TE content. However, on the basis of the most likely sources of error, we suggest that this very large genome is not largely composed of recently amplified, undetected TEs but may instead include a large component of older degenerate TEs. Based on these estimates, and on Thomson's (Thomson K. 1972. An attempt to reconstruct evolutionary changes in the cellular DNA content of lungfish. J Exp Zool. 180:363-372) inference that in the lineage leading to the extant Australian lungfish, there was massive increase in genome size between 350 and 200 mya, after which the size of the genome changed little, we speculate that the very large Australian lungfish genome may be the result of a massive amplification of TEs followed by a long period with a very low rate of sequence removal and some ongoing TE activity. PMID:22734051

  19. A method for the large scale isolation of high transformation efficiency fungal genomic DNA.

    PubMed

    Zhang, D; Yang, Y; Castlebury, L A; Cerniglia, C E

    1996-12-01

    A procedure for isolation of genomic DNA from the zygomycete Cunninghamella elegans and other filamentous fungi and yeasts is reported. This procedure involves disruption of cells by grinding using dry ice, removal of polysaccharides using cetyltrimethylammonium bromide and by phenol extractions, and precipitation of DNA with isopropanol at room temperature. The isolation method produced large scale (approximate 1 mg DNA/5 g wet cells) and highly purified high molecular mass DNA. Sau3AI partially digested DNA showed high transformation efficiency (> 10(6)/100 ng DNA) when ligated to ZAP-express lambda vector. PMID:8961565

  20. The gradient boosting algorithm and random boosting for genome-assisted evaluation in large data sets.

    PubMed

    González-Recio, O; Jiménez-Montero, J A; Alenda, R

    2013-01-01

    In the next few years, with the advent of high-density single nucleotide polymorphism (SNP) arrays and genome sequencing, genomic evaluation methods will need to deal with a large number of genetic variants and an increasing sample size. The boosting algorithm is a machine-learning technique that may alleviate the drawbacks of dealing with such large data sets. This algorithm combines different predictors in a sequential manner with some shrinkage on them; each predictor is applied consecutively to the residuals from the committee formed by the previous ones to form a final prediction based on a subset of covariates. Here, a detailed description is provided and examples using a toy data set are included. A modification of the algorithm called "random boosting" was proposed to increase predictive ability and decrease computation time of genome-assisted evaluation in large data sets. Random boosting uses a random selection of markers to add a subsequent weak learner to the predictive model. These modifications were applied to a real data set composed of 1,797 bulls genotyped for 39,714 SNP. Deregressed proofs of 4 yield traits and 1 type trait from January 2009 routine evaluations were used as dependent variables. A 2-fold cross-validation scenario was implemented. Sires born before 2005 were used as a training sample (1,576 and 1,562 for production and type traits, respectively), whereas younger sires were used as a testing sample to evaluate predictive ability of the algorithm on yet-to-be-observed phenotypes. Comparison with the original algorithm was provided. The predictive ability of the algorithm was measured as Pearson correlations between observed and predicted responses. Further, estimated bias was computed as the average difference between observed and predicted phenotypes. The results showed that the modification of the original boosting algorithm could be run in 1% of the time used with the original algorithm and with negligible differences in accuracy

  1. Managing Large-Scale Genomic Datasets and Translation into Clinical Practice

    PubMed Central

    2014-01-01

    Summary Objective To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain. Method We provide a synopsis of the articles selected for the IMIA Yearbook 2014, from which we attempt to derive a synthetic overview of current and future activities in the field. A first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section. Each section editor evaluated independently the set of 1,851 articles and 15 articles were retained for peer-review. Results The selection and evaluation process of this Yearbook’s section on Bioinformatics and Translational Informatics yielded three excellent articles regarding data management and genome medicine. In the first article, the authors present VEST (Variant Effect Scoring Tool) which is a supervised machine learning tool for prioritizing variants found in exome sequencing projects that are more likely involved in human Mendelian diseases. In the second article, the authors show how to infer surnames of male individuals by crossing anonymous publicly available genomic data from the Y chromosome and public genealogy data banks. The third article presents a statistical framework called iCluster+ that can perform pattern discovery in integrated cancer genomic data. This framework was able to determine different tumor subtypes in colon cancer. Conclusions The current research activities still attest the continuous convergence of Bioinformatics and Medical Informatics, with a focus this year on large-scale biological, genomic, and Electronic Health Records data. Indeed, there is a need for powerful tools for managing and interpreting complex data, but also a need for user-friendly tools developed for the clinicians in their daily practice. All the recent research and development efforts are contributing to the challenge of impacting clinically the results and even going towards a

  2. Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics

    PubMed Central

    Cherkasov, Artem; Ho Sui, Shannan J; Brunham, Robert C; Jones, Steven JM

    2004-01-01

    Background We establish that the occurrence of protein folds among genomes can be accurately described with a Weibull function. Systems which exhibit Weibull character can be interpreted with reliability theory commonly used in engineering analysis. For instance, Weibull distributions are widely used in reliability, maintainability and safety work to model time-to-failure of mechanical devices, mechanisms, building constructions and equipment. Results We have found that the Weibull function describes protein fold distribution within and among genomes more accurately than conventional power functions which have been used in a number of structural genomic studies reported to date. It has also been found that the Weibull reliability parameter β for protein fold distributions varies between genomes and may reflect differences in rates of gene duplication in evolutionary history of organisms. Conclusions The results of this work demonstrate that reliability analysis can provide useful insights and testable predictions in the fields of comparative and structural genomics. PMID:15274750

  3. A new tool called DISSECT for analysing large genomic data sets using a Big Data approach

    PubMed Central

    Canela-Xandri, Oriol; Law, Andy; Gray, Alan; Woolliams, John A.; Tenesa, Albert

    2015-01-01

    Large-scale genetic and genomic data are increasingly available and the major bottleneck in their analysis is a lack of sufficiently scalable computational tools. To address this problem in the context of complex traits analysis, we present DISSECT. DISSECT is a new and freely available software that is able to exploit the distributed-memory parallel computational architectures of compute clusters, to perform a wide range of genomic and epidemiologic analyses, which currently can only be carried out on reduced sample sizes or under restricted conditions. We demonstrate the usefulness of our new tool by addressing the challenge of predicting phenotypes from genotype data in human populations using mixed-linear model analysis. We analyse simulated traits from 470,000 individuals genotyped for 590,004 SNPs in ∼4 h using the combined computational power of 8,400 processor cores. We find that prediction accuracies in excess of 80% of the theoretical maximum could be achieved with large sample sizes. PMID:26657010

  4. A new tool called DISSECT for analysing large genomic data sets using a Big Data approach.

    PubMed

    Canela-Xandri, Oriol; Law, Andy; Gray, Alan; Woolliams, John A; Tenesa, Albert

    2015-01-01

    Large-scale genetic and genomic data are increasingly available and the major bottleneck in their analysis is a lack of sufficiently scalable computational tools. To address this problem in the context of complex traits analysis, we present DISSECT. DISSECT is a new and freely available software that is able to exploit the distributed-memory parallel computational architectures of compute clusters, to perform a wide range of genomic and epidemiologic analyses, which currently can only be carried out on reduced sample sizes or under restricted conditions. We demonstrate the usefulness of our new tool by addressing the challenge of predicting phenotypes from genotype data in human populations using mixed-linear model analysis. We analyse simulated traits from 470,000 individuals genotyped for 590,004 SNPs in ∼4 h using the combined computational power of 8,400 processor cores. We find that prediction accuracies in excess of 80% of the theoretical maximum could be achieved with large sample sizes. PMID:26657010

  5. Cross-Platform Assessment of Genomic Imbalance Confirms the Clinical Relevance of Genomic Complexity and Reveals Loci with Potential Pathogenic Roles in Diffuse Large B-Cell Lymphoma

    PubMed Central

    Dias, Lizalynn M.; Thodima, Venkata; Friedman, Julia; Ma, Charles; Guttapalli, Asha; Mendiratta, Geetu; Siddiqi, Imran N.; Syrbu, Sergei; Chaganti, R. S. K.; Houldsworth, Jane

    2016-01-01

    Genomic copy number alterations (CNAs) in diffuse large B-cell lymphoma (DLBCL) have roles in disease pathogenesis but overall clinical relevance remains unclear. Herein, an unbiased algorithm was uniformly applied across three genome profiling datasets comprising 392 newly-diagnosed DLBCL specimens that defined 32 overlapping CNAs, involving 36 minimal common regions (MCRs). Scoring criteria were established for 50 aberrations within the MCRs while considering peak gains/losses. Application of these criteria to independent datasets revealed novel candidate genes with coordinated expression, such as CNOT2, potentially with pathogenic roles. No one single aberration significantly associated with patient outcome across datasets, but genomic complexity, defined by imbalance in more than one MCR, significantly portended adverse outcome in two of three independent datasets. Thus, the standardized scoring of CNAs currently developed can be uniformly applied across platforms, affording robust validation of genomic imbalance and complexity in DLBCL and overall clinical utility as biomarkers of patient outcome. PMID:26294112

