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Find video protocols related to scientific articles indexed in Pubmed.
Phylotranscriptomic analysis of the origin and early diversification of land plants.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-29-2014
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Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Understanding the spectacular failure of DNA barcoding in willows (Salix): does this result from a trans-specific selective sweep?
Mol. Ecol.
PUBLISHED: 05-29-2014
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Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive nonrandom coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographical (isolation by distance) effects in the haplotype distributions of this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.
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Paralogous radiations of PIN proteins with multiple origins of noncanonical PIN structure.
Mol. Biol. Evol.
PUBLISHED: 04-23-2014
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The plant hormone auxin is a conserved regulator of development which has been implicated in the generation of morphological novelty. PIN-FORMED1 (PIN) auxin efflux carriers are central to auxin function by regulating its distribution. PIN family members have divergent structures and cellular localizations, but the origin and evolutionary significance of this variation is unresolved. To characterize PIN family evolution, we have undertaken phylogenetic and structural analyses with a massive increase in taxon sampling over previous studies. Our phylogeny shows that following the divergence of the bryophyte and lycophyte lineages, two deep duplication events gave rise to three distinct lineages of PIN proteins in euphyllophytes. Subsequent independent radiations within each of these lineages were taxonomically asymmetric, giving rise to at least 21 clades of PIN proteins, of which 15 are revealed here for the first time. Although most PIN protein clades share a conserved canonical structure with a modular central loop domain, a small number of noncanonical clades dispersed across the phylogeny have highly divergent protein structure. We propose that PIN proteins underwent sub- and neofunctionalization with substantial modification to protein structure throughout plant evolution. Our results have important implications for plant evolution as they suggest that structurally divergent PIN proteins that arose in paralogous radiations contributed to the convergent evolution of organ systems in different land plant lineages.
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Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 04-14-2014
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Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor--neochrome--that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.
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Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor.
Mol. Phylogenet. Evol.
PUBLISHED: 04-04-2014
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It is commonly believed that gene duplications provide the raw material for morphological evolution. Both the number of genes and size of gene families have increased during the diversification of land plants. Several small proteins that regulate transcription factors have recently been identified in plants, including the LITTLE ZIPPER (ZPR) proteins. ZPRs are post-translational negative regulators, via heterodimerization, of class III Homeodomain Leucine Zipper (C3HDZ) proteins that play a key role in directing plant form and growth. We show that ZPR genes originated as a duplication of a C3HDZ transcription factor paralog in the common ancestor of euphyllophytes (ferns and seed plants). The ZPRs evolved by degenerative mutations resulting in loss all of the C3HDZ functional domains, except the leucine zipper that modulates dimerization. ZPRs represent a novel regulatory module of the C3HDZ network unique to the euphyllophyte lineage, and their origin correlates to a period of rapid morphological changes and increased complexity in land plants. The origin of the ZPRs illustrates the significance of gene duplications in creating developmental complexity during land plant evolution that likely led to morphological evolution.
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Variation in mating systems of salamanders: mate guarding or territoriality?
Behav. Processes
PUBLISHED: 03-21-2014
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Two of the most common mating tactics in vertebrates are mate guarding and territoriality, yet much of the research on these strategies has focused on mating systems in birds, despite novel insights gained from studying less traditional systems. North American stream salamanders that comprise the Eurycea bislineata complex represent an excellent nontraditional system for comparing mating strategies because these species exhibit a continuum of male morphologies, diverse habitat associations, and various potential mating strategies. We studied two species within this complex that exhibit the extremes of this continuum, Eurycea aquatica (robust morph) and Eurycea cirrigera (slender morph). The larger head in males of E. aquatica is due to larger musculature around the jaw and may be associated with aggressive behavior. Therefore, we hypothesized that the robust morphology exhibited by males of E. aquatica provides benefits during either territorial defense or mate defense and that males of E. cirrigera would not exhibit aggression in either scenario. We found that neither species exhibited aggressive behavior to defend a territory. However, in the presence of a female, males of E. aquatica were significantly more aggressive toward intruding males than were males of E. cirrigera. Therefore, mate-guarding behavior occurs in E. aquatica, and the enlarged head of males likely aids in deterring rivals. This is the first demonstration of mate-guarding behavior in a plethodontid, the most speciose family of salamanders.