  6. Gene map of large yellow croaker (Larimichthys crocea) provides insights into teleost genome evolution and conserved regions associated with growth

    PubMed Central

    Xiao, Shijun; Wang, Panpan; Zhang, Yan; Fang, Lujing; Liu, Yang; Li, Jiong-Tang; Wang, Zhi-Yong

    2015-01-01

    The genetic map of a species is essential for its whole genome assembly and can be applied to the mapping of important traits. In this study, we performed RNA-seq for a family of large yellow croakers (Larimichthys crocea) and constructed a high-density genetic map. In this map, 24 linkage groups comprised 3,448 polymorphic SNP markers. Approximately 72.4% (2,495) of the markers were located in protein-coding regions. Comparison of the croaker genome with those of five model fish species revealed that the croaker genome structure was closer to that of the medaka than to the remaining four genomes. Because the medaka genome preserves the teleost ancestral karyotype, this result indicated that the croaker genome might also maintain the teleost ancestral genome structure. The analysis also revealed different genome rearrangements across teleosts. QTL mapping and association analysis consistently identified growth-related QTL regions and associated genes. Orthologs of the associated genes in other species were demonstrated to regulate development, indicating that these genes might regulate development and growth in croaker. This gene map will enable us to construct the croaker genome for comparative studies and to provide an important resource for selective breeding of croaker. PMID:26689832

  7. Telocytes in ileum of the Chinese giant salamander: ultrastructural evidence.

    PubMed

    Zhang, Hui; Zhong, Shengwei; Ge, Tingting; Peng, Shasha; Yu, Pengcheng; Zhou, Zuohong; Guo, Xiaoquan

    2016-03-01

    Telocytes (TCs) and their telopodes (Tps) have been found in various organs of many mammals, including in lower animals. However, knowledge of TCs in lower animals is still very limited. This study identified TCs and their Tps in the ileum of the Chinese giant salamander, Andrias davidianus (Amphibia: Caudata), by transmission electron microscopy. The TCs/Tps were found near epithelial cells, glandular cells and unmyelinated nerve fibres. Moreover, exosomes were also found to be present in between TCs/Tps and these cells. PMID:26805522

  8. Detecting a hierarchical genetic population structure: the case study of the Fire Salamander (Salamandra salamandra) in Northern Italy

    PubMed Central

    Pisa, Giulia; Orioli, Valerio; Spilotros, Giulia; Fabbri, Elena; Randi, Ettore; Bani, Luciano

    2015-01-01

    The multistep method here applied in studying the genetic structure of a low dispersal and philopatric species, such as the Fire Salamander Salamandra salamandra, was proved to be effective in identifying the hierarchical structure of populations living in broad-leaved forest ecosystems in Northern Italy. In this study, 477 salamander larvae, collected in 28 sampling populations (SPs) in the Prealpine and in the foothill areas of Northern Italy, were genotyped at 16 specie-specific microsatellites. SPs showed a significant overall genetic variation (Global FST = 0.032, P < 0.001). The genetic population structure was assessed by using STRUCTURE 2.3.4. We found two main genetic groups, one represented by SPs inhabiting the Prealpine belt, which maintain connections with those of the Eastern foothill lowland (PEF), and a second group with the SPs of the Western foothill lowland (WF). The two groups were significantly distinct with a Global FST of 0.010 (P < 0.001). While the first group showed a moderate structure, with only one divergent SP (Global FST = 0.006, P < 0.001), the second group proved more structured being divided in four clusters (Global FST = 0.017, P = 0.058). This genetic population structure should be due to the large conurbations and main roads that separate the WF group from the Prealpine belt and the Eastern foothill lowland. The adopted methods allowed the analysis of the genetic population structure of Fire Salamander from wide to local scale, identifying different degrees of genetic divergence of their populations derived from forest fragmentation induced by urban and infrastructure sprawl. PMID:25691995

  9. Detecting a hierarchical genetic population structure: the case study of the Fire Salamander (Salamandra salamandra) in Northern Italy.

    PubMed

    Pisa, Giulia; Orioli, Valerio; Spilotros, Giulia; Fabbri, Elena; Randi, Ettore; Bani, Luciano

    2015-02-01

    The multistep method here applied in studying the genetic structure of a low dispersal and philopatric species, such as the Fire Salamander Salamandra salamandra, was proved to be effective in identifying the hierarchical structure of populations living in broad-leaved forest ecosystems in Northern Italy. In this study, 477 salamander larvae, collected in 28 sampling populations (SPs) in the Prealpine and in the foothill areas of Northern Italy, were genotyped at 16 specie-specific microsatellites. SPs showed a significant overall genetic variation (Global F ST = 0.032, P < 0.001). The genetic population structure was assessed by using STRUCTURE 2.3.4. We found two main genetic groups, one represented by SPs inhabiting the Prealpine belt, which maintain connections with those of the Eastern foothill lowland (PEF), and a second group with the SPs of the Western foothill lowland (WF). The two groups were significantly distinct with a Global F ST of 0.010 (P < 0.001). While the first group showed a moderate structure, with only one divergent SP (Global F ST = 0.006, P < 0.001), the second group proved more structured being divided in four clusters (Global F ST = 0.017, P = 0.058). This genetic population structure should be due to the large conurbations and main roads that separate the WF group from the Prealpine belt and the Eastern foothill lowland. The adopted methods allowed the analysis of the genetic population structure of Fire Salamander from wide to local scale, identifying different degrees of genetic divergence of their populations derived from forest fragmentation induced by urban and infrastructure sprawl. PMID:25691995

  10. Earthworms, as ecosystem engineers, influence multiple aspects of a salamander's ecology.

    PubMed

    Ransom, Tami S

    2011-03-01

    Ecosystem engineers create habitat that can be used by other species in multiple ways, such as refugees from predators, places to breed, or areas with increased prey resources. I conducted a series of enclosure experiments to: (1) determine if salamanders use earthworm burrows, and (2) examine the potential influence of earthworm burrow use and indirect effects on salamander intra- and interspecific competition, predator avoidance, and seasonal performance. I found that one species of woodland salamander, Plethodon cinereus, used earthworm burrows 50% of the time when burrows were present. Neither adults nor juveniles of the congeneric P. glutinosus used earthworm burrows. Intraspecific, but not interspecific, competition by P. cinereus affected salamander behavior when earthworms were absent, with P. cinereus found under cover objects >70% of the time when alone or with a P. glutinosus, but only 40% of the time when with another P. cinereus. When earthworms were present, the behavior of P. cinereus was similar across salamander treatments. Earthworms decreased the amount of leaf litter and microinvertebrates, although this did not affect salamander mass. In subsequent experiments using only P. cinereus, the refuge provided by earthworm burrows increased the survival of P. cinereus over the winter and allowed P. cinereus to avoid being consumed by the common garter snake (Thamnophis sirtalis). Because earthworm burrows provide a refuge for P. cinereus during intraspecific encounters, in the presence of a predator and over the winter, they may serve as an important belowground-aboveground linkage in eastern forests where salamanders are common. PMID:20848134

  11. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0

    PubMed Central

    2010-01-01

    Background The growing whole genome sequence databases necessitate the development of user-friendly software tools to mine these data. Web-based tools are particularly useful to wet-bench biologists as they enable platform-independent analysis of sequence data, without having to perform complex programming tasks and software compiling. Findings GeneOrder4.0 is a web-based "on-the-fly" synteny and gene order analysis tool for comparative bacterial genomics (ca. 8 Mb). It enables the visualization of synteny by plotting protein similarity scores between two genomes and it also provides visual annotation of "hypothetical" proteins from older archived genomes based on more recent annotations. Conclusions The web-based software tool GeneOrder4.0 is a user-friendly application that has been updated to allow the rapid analysis of synteny and gene order in large bacterial genomes. It is developed with the wet-bench researcher in mind. PMID:20178631

  12. Genomic mechanisms underlying PARK2 large deletions identified in a cohort of patients with PD

    PubMed Central

    Morais, Sara; Bastos-Ferreira, Rita; Sequeiros, Jorge

    2016-01-01

    Objectives: To identify the genomic mechanisms that result in PARK2 large gene deletions. Methods: We conducted mutation screening using PCR amplification of PARK2-coding regions and exon-intron boundaries, followed by sequencing to evaluate a large series of 244 unrelated Portuguese patients with symptoms of Parkinson disease. For the detection of large gene rearrangements, we performed multiplex ligation-dependent probe amplification, followed by long-range PCR and sequencing to map deletion breakpoints. Results: We identified biallelic pathogenic parkin mutations in 40 of the 244 patients. There were 18 different mutations, some of them novel. This study included mapping of 17 deletion breakpoints showing that nonhomologous end joining is the most common mechanism responsible for these gene rearrangements. None of these deletion breakpoints were previously described, and only one was present in 2 unrelated families, indicating that most of the deletions result from independent events. Conclusions: The c.155delA mutation is highly prevalent in the Portuguese population (62.5% of the cases). Large deletions were present in 42.5% of the patients. We present the largest study on the molecular mechanisms that mediate PARK2 deletions in a homogeneous population. PMID:27182553

  13. Differentially expressed genes match bill morphology and plumage despite largely undifferentiated genomes in a Holarctic songbird.

    PubMed

    Mason, Nicholas A; Taylor, Scott A

    2015-06-01

    Understanding the patterns and processes that contribute to phenotypic diversity and speciation is a central goal of evolutionary biology. Recently, high-throughput sequencing has provided unprecedented phylogenetic resolution in many lineages that have experienced rapid diversification. The Holarctic redpoll finches (Genus: Acanthis) provide an intriguing example of a recent, phenotypically diverse lineage; traditional sequencing and genotyping methods have failed to detect any genetic differences between currently recognized species, despite marked variation in plumage and morphology within the genus. We examined variation among 20 712 anonymous single nucleotide polymorphisms (SNPs) distributed throughout the redpoll genome in combination with 215 825 SNPs within the redpoll transcriptome, gene expression data and ecological niche modelling to evaluate genetic and ecological differentiation among currently recognized species. Expanding upon previous findings, we present evidence of (i) largely undifferentiated genomes among currently recognized species; (ii) substantial niche overlap across the North American Acanthis range; and (iii) a strong relationship between polygenic patterns of gene expression and continuous phenotypic variation within a sample of redpolls from North America. The patterns we report may be caused by high levels of ongoing gene flow between polymorphic populations, incomplete lineage sorting accompanying very recent or ongoing divergence, variation in cis-regulatory elements, or phenotypic plasticity, but do not support a scenario of prolonged isolation and subsequent secondary contact. Together, these findings highlight ongoing theoretical and computational challenges presented by recent, rapid bouts of phenotypic diversification and provide new insight into the evolutionary dynamics of an intriguing, understudied non-model system. PMID:25735539

  14. Large-scale analysis of tandem repeat variability in the human genome

    PubMed Central

    Duitama, Jorge; Zablotskaya, Alena; Gemayel, Rita; Jansen, An; Belet, Stefanie; Vermeesch, Joris R.; Verstrepen, Kevin J.; Froyen, Guy

    2014-01-01

    Tandem repeats are short DNA sequences that are repeated head-to-tail with a propensity to be variable. They constitute a significant proportion of the human genome, also occurring within coding and regulatory regions. Variation in these repeats can alter the function and/or expression of genes allowing organisms to swiftly adapt to novel environments. Importantly, some repeat expansions have also been linked to certain neurodegenerative diseases. Therefore, accurate sequencing of tandem repeats could contribute to our understanding of common phenotypic variability and might uncover missing genetic factors in idiopathic clinical conditions. However, despite long-standing evidence for the functional role of repeats, they are largely ignored because of technical limitations in sequencing, mapping and typing. Here, we report on a novel capture technique and data filtering protocol that allowed simultaneous sequencing of thousands of tandem repeats in the human genomes of a three generation family using GS-FLX-plus Titanium technology. Our results demonstrated that up to 7.6% of tandem repeats in this family (4% in coding sequences) differ from the reference sequence, and identified a de novo variation in the family tree. The method opens new routes to look at this underappreciated type of genetic variability, including the identification of novel disease-related repeats. PMID:24682812

  15. The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

    PubMed Central

    Brouard, Jean-Simon; Otis, Christian; Lemieux, Claude; Turmel, Monique

    2010-01-01

    The Chlorophyceae, an advanced class of chlorophyte green algae, comprises five lineages that form two major clades (Chlamydomonadales + Sphaeropleales and Oedogoniales + Chaetopeltidales + Chaetophorales). The four complete chloroplast DNA (cpDNA) sequences currently available for chlorophyceans uncovered an extraordinarily fluid genome architecture as well as many structural features distinguishing this group from other green algae. We report here the 521,168-bp cpDNA sequence from a member of the Chaetopeltidales (Floydiella terrestris), the sole chlorophycean lineage not previously sampled for chloroplast genome analysis. This genome, which contains 97 conserved genes and 26 introns (19 group I and 7 group II introns), is the largest chloroplast genome ever sequenced. Intergenic regions account for 77.8% of the genome size and are populated by short repeats. Numerous genomic features are shared with the cpDNA of the chaetophoralean Stigeoclonium helveticum, notably the absence of a large inverted repeat and the presence of unique gene clusters and trans-spliced group II introns. Although only one of the Floydiella group I introns encodes a homing endonuclease gene, our finding of five free-standing reading frames having similarity with such genes suggests that chloroplast group I introns endowed with mobility were once more abundant in the Floydiella lineage. Parsimony analysis of structural genomic features and phylogenetic analysis of chloroplast sequence data unambiguously resolved the Oedogoniales as sister to the Chaetopeltidales and Chaetophorales. An evolutionary scenario of the molecular events that shaped the chloroplast genome in the Chlorophyceae is presented. PMID:20624729

  16. Extreme negative temperatures and body mass loss in the Siberian salamander (Salamandrella keyserlingii, amphibia, hynobiidae).

    PubMed

    Berman, D I; Meshcheryakova, E N; Bulakhova, N A

    2016-05-01

    Frozen Siberian salamander safely tolerates long (45 days) stay at-35°C. Short-term (3 days) cooling down to-50°C was tolerable for 40% of adult individuals; down to-55°C, for 80% of the underyearlings. Generally, the salamanders lose about 28% of the body mass during the pre-hibernating period (before winter, at temperatures as low as 0°C) and during the process of freezing (as low as-5°C). The body weight remained constant upon further cooling (to-35°C). The frozen salamanders have no physiological mechanisms protecting from sublimation. PMID:27411827

  17. A field test of the effect of acidic rain on ion balance in a woodland salamander

    SciTech Connect

    Frisbie, M.P.; Wyman, R.L. )

    1994-06-01

    Earlier laboratory studies demonstrated that red-backed salamanders, Plethodon cinereus, are susceptible to osmotic disruption by low pH substrates. In natural systems, however, acidic input from precipitation may be mediated by soils before it impacts salamanders. We tested the effect of acidic rain on sodium balance in salamanders by confining individuals in enclosure in two forest types (hemlock, beech) for 34 d. Enclosures received artificial rain of either pH 3 or 5 every 3-4 d. Soils inside enclosures in the hemlock forest were more acidic than those in the beech forest at the outset. At termination, [H[sup +

  18. Conservation genetics of the endangered Shenandoah salamander (Plethodon shenandoah, Plethodontidae)

    USGS Publications Warehouse

    Carpenter, D.W.; Jung, R.E.; Sites, J.W., Jr.

    2001-01-01

    The Shenandoah salamander (Plethodon shenandoah) is restricted to three isolated talus outcrops in Shenandoah National Park, VA, USA and has one of the smallest ranges of any tetrapod vertebrate. This species was listed as endangered under the US Endangered Species Act in 1989 over concern that direct competition with the red-backed salamander (Plethodon cinereus), successional habitat changes, and human impacts may cause its decline and possible extinction. We address two issues herein: (1) whether extensive introgression (through long-term hybridization) is present between the two species and threatens the survival of P. shenandoah, and (2) the level of population structure within P. shenandoah. We provide evidence from mtDNA haplotypes that shows no genetic differentiation among the three isolates of P. shenandoah, suggesting that their fragmentation is a geologically recent event, and/or that the isolates are still connected by occasional gene flow. There is also no evidence for extensive introgression of alleles in either direction between P. cinereus and P. shenandoah, which suggests that P. shenandoah may not be in danger of being genetically swamped out through hybridization with P. cinereus.