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Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales).
BMC Evol. Biol.
PUBLISHED: 02-21-2014
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The aquatic flowering-plant family Hydatellaceae has a classic Gondwanan distribution, as it is found in Australia, India and New Zealand. To shed light on the biogeographic history of this apparently ancient branch of angiosperm phylogeny, we dated the family in the context of other seed-plant divergences, and evaluated its biogeography using parsimony and likelihood methods. We also explicitly tested the effect of different extinction rates on biogeographic inferences.
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Impacts of Macondo oil from Deepwater Horizon spill on the growth response of the common reed Phragmites australis: a mesocosm study.
Mar. Pollut. Bull.
PUBLISHED: 01-20-2014
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We investigated impacts of Macondo MC252 oil from the Deepwater Horizon (DWH) spill on the common reed Phragmites australis (Cav.) Trin. ex Steud., a dominant species of the Mississippi River Delta. In greenhouse experiments, we simulated the most common DWH oiling scenarios by applying weathered and emulsified Macondo oil to aboveground shoots at varying degrees of coverage (0-100%) or directly to marsh soil at different dosages (0-16 Lm(-)(2)). P. australis exhibited strong resistance to negative impacts when oil was applied to shoots alone, while reductions in above- and belowground plant growth were apparent when oil was applied to the soil or with repeated shoot-oiling. Although soil-oiling compromised plant function, mortality of P. australis did not occur. Our results demonstrate that P. australis has a high tolerance to weathered and emulsified Macondo oil, and that mode of exposure (aboveground versus belowground) was a primary determinant of impact severity.
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Between two fern genomes.
Gigascience
PUBLISHED: 01-01-2014
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Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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Resting environments of some Costa Rican mosquitoes.
J. Vector Ecol.
PUBLISHED: 05-25-2013
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The resting sites of tropical American mosquitoes are poorly documented, and the few reports that do exist are largely from opportunistic collections. Since blood-engorged females (used in determining host associations) are more efficiently collected from resting sites than attractive traps, information on resting site utilization has practical value. To investigate differences in the resting sites utilized by tropical mosquitoes, we collected and identified female mosquitoes from one man-made (resting shelter) and three natural (buttress tree roots, hollow trees, and understory vegetation) resting environments at a tropical dry forest location in western Costa Rica. All of the most common species collected demonstrated associations with one or more resting environments. Females of five species (blood-engorged Anopheles albimanus, Uranotaenia apicalis, Uranotaenia lowii, Uranotaenia orthodoxa, and blood-engorged Mansonia titillans) were collected in significantly greater numbers from understory vegetation than other resting environments. Culex erraticus and other members of the subgenus Melanoconion were encountered more often in resting shelters, hollow trees, and buttress roots, while Culex restrictor (blood-engorged) females were associated with hollow trees. Similarity indices indicate that buttress tree roots, hollow trees, and resting shelters are similar with respect to the mosquito communities that utilize them as resting sites, while understory vegetation has a resting fauna that is different than the other environments surveyed here. These results add to the body of information regarding resting sites utilized by tropical American mosquitoes.
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Transcriptome-mining for single-copy nuclear markers in ferns.
PLoS ONE
PUBLISHED: 01-01-2013
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Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales.
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Fluence field optimization for noise and dose objectives in CT.