  19. Elevated plasma corticosterone increases metabolic rate in a terrestrial salamander.

    PubMed

    Wack, Corina L; DuRant, Sarah E; Hopkins, William A; Lovern, Matthew B; Feldhoff, Richard C; Woodley, Sarah K

    2012-02-01

    Plasma glucocorticoid hormones (GCs) increase intermediary metabolism, which may be reflected in whole-animal metabolic rate. Studies in fish, birds, and reptiles have shown that GCs may alter whole-animal energy expenditure, but results are conflicting and often involve GC levels that are not physiologically relevant. A previous study in red-legged salamanders found that male courtship pheromone increased plasma corticosterone (CORT; the primary GC in amphibians) concentrations in males, which could elevate metabolic processes to sustain courtship behaviors. To understand the possible metabolic effect of elevated plasma CORT, we measured the effects of male courtship pheromone and exogenous application of CORT on oxygen consumption in male red-legged salamanders (Plethodon shermani). Exogenous application of CORT elevated plasma CORT to physiologically relevant levels. Compared to treatment with male courtship pheromone and vehicle, treatment with CORT increased oxygen consumption rates for several hours after treatment, resulting in 12% more oxygen consumed (equivalent to 0.33 J) during our first 2h sampling period. Contrary to our previous work, treatment with pheromone did not increase plasma CORT, perhaps because subjects used in this study were not in breeding condition. Pheromone application did not affect respiration rates. Our study is one of the few to evaluate the influence of physiologically relevant elevations in CORT on whole-animal metabolism in vertebrates, and the first to show that elevated plasma CORT increases metabolism in an amphibian. PMID:22047668

  20. Strong selection barriers explain microgeographic adaptation in wild salamander populations.

    PubMed

    Richardson, Jonathan L; Urban, Mark C

    2013-06-01

    Microgeographic adaptation occurs when populations evolve divergent fitness advantages across the spatial scales at which focal organisms regularly disperse. Although an increasing number of studies find evidence for microgeographic adaptation, the underlying causes often remain unknown. Adaptive divergence requires some combination of limited gene flow and strong divergent natural selection among populations. In this study, we estimated the relative influence of selection, gene flow, and the spatial arrangement of populations in shaping patterns of adaptive divergence in natural populations of the spotted salamander (Ambystoma maculatum). Within the study region, A. maculatum co-occur with the predatory marbled salamander (Ambystoma opacum) in some ponds, and past studies have established a link between predation risk and adaptive trait variation in A. maculatum. Using 14 microsatellite loci, we found a significant pattern of genetic divergence among A. maculatum populations corresponding to levels of A. opacum predation risk. Additionally, A. maculatum foraging rate was strongly associated with predation risk, genetic divergence, and the spatial relationship of ponds on the landscape. Our results indicate the sorting of adaptive genotypes by selection regime and strongly suggest that substantial selective barriers operate against gene flow. This outcome suggests that microgeographic adaptation in A. maculatum is possible because strong antagonistic selection quickly eliminates maladapted phenotypes despite ongoing and substantial immigration. Increasing evidence for microgeographic adaptation suggests a strong role for selective barriers in counteracting the homogenizing influence of gene flow. PMID:23730765

  1. Spermatogenic cycle of a plethodontid salamander, Eurycea longicauda (Amphibia, Urodela)

    PubMed Central

    Siegel, Dustin S; Alvino, Sam; Trauth, Stanley E; Sever, David M; Gribbins, Kevin M

    2014-01-01

    Previous investigators have described the spermatogenic cycles of numerous species of plethodontid salamanders. Most studies describe a fairly stereotypical cycle with meiotic divisions of spermatogenesis commencing in the spring/summer. However, many studies lack details obtainable from histological examination and/or testicular squashes and, instead, provide only mensural data from the testes. Studies that lacked microscopic evaluation often revealed spermatogenic cycles that varied greatly from that of the stereotypical cycle with meiotic divisions commencing in the fall/winter. Those studies hamper comparisons between the spermatogenic cycles of different species and their environments, as they do not provide a correlation between testicular size and any aspect of the spermatogenic cycle. In the following manuscript, we elucidate the spermatogenic cycle of Eurycea longicauda longicauda in an effort to outline an appropriate protocol for analyzing spermatogenesis in salamanders that will facilitate future comparative studies. Like many Nearctic plethodontids, E. l. longicauda exhibits a meiotic wave that travels through the testes during the summer; this process is followed by spermiogenesis, spermiation, and recrudescence in the fall, winter, and spring. PMID:26413402

  2. Population dynamics and regulation in the cave salamander Speleomantes strinatii

    NASA Astrophysics Data System (ADS)

    Salvidio, Sebastiano

    2007-05-01

    Time series analysis has been used to evaluate the mechanisms regulating population dynamics of mammals and insects, but has been rarely applied to amphibian populations. In this study, the influence of endogenous (density-dependent) and exogenous (density-independent) factors regulating population dynamics of the terrestrial plethodontid salamander Speleomantes strinatii was analysed by means of time series and multiple regression analyses. During the period 1993 2005, S. strinatii population abundance, estimated by a standardised temporary removal method, displayed relatively low fluctuations, and the autocorrelation function (ACF) analysis showed that the time series had a noncyclic structure. The partial rate correlation function (PRCF) indicated that a strong first-order negative feedback dominated the endogenous dynamics. Stepwise multiple regression analysis showed that the only climatic factor influencing population growth rate was the minimum winter temperature. Thus, at least during the study period, endogenous, density-dependent negative feedback was the main factor affecting the growth rate of the salamander population, whereas stochastic environmental variables, such as temperature and rainfall, seemed to play a minor role in regulation. These results stress the importance of considering both exogenous and endogenous factors when analysing amphibian long-term population dynamics.

  3. Sensitivity of two salamander (Ambystoma) species to ultraviolet radiation

    USGS Publications Warehouse

    Calfee, R.D.; Bridges, C.M.; Little, E.E.

    2006-01-01

    Increased ultraviolet-B (UV-B) radiation reaching the Earth's surface has been implicated in amphibian declines. Recent studies have shown that many amphibian species have differences in sensitivity depending on developmental stage. Embryos and larvae of Ambystoma maculatum (Spotted Salamander) and larvae of Ambystoma talpoideum (Mole Salamander) were exposed to five simulated UV-B treatments in controlled laboratory experiments to determine the relative sensitivity of different lifestages. Hatching success of the embryos exceeded 95% in all treatments; however, the larvae of both species exhibited greater sensitivity to UV-B exposure. Older larvae of A. maculatum that were not exposed to UV-B as embryos were more sensitive than larvae that had hatched during exposure to UV-B. Growth of surviving larvae of A. maculatum was significantly reduced as UV-B intensity increased, whereas growth of A. talpoideum was unaffected. These results were compared to ambient UV-B conditions in natural environments. It appears that the embryo stage is relatively unaffected by UV-B levels observed in natural habitats, probably because of protection from vegetation, organic matter in the water column, oviposition depth, and egg jelly. The larval stage of these species may be at greater risk, particularly if there is an increase in UV-B radiation exposure caused by increases in water clarity and/or decreases in dissolved organic carbon.

  4. Software engineering the mixed model for genome-wide association studies on large samples.

    PubMed

    Zhang, Zhiwu; Buckler, Edward S; Casstevens, Terry M; Bradbury, Peter J

    2009-11-01

    Mixed models improve the ability to detect phenotype-genotype associations in the presence of population stratification and multiple levels of relatedness in genome-wide association studies (GWAS), but for large data sets the resource consumption becomes impractical. At the same time, the sample size and number of markers used for GWAS is increasing dramatically, resulting in greater statistical power to detect those associations. The use of mixed models with increasingly large data sets depends on the availability of software for analyzing those models. While multiple software packages implement the mixed model method, no single package provides the best combination of fast computation, ability to handle large samples, flexible modeling and ease of use. Key elements of association analysis with mixed models are reviewed, including modeling phenotype-genotype associations using mixed models, population stratification, kinship and its estimation, variance component estimation, use of best linear unbiased predictors or residuals in place of raw phenotype, improving efficiency and software-user interaction. The available software packages are evaluated, and suggestions made for future software development. PMID:19933212

  5. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans

    PubMed Central

    Shoguchi, Eiichi; Shinzato, Chuya; Hisata, Kanako; Satoh, Nori; Mungpakdee, Sutada

    2015-01-01

    Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures. PMID:26199191

  6. The Large Mitochondrial Genome of Symbiodinium minutum Reveals Conserved Noncoding Sequences between Dinoflagellates and Apicomplexans.

    PubMed

    Shoguchi, Eiichi; Shinzato, Chuya; Hisata, Kanako; Satoh, Nori; Mungpakdee, Sutada

    2015-08-01

    Even though mitochondrial genomes, which characterize eukaryotic cells, were first discovered more than 50 years ago, mitochondrial genomics remains an important topic in molecular biology and genome sciences. The Phylum Alveolata comprises three major groups (ciliates, apicomplexans, and dinoflagellates), the mitochondrial genomes of which have diverged widely. Even though the gene content of dinoflagellate mitochondrial genomes is reportedly comparable to that of apicomplexans, the highly fragmented and rearranged genome structures of dinoflagellates have frustrated whole genomic analysis. Consequently, noncoding sequences and gene arrangements of dinoflagellate mitochondrial genomes have not been well characterized. Here we report that the continuous assembled genome (∼326 kb) of the dinoflagellate, Symbiodinium minutum, is AT-rich (∼64.3%) and that it contains three protein-coding genes. Based upon in silico analysis, the remaining 99% of the genome comprises transcriptomic noncoding sequences. RNA edited sites and unique, possible start and stop codons clarify conserved regions among dinoflagellates. Our massive transcriptome analysis shows that almost all regions of the genome are transcribed, including 27 possible fragmented ribosomal RNA genes and 12 uncharacterized small RNAs that are similar to mitochondrial RNA genes of the malarial parasite, Plasmodium falciparum. Gene map comparisons show that gene order is only slightly conserved between S. minutum and P. falciparum. However, small RNAs and intergenic sequences share sequence similarities with P. falciparum, suggesting that the function of noncoding sequences has been preserved despite development of very different genome structures. PMID:26199191

  7. Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.

    PubMed

    Paux, Etienne; Legeai, Fabrice; Guilhot, Nicolas; Adam-Blondon, Anne-Françoise; Alaux, Michaël; Salse, Jérôme; Sourdille, Pierre; Leroy, Philippe; Feuillet, Catherine

    2008-02-01

    Anchored physical maps represent essential frameworks for map-based cloning, comparative genomics studies, and genome sequencing projects. High throughput anchoring can be achieved by polymerase chain reaction (PCR) screening of bacterial artificial chromosome (BAC) library pools with molecular markers. However, for large genomes such as wheat, the development of high dimension pools and the number of reactions that need to be performed can be extremely large making the screening laborious and costly. To improve the cost efficiency of anchoring in such large genomes, we have developed a new software named Elephant (electronic physical map anchoring tool) that combines BAC contig information generated by FingerPrinted Contig with results of BAC library pools screening to identify BAC addresses with a minimal amount of PCR reactions. Elephant was evaluated during the construction of a physical map of chromosome 3B of hexaploid wheat. Results show that a one dimensional pool screening can be sufficient to anchor a BAC contig while reducing the number of PCR by 384-fold thereby demonstrating that Elephant is an efficient and cost-effective tool to support physical mapping in large genomes. PMID:18038165

  8. The genomic and physical organization of Ty1-copia-like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms.

    PubMed Central

    Kamm, A; Doudrick, R L; Heslop-Harrison, J S; Schmidt, T

    1996-01-01

    A DNA sequence, TPE1, representing the internal domain of a Ty1-copia retroelement, was isolated from genomic DNA of Pinus elliottii Engelm. var. elliottii (slash pine). Genomic Southern analysis showed that this sequence, carrying partial reverse transcriptase and integrase gene sequences, is highly amplified within the genome of slash pine and part of a dispersed element >4.8 kbp. Fluorescent in situ hybridization to metaphase chromosomes shows that the element is relatively uniformly dispersed over all 12 chromosome pairs and is highly abundant in the genome. It is largely excluded from centromeric regions and intercalary chromosomal sites representing the 18S-5.8S-25S rRNA genes. Southern hybridization with specific DNA probes for the reverse transcriptase gene shows that TPE1 represents a large subgroup of heterogeneous Ty1-copia retrotransposons in Pinus species. Because no TPE1 transcription could be detected, it is most likely an inactive element--at least in needle tissue. Further evidence for inactivity was found in recombinant reverse transcriptase and integrase sequences. The distribution of TPE1 within different gymnosperms that contain Ty1-copia group retrotransposons, as shown by a PCR assay, was investigated by Southern hybridization. The TPE1 family is highly amplified and conserved in all Pinus species analyzed, showing a similar genomic organization in the three- and five-needle pine species investigated. It is also present in spruce, bald cypress (swamp cypress), and in gingko but in fewer copies and a different genomic organization. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8610105

  9. Larval salamanders and channel geomorphology are indicators of hydrologic permanence in forested headwater streams

    EPA Science Inventory

    Regulatory agencies need rapid indicators of hydrologic permanence for jurisdictional determinations of headwater streams. Our study objective was to assess the utility of larval salamander presence and assemblage structure and habitat variables for determining stream permanence ...

  10. SPATIALLY AUTOCORRELATED DEMOGRAPHY AND INTERPOND MIGRATION IN THE CALIFORNIA TIGER SALAMANDER (AMBYSTOME CALIFORNIENSE)

    EPA Science Inventory

    We investigated the metapopulation structure of the California tiger salamander (Ambystoma californiense) using a combination of indirect and direct methods to evaluate two key requirements of modern metapopulation models: 1) that patches support somewhat independent populations ...

  11. Tracing the first step to speciation: ecological and genetic differentiation of a salamander population in a small forest.

    PubMed

    Steinfartz, Sebastian; Weitere, Markus; Tautz, Diethard

    2007-11-01

    Mechanisms and processes of ecologically driven adaptive speciation are best studied in natural situations where the splitting process is still occurring, i.e. before complete reproductive isolation is achieved. Here, we present a case of an early stage of adaptive differentiation under sympatric conditions in the fire salamander, Salamandra salamandra, that allows inferring the underlying processes for the split. Larvae of S. salamandra normally mature in small streams until metamorphosis, but in an old, continuous forest area near Bonn (the Kottenforst), we found salamander larvae not only in small streams but also in shallow ponds, which are ecologically very different from small streams. Common-environment experiments with larvae from both habitat types reveal specific adaptations to these different ecological conditions. Mitochondrial and microsatellite analyses show that the two ecologically differentiated groups also show signs of genetic differentiation. A parallel analysis of animals from a neighbouring much larger forest area (the Eifel), in which larvae mature only in streams, shows no signs of genetic differentiation, indicating that gene flow between ecologically similar types can occur over large distances. Hence, geographical factors cannot explain the differential larval habitat adaptations in the Kottenforst, in particular since adult life and mating of S. salamandra is strictly terrestrial and not associated with larval habitats. We propose therefore that the evolution of these adaptations was coupled with the evolution of cues for assortative mating which would be in line with models of sympatric speciation that suggest a co-evolution of habitat adaptations and associated mating signals. PMID:17877714

  12. Needles: Toward Large-Scale Genomic Prediction with Marker-by-Environment Interaction.

    PubMed

    De Coninck, Arne; De Baets, Bernard; Kourounis, Drosos; Verbosio, Fabio; Schenk, Olaf; Maenhout, Steven; Fostier, Jan

    2016-05-01

    Genomic prediction relies on genotypic marker information to predict the agronomic performance of future hybrid breeds based on trial records. Because the effect of markers may vary substantially under the influence of different environmental conditions, marker-by-environment interaction effects have to be taken into account. However, this may lead to a dramatic increase in the computational resources needed for analyzing large-scale trial data. A high-performance computing solution, called Needles, is presented for handling such data sets. Needles is tailored to the particular properties of the underlying algebraic framework by exploiting a sparse matrix formalism where suited and by utilizing distributed computing techniques to enable the use of a dedicated computing cluster. It is demonstrated that large-scale analyses can be performed within reasonable time frames with this framework. Moreover, by analyzing simulated trial data, it is shown that the effects of markers with a high environmental interaction can be predicted more accurately when more records per environment are available in the training data. The availability of such data and their analysis with Needles also may lead to the discovery of highly contributing QTL in specific environmental conditions. Such a framework thus opens the path for plant breeders to select crops based on these QTL, resulting in hybrid lines with optimized agronomic performance in specific environmental conditions. PMID:26936924

  13. Diversity and relationships of cocirculating modern human rotaviruses revealed using large-scale comparative genomics.

    PubMed

    McDonald, Sarah M; McKell, Allison O; Rippinger, Christine M; McAllen, John K; Akopov, Asmik; Kirkness, Ewen F; Payne, Daniel C; Edwards, Kathryn M; Chappell, James D; Patton, John T

    2012-09-01

    Group A rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses and are primary causes of gastroenteritis in young children. Despite their medical relevance, the genetic diversity of modern human RVs is poorly understood, and the impact of vaccine use on circulating strains remains unknown. In this study, we report the complete genome sequence analysis of 58 RVs isolated from children with severe diarrhea and/or vomiting at Vanderbilt University Medical Center (VUMC) in Nashville, TN, during the years spanning community vaccine implementation (2005 to 2009). The RVs analyzed include 36 G1P[8], 18 G3P[8], and 4 G12P[8] Wa-like genogroup 1 strains with VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 genotype constellations of I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees, we identified 2 to 5 subgenotype alleles for each gene. The results show evidence of intragenogroup gene reassortment among the cocirculating strains. However, several isolates from different seasons maintained identical allele constellations, consistent with the notion that certain RV clades persisted in the community. By comparing the genes of VUMC RVs to those of other archival and contemporary RV strains for which sequences are available, we defined phylogenetic lineages and verified that the diversity of the strains analyzed in this study reflects that seen in other regions of the world. Importantly, the VP4 and VP7 proteins encoded by VUMC RVs and other contemporary strains show amino acid changes in or near neutralization domains, which might reflect antigenic drift of the virus. Thus, this large-scale, comparative genomic study of modern human RVs provides significant insight into how this pathogen evolves during its spread in the community. PMID:22696651

  14. Diversity and Relationships of Cocirculating Modern Human Rotaviruses Revealed Using Large-Scale Comparative Genomics

    PubMed Central

    McKell, Allison O.; Rippinger, Christine M.; McAllen, John K.; Akopov, Asmik; Kirkness, Ewen F.; Payne, Daniel C.; Edwards, Kathryn M.; Chappell, James D.; Patton, John T.

    2012-01-01

    Group A rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses and are primary causes of gastroenteritis in young children. Despite their medical relevance, the genetic diversity of modern human RVs is poorly understood, and the impact of vaccine use on circulating strains remains unknown. In this study, we report the complete genome sequence analysis of 58 RVs isolated from children with severe diarrhea and/or vomiting at Vanderbilt University Medical Center (VUMC) in Nashville, TN, during the years spanning community vaccine implementation (2005 to 2009). The RVs analyzed include 36 G1P[8], 18 G3P[8], and 4 G12P[8] Wa-like genogroup 1 strains with VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 genotype constellations of I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees, we identified 2 to 5 subgenotype alleles for each gene. The results show evidence of intragenogroup gene reassortment among the cocirculating strains. However, several isolates from different seasons maintained identical allele constellations, consistent with the notion that certain RV clades persisted in the community. By comparing the genes of VUMC RVs to those of other archival and contemporary RV strains for which sequences are available, we defined phylogenetic lineages and verified that the diversity of the strains analyzed in this study reflects that seen in other regions of the world. Importantly, the VP4 and VP7 proteins encoded by VUMC RVs and other contemporary strains show amino acid changes in or near neutralization domains, which might reflect antigenic drift of the virus. Thus, this large-scale, comparative genomic study of modern human RVs provides significant insight into how this pathogen evolves during its spread in the community. PMID:22696651

  15. Reintroduction and Post-Release Survival of a Living Fossil: The Chinese Giant Salamander

    PubMed Central

    Zhang, Lu; Jiang, Wei; Wang, Qi-Jun; Zhao, Hu; Zhang, Hong-Xing; Marcec, Ruth M.; Willard, Scott T.; Kouba, Andrew J.

    2016-01-01

    Captive rearing and reintroduction / translocation are increasingly used as tools to supplement wild populations of threatened species. Reintroducing captive-reared Chinese giant salamanders may help to augment the declining wild populations and conserve this critically endangered amphibian. We released 31 captive-reared juvenile giant salamanders implanted with VHF radio transmitters at the Heihe River (n = 15) and the Donghe River (n = 16) in the Qinling Mountains of central China. Salamanders were monitored every day for survival from April 28th 2013 to September 3rd 2014. We attempted to recapture all living individuals by the end of the study, measured their body mass and total body length, and checked for abnormalities and presence of external parasites. Two salamanders at the Heihe River and 10 animals at the Donghe River survived through the project timeline. Nine salamanders were confirmed dead, while the status of the other 10 animals was undetermined. The annual survival rate of giant salamanders at the Donghe River (0.702) was 1.7-fold higher than that at the Heihe River (0.405). Survival increased as individuals were held longer following surgery, whereas body mass did not have a significant impact on survival rate. All salamanders recaptured from the Donghe River (n = 8) increased in mass (0.50 ± 0.13 kg) and length (5.5 ± 1.5 cm) after approximately 11 months in the wild, and they were only 7% lighter than wild animals of the same length (mean residual = -0.033 ± 0.025). Our results indicate that captive-reared Chinese giant salamanders can survive in the wild one year after release and adequate surgical recovery time is extremely important to post-release survival. Future projects may reintroduce older juveniles to achieve better survival and longer monitoring duration. PMID:27258650

  16. Reintroduction and Post-Release Survival of a Living Fossil: The Chinese Giant Salamander.

    PubMed

    Zhang, Lu; Jiang, Wei; Wang, Qi-Jun; Zhao, Hu; Zhang, Hong-Xing; Marcec, Ruth M; Willard, Scott T; Kouba, Andrew J

    2016-01-01

    Captive rearing and reintroduction / translocation are increasingly used as tools to supplement wild populations of threatened species. Reintroducing captive-reared Chinese giant salamanders may help to augment the declining wild populations and conserve this critically endangered amphibian. We released 31 captive-reared juvenile giant salamanders implanted with VHF radio transmitters at the Heihe River (n = 15) and the Donghe River (n = 16) in the Qinling Mountains of central China. Salamanders were monitored every day for survival from April 28th 2013 to September 3rd 2014. We attempted to recapture all living individuals by the end of the study, measured their body mass and total body length, and checked for abnormalities and presence of external parasites. Two salamanders at the Heihe River and 10 animals at the Donghe River survived through the project timeline. Nine salamanders were confirmed dead, while the status of the other 10 animals was undetermined. The annual survival rate of giant salamanders at the Donghe River (0.702) was 1.7-fold higher than that at the Heihe River (0.405). Survival increased as individuals were held longer following surgery, whereas body mass did not have a significant impact on survival rate. All salamanders recaptured from the Donghe River (n = 8) increased in mass (0.50 ± 0.13 kg) and length (5.5 ± 1.5 cm) after approximately 11 months in the wild, and they were only 7% lighter than wild animals of the same length (mean residual = -0.033 ± 0.025). Our results indicate that captive-reared Chinese giant salamanders can survive in the wild one year after release and adequate surgical recovery time is extremely important to post-release survival. Future projects may reintroduce older juveniles to achieve better survival and longer monitoring duration. PMID:27258650

  17. Tiger salamanders' (Ambystoma tigrinum) response learning and usage of visual cues.

    PubMed

    Kundey, Shannon M A; Millar, Roberto; McPherson, Justin; Gonzalez, Maya; Fitz, Aleyna; Allen, Chadbourne

    2016-05-01

    We explored tiger salamanders' (Ambystoma tigrinum) learning to execute a response within a maze as proximal visual cue conditions varied. In Experiment 1, salamanders learned to turn consistently in a T-maze for reinforcement before the maze was rotated. All learned the initial task and executed the trained turn during test, suggesting that they learned to demonstrate the reinforced response during training and continued to perform it during test. In a second experiment utilizing a similar procedure, two visual cues were placed consistently at the maze junction. Salamanders were reinforced for turning towards one cue. Cue placement was reversed during test. All learned the initial task, but executed the trained turn rather than turning towards the visual cue during test, evidencing response learning. In Experiment 3, we investigated whether a compound visual cue could control salamanders' behaviour when it was the only cue predictive of reinforcement in a cross-maze by varying start position and cue placement. All learned to turn in the direction indicated by the compound visual cue, indicating that visual cues can come to control their behaviour. Following training, testing revealed that salamanders attended to stimuli foreground over background features. Overall, these results suggest that salamanders learn to execute responses over learning to use visual cues but can use visual cues if required. Our success with this paradigm offers the potential in future studies to explore salamanders' cognition further, as well as to shed light on how features of the tiger salamanders' life history (e.g. hibernation and metamorphosis) impact cognition. PMID:26796198

  18. Diagnostic and molecular evaluation of three iridovirus-associated salamander mortality events

    USGS Publications Warehouse

    Docherty, D.E.; Meteyer, C.U.; Wang, Jingyuan; Mao, J.; Case, S.T.; Chinchar, V.G.

    2003-01-01

    In 1998 viruses were isolated from tiger salamander larvae (Ambystoma tigrinum diaboli and A. tigrinum melanostictum) involved in North Dakota and Utah (USA) mortality events and spotted salamander (A. maculatum) larvae in a third event in Maine (USA). Although sympatric caudates and anurans were present at all three sites only ambystomid larvae appeared to be affected. Mortality at the North Dakota site was in the thousands while at the Utah and Maine sites mortality was in the hundreds. Sick larvae were lethargic and slow moving. They swam in circles with obvious buoyancy problems and were unable to remain upright. On the ventral surface, near the gills and hind limbs, red spots or swollen areas were noted. Necropsy findings included: hemorrhages and ulceration of the skin, subcutaneous and intramuscular edema, swollen and pale livers with multifocal hemorrhage, and distended fluid-filled intestines with areas of hemorrhage. Light microscopy revealed intracytoplasmic inclusions, suggestive of a viral infection, in a variety of organs. Electron microscopy of ultra thin sections of the same tissues revealed iridovirus-like particles within the inclusions. These viruses were isolated from a variety of organs, indicating a systemic infection. Representative viral isolates from the three mortality events were characterized using molecular assays. Characterization confirmed that the viral isolates were iridoviruses and that the two tiger salamander isolates were similar and could be distinguished from the spotted salamander isolate. The spotted salamander isolate was similar to frog virus 3, the type species of the genus Ranavirus, while the tiger salamander isolates were not. These data indicate that different species of salamanders can become infected and die in association with different iridoviruses. Challenge assays are required to determine the fish and amphibian host range of these isolates and to assess the susceptibility of tiger and spotted salamanders to

  19. Plethodon cinerius (eastern red-backed salamander) movement

    USGS Publications Warehouse

    Sterrett, Sean; Brand, Adrianne; Fields, William R.; Katz, Rachel A.; Grant, Evan H. Campbell

    2015-01-01

    Lungless salamanders (family Plethodontidae) are relatively sedentary and are presumed to have limited dispersal ability (Marsh et al. 2004. Ecology 85:3396–3405). Site fidelity in Plethodontidae is high, and individuals displaced 90 m return to home territories (Kleeberger and Werner 1982. Copeia 1982:409–415). Individuals defend territories (Jaeger et al. 1982. Anim. Behav. 30:490–496) and female home ranges have been estimated to be 24.34 m2 (Kleeberger and Werner 1982, op. cit.). Females may seek out suitable subsurface habitat to oviposit eggs, yet little is known about their maximum movement distances (Petranka 1998. Salamanders of the United States and Canada. Smithsonian Institution Press, Washington. 587 pp.).On 18 September 2014, a female P. cinereus (lead back morphotype; SVL = 44.68 mm; 0.89 g) was found under a coverboard during a standard sampling event and uniquely marked using visual implant elastomer at the S.O. Conte Anadromous Fish Research Center, Massachusetts, USA (42.59280°N, 72.58070°W, datum WGS84; elev. 74 m). This individual was subsequently recaptured at ~1500 h on 8 October 2014 under a coverboard within 3 m of the original capture location and then again ~1430 h on 16 October 2014 under a log, within the same forest patch, though in a 50 x 150 m area adjacent to the original study area. Because we found the marked salamander while collecting multiple individuals for a laboratory study, the exact recapture location of the marked individual is not known. However, the distance between the 8 October capture location and the nearest edge of the 16 October search area (i.e. 50 x 150 m) was 143 m, indicating a minimum movement distance. As far as we are aware, this is the longest recorded movement for P. cinereus by more than 53 m (Kleeberger and Werner 1982, op. cit.). This finding followed a rain event of 1.63 cm within 24 h and the second largest sustained rain event during October. The movement we observed may have been due to

  20. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq.

    PubMed

    Karam, M-J; Lefèvre, F; Dagher-Kharrat, M Bou; Pinosio, S; Vendramin, G G

    2015-05-01

    We combined restriction site associated DNA sequencing (RADseq) using a hypomethylation-sensitive enzyme and messenger RNA sequencing (mRNAseq) to develop molecular markers for the 16 gigabase genome of Cedrus atlantica, a conifer tree species. With each method, Illumina(®) reads from one individual were used to generate de novo assemblies. SNPs from the RADseq data set were detected in a panel of one single individual and three pools of three individuals each. We developed a flexible script to estimate the ascertainment bias in SNP detection considering the pooling and sampling effects on the probability of not detecting an existing polymorphism. Gene Ontology (GO) and transposable element (TE) search analyses were applied to both data sets. The RADseq and the mRNAseq assemblies represented 0.1% and 0.6% of the genome, respectively. Genome complexity reduction resulted in 17% of the RADseq contigs potentially coding for proteins. This rate was doubled in the mRNAseq data set, suggesting that RADseq also explores noncoding low-repeat regions. The two methods gave very similar GO-slim profiles. As expected, the two assemblies were poor in TE-like sequences (<4% of contigs length). We identified 17,348 single nucleotide polymorphisms (SNPs) in the RADseq data set and 5,714 simple sequence repeats (SSRs) in the transcriptome. A subset of 282 SNPs was validated using the Fluidigm genotyping technology, giving a conversion rate of 50.4%, falling within the expected range for conifers. Increasing sample size had the greatest effect for ascertainment bias reduction. These results validated the utility of the RADseq approach for highly complex genomes such as conifers. PMID:25224750

  1. Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum.

    PubMed

    Hardigan, Michael A; Crisovan, Emily; Hamilton, John P; Kim, Jeongwoon; Laimbeer, Parker; Leisner, Courtney P; Manrique-Carpintero, Norma C; Newton, Linsey; Pham, Gina M; Vaillancourt, Brieanne; Yang, Xueming; Zeng, Zixian; Douches, David S; Jiang, Jiming; Veilleux, Richard E; Buell, C Robin

    2016-02-01

    Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways. PMID:26772996

  2. Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

    PubMed Central

    Seidl, Michael F.; Van den Ackerveken, Guido; Govers, Francine; Snel, Berend

    2012-01-01

    The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have not yet been studied by applying systematic tree reconciliation of the phylome of these species. We analyzed evolutionary dynamics of ten Stramenopiles. Gene gains, duplications, and losses were inferred by tree reconciliation of 18,459 gene trees constituting the phylome with a highly supported species phylogeny. We reconstructed a strikingly large last common ancestor of the Stramenopiles that contained ∼10,000 genes. Throughout evolution, the genomes of pathogenic oomycetes have constantly gained and lost genes, though gene gains through duplications outnumber the losses. The branch leading to the plant pathogenic Phytophthora genus was identified as a major transition point characterized by increased frequency of duplication events that has likely driven the speciation within this genus. Large gene families encoding different classes of enzymes associated with pathogenicity such as glycoside hydrolases are formed by complex and distinct patterns of duplications and losses leading to their expansion in extant oomycetes. This study unveils the large-scale evolutionary dynamics that shaped the genomes of pathogenic oomycetes. By the application of phylogenetic based analyses methods, it provides additional insights that shed light on the complex history of oomycete genome evolution and the emergence of large gene families characteristic for this important class of pathogens. PMID:22230142

  3. Spatial variation in water loss predicts terrestrial salamander distribution and population dynamics.

    PubMed

    Peterman, W E; Semlitsch, R D

    2014-10-01

    Many patterns observed in ecology, such as species richness, life history variation, habitat use, and distribution, have physiological underpinnings. For many ectothermic organisms, temperature relationships shape these patterns, but for terrestrial amphibians, water balance may supersede temperature as the most critical physiologically limiting factor. Many amphibian species have little resistance to water loss, which restricts them to moist microhabitats, and may significantly affect foraging, dispersal, and courtship. Using plaster models as surrogates for terrestrial plethodontid salamanders (Plethodon albagula), we measured water loss under ecologically relevant field conditions to estimate the duration of surface activity time across the landscape. Surface activity time was significantly affected by topography, solar exposure, canopy cover, maximum air temperature, and time since rain. Spatially, surface activity times were highest in ravine habitats and lowest on ridges. Surface activity time was a significant predictor of salamander abundance, as well as a predictor of successful recruitment; the probability of a juvenile salamander occupying an area with high surface activity time was two times greater than an area with limited predicted surface activity. Our results suggest that survival, recruitment, or both are demographic processes that are affected by water loss and the ability of salamanders to be surface-active. Results from our study extend our understanding of plethodontid salamander ecology, emphasize the limitations imposed by their unique physiology, and highlight the importance of water loss to spatial population dynamics. These findings are timely for understanding the effects that fluctuating temperature and moisture conditions predicted for future climates will have on plethodontid salamanders. PMID:25154754

  4. A re-examination and re-evaluation of salamander orbital glands.

    PubMed

    Rehorek, Susan J; Grand-Pierre, Alix E; Cummings, Joshua R; Jewell, Bridgette; Constantine, Julieanne; Hillenius, W Jaap

    2013-11-01

    The amphibian integument contains numerous multicellular glands. Although two of these, the nasolabial and orbital glands and the associated nasolacrimal duct (NLD), have historically received considerable attention, interpretation of the original observations can be problematic in the context of current literature. Salamanders, in particular, are frequently regarded as at least indicative of aspects of the morphology of the common ancestor to all extant tetrapods; hence, an understanding of these glands in salamanders might prove to be informative about their evolution. For this study, the orbitonasal region of salamanders from three families was histologically examined. Three themes emerged: (1) examination of the effect of phylogeny on the nasolabial gland and NLD revealed a combination of features that may be unique to plethodontid salamanders, and may be correlated to their nose-tapping behavior by which substances are moved into the vomeronasal organ; (2) ecology appears to impact the relative development of the orbital glands, but not necessarily the nasolabial gland, with smaller glands being present in the aquatic species; (3) the nomenclature of the salamander orbital gland remains problematic, especially in light of comparative studies, as several alternate possibilities are viable. From this nomenclatural conundrum, however, it could be concluded that there may be a global pattern in the location of tetrapod orbital gland development. Molecular questions in terms of ontogeny and genetic homology affect the nature of the debate on orbital gland nomenclature. These observations suggest that rather than reflecting an ancestral condition, salamanders may instead represent a case of specialized, convergent evolution. PMID:24106029

  5. Three decades of urbanization: Estimating the impact of land-cover change on stream salamander populations

    USGS Publications Warehouse

    Price, S.J.; Dorcas, M.E.; Gallant, A.L.; Klaver, R.W.; Willson, J.D.

    2006-01-01

    Urbanization has become the dominant form of landscape disturbance in parts of the United States. Small streams in the Piedmont region of the eastern United States support high densities of salamanders and are often the first habitats to be affected by landscape-altering factors such as urbanization. We used US Geological Survey land cover data from 1972 to 2000 and a relation between stream salamanders and land cover, established from recent research, to estimate the impact of contemporary land-cover change on the abundance of stream salamanders near Davidson, North Carolina, a Piedmont locale that has experienced rapid urbanization during this time. Our analysis indicates that southern two-lined salamander (Eurycea cirrigera) populations have decreased from 32% to 44% while northern dusky salamanders (Desmognathus fuscus) have decreased from 21% to 30% over the last three decades. Our results suggest that the widespread conversion of forest to urban land in small catchments has likely resulted in a substantial decline of populations of stream salamanders and could have serious effects on stream ecosystems. ?? 2006 Elsevier Ltd. All rights reserved.

  6. Soil acidity affects distribution, behavior, and physiology of the salamander Plethodon cinereus

    SciTech Connect

    Wyman, R.L.; Hawksley-Lescault, D.S.

    1987-12-01

    Censuses at two sites in Delaware County, New York from spring 1981 through spring 1985 indicated that the density and distribution of Plethodon cinereus were influenced by soil pH but not by soil temperature or moisture. Of 1044 1-m/sup 2/ quadrats of forest litter searched, 284 had a pH of 3.7 or less and only 25 of these (8.8%) contained salamanders. Of 760 quadrats with a pH 3.8 or more, 386 (50.8%) contained salamanders. Juvenile salamanders were never found on soils with a pH less than or equal to 3.7. Seasonal salamander density was correlated (r = -0.92) with the percentage of quadrats with a pH of 3.7 and less. Salamanders apparently were excluded from 27% of forest habitat because of low soil pH. In the laboratory, P. cinereus preferred to occupy substrates near neutral pH when given a choice among three levels of substrate acidity. The acutely lethal pH was between 2.5 and 3 and the 8-mo chronically lethal pH was between 3 and 4. Growth and respiration were reduced at low pHs. The influence of soil pH on salamander distribution might fundamentally change the forest floor decomposer food web of which P. cinereus is an upper-level consumer.

  7. Leaf litter bags as an index to populations of northern two-lined salamanders (Eurycea bislineata)

    USGS Publications Warehouse

    Chalmers, R.J.; Droege, S.

    2002-01-01

    Concern about recent amphibian declines has led to research on amphibian populations, but few statistically tested, standardized methods of counting amphibians exist. We tested whether counts of northern two-lined salamander larvae (Eurycea bislineata) sheltered in leaf litter bags--a relatively new, easily replicable survey technique--had a linear correlation to total number of larvae. Using experimental enclosures placed in streams, we compared number of salamanders found in artificial habitat (leaf litter bags) with total number of salamanders in each enclosure. Low numbers of the animals were found in leaf litter bags, and the relative amount of variation in the index (number of animals in leaf litter bags compared to total number of animals in stream enclosures) was high. The index of salamanders in leaf litter bags was not significantly related to total number of salamanders in enclosures for two-thirds of the replicates or with pooled replicates (P= 0.066). Consequently, we cannot recommend using leaf litter bags to index populations of northern two-lined salamanders.

  8. Woodland salamander responses to a shelterwood harvest-prescribed burn silvicultural treatment within Appalachian mixed-oak forests

    USGS Publications Warehouse

    Ford, W. Mark; Mahoney, Kathleen R.; Russell, Kevin R.; Rodrigue, Jane L.; Riddle, Jason D.; Schuler, Thomas M.; Adams, Mary Beth

    2015-01-01

    Forest management practices that mimic natural canopy disturbances, including prescribed fire and timber harvests, may reduce competition and facilitate establishment of favorable vegetative species within various ecosystems. Fire suppression in the central Appalachian region for almost a century has contributed to a transition from oak-dominated to more mesophytic, fire-intolerant forest communities. Prescribed fire coupled with timber removal is currently implemented to aid in oak regeneration and establishment but responses of woodland salamanders to this complex silvicultural system is poorly documented. The purpose of our research was to determine how woodland salamanders respond to shelterwood harvests following successive burns in a central Appalachian mixed-oak forest. Woodland salamanders were surveyed using coverboard arrays in May, July, and August–September 2011 and 2012. Surveys were conducted within fenced shelterwood-burn (prescribed fires, shelterwood harvest, and fencing to prevent white-tailed deer [Odocoileus virginianus] herbivory), shelterwood-burn (prescribed fires and shelterwood harvest), and control plots. Relative abundance was modeled in relation to habitat variables measured within treatments for mountain dusky salamanders (Desmognathus ochrophaeus), slimy salamanders (Plethodon glutinosus), and eastern red-backed salamanders (Plethodon cinereus). Mountain dusky salamander relative abundance was positively associated with canopy cover and there were significantly more individuals within controls than either shelterwood-burn or fenced shelterwood-burn treatments. Conversely, habitat variables associated with slimy salamanders and eastern red-backed salamanders did not differ among treatments. Salamander age-class structure within controls did not differ from shelterwood-burn or fenced shelterwood-burn treatments for any species. Overall, the woodland salamander assemblage remained relatively intact throughout the shelterwoodburn

  9. Large Genomic Fragment Deletions and Insertions in Mouse Using CRISPR/Cas9

    PubMed Central

    Satheka, Achim Cchitvsanzwhoh; Togo, Jacques; An, Yao; Humphrey, Mabwi; Ban, Luying; Ji, Yan; Jin, Honghong; Feng, Xuechao; Zheng, Yaowu

    2015-01-01

    ZFN, TALENs and CRISPR/Cas9 system have been used to generate point mutations and large fragment deletions and insertions in genomic modifications. CRISPR/Cas9 system is the most flexible and fast developing technology that has been extensively used to make mutations in all kinds of organisms. However, the most mutations reported up to date are small insertions and deletions. In this report, CRISPR/Cas9 system was used to make large DNA fragment deletions and insertions, including entire Dip2a gene deletion, about 65kb in size, and β-galactosidase (lacZ) reporter gene insertion of larger than 5kb in mouse. About 11.8% (11/93) are positive for 65kb deletion from transfected and diluted ES clones. High targeting efficiencies in ES cells were also achieved with G418 selection, 46.2% (12/26) and 73.1% (19/26) for left and right arms respectively. Targeted large fragment deletion efficiency is about 21.4% of live pups or 6.0% of injected embryos. Targeted insertion of lacZ reporter with NEO cassette showed 27.1% (13/48) of targeting rate by ES cell transfection and 11.1% (2/18) by direct zygote injection. The procedures have bypassed in vitro transcription by directly co-injection of zygotes or co-transfection of embryonic stem cells with circular plasmid DNA. The methods are technically easy, time saving, and cost effective in generating mouse models and will certainly facilitate gene function studies. PMID:25803037

  10. Using large-scale genome variation cohorts to decipher the molecular mechanism of cancer.

    PubMed

    Habermann, Nina; Mardin, Balca R; Yakneen, Sergei; Korbel, Jan O

    2016-01-01

    Characterizing genomic structural variations (SVs) in the human genome remains challenging, and there is a growing interest to understand somatic SVs occurring in cancer, a disease of the genome. A havoc-causing SV process known as chromothripsis scars the genome when localized chromosome shattering and repair occur in a one-off catastrophe. Recent efforts led to the development of a set of conceptual criteria for the inference of chromothripsis events in cancer genomes and to the development of experimental model systems for studying this striking DNA alteration process in vitro. We discuss these approaches, and additionally touch upon current "Big Data" efforts that employ hybrid cloud computing to enable studies of numerous cancer genomes in an effort to search for commonalities and differences in molecular DNA alteration processes in cancer. PMID:27342254