Med Phys
PUBLISHED: 10-08-2011
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Selecting the appropriate imaging technique in computed tomography (CT) inherently involves balancing the tradeoff between image quality and imaging dose. Modulation of the x-ray fluence field, laterally across the beam, and independently for each projection, may potentially meet user-prescribed, regional image quality objectives, while reducing radiation to the patient. The proposed approach, called fluence field modulated CT (FFMCT), parallels the approach commonly used in intensity-modulated radiation therapy (IMRT), except "image quality plans" replace the "dose plans" of IMRT. This work studies the potential noise and dose benefits of FFMCT via objective driven optimization of fluence fields.
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Comparison of ultrasound and nerve stimulation techniques for interscalene brachial plexus block for shoulder surgery in a residency training environment: a randomized, controlled, observer-blinded trial.
Ochsner J
PUBLISHED: 10-01-2011
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The ability to provide adequate intraoperative anesthesia and postoperative analgesia for orthopedic shoulder surgery continues to be a procedural challenge. Anesthesiology training programs constantly balance the time needed for procedural education versus associated costs. The administration of brachial plexus anesthesia can be facilitated through nerve stimulation or by ultrasound guidance. The benefits of using a nerve stimulator include a high incidence of success and less cost when compared to ultrasonography. Recent studies with ultrasonography suggest high success rates and decreased procedural times, but less is known about the comparison of these procedural times in training programs. We conducted a prospective, randomized, observer-blinded study with inexperienced clinical anesthesia (CA) residents-CA-1 to CA-3-to compare differences in these 2 guidance techniques in patients undergoing interscalene brachial plexus block for orthopedic surgery.
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Competency of reptiles and amphibians for eastern equine encephalitis virus.
Am. J. Trop. Med. Hyg.
PUBLISHED: 09-08-2011
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Eastern equine encephalitis virus (EEEV) is endemic throughout most of the eastern United States. Although it is transmitted year round in Florida, transmission elsewhere is seasonal. The mechanism that enables EEEV to overwinter in seasonal foci remains obscure. In previous field studies, early season EEEV activity was detected in mosquito species that feed primarily upon ectothermic hosts, suggesting that reptiles and amphibians might represent overwintering reservoir hosts for EEEV. To determine if this might be possible, two commonly fed upon amphibian and reptile species were evaluated as hosts for the North American subtype I strain of EEEV. Neither amphibian species was a competent host. However, circulating viremias were detected in both reptile species examined. Hibernating infected garter snakes remained viremic after exiting hibernation. These data suggest that snakes may represent an overwintering host for North American EEEV.
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The impacts of invaders: basal and acute stress glucocorticoid profiles and immune function in native lizards threatened by invasive ants.
Gen. Comp. Endocrinol.
PUBLISHED: 09-06-2011
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As anthropogenic stressors increase exponentially in the coming decades, native vertebrates will likely face increasing threats from these novel challenges. The success or failure of the primary physiological mediator of these stressors--the HPA axis--will likely involve numerous and chaotic outcomes. Among the most challenging of these new threats are invasive species. These have the capacity to simultaneously challenge the HPA axis and the immune system as they are often associated with, or the cause of, emerging infectious diseases, and energetic tradeoffs with the HPA response can have immunosuppressive effects. To determine the effects of invasive species on the vertebrate GC response to a novel stressor, and on immunity, we examined the effects of invasive fire ants on native lizards, comparing lizards from sites with long histories with fire ants to those outside the invasion zone. We demonstrated higher baseline and acute stress (captive restraint) CORT levels in lizards from within fire ant invaded areas; females are more strongly affected than males, suggesting context-specific effects of invasion. We found no effect of fire ant invasion on the immune parameters we measured (complement bacterial lysis and antibody hemagglutination) with the exception of ectoparasite infestation. Mites were far less prevalent on lizards within fire ant invaded sites, suggesting fire ants may actually benefit lizards in this regard. This study suggests that invasive species may impose physiological stress on native vertebrates, but that the consequences of this stress may be complicated and unpredictable.
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Reconciling gene and genome duplication events: using multiple nuclear gene families to infer the phylogeny of the aquatic plant family Pontederiaceae.
Mol. Biol. Evol.
PUBLISHED: 06-01-2011
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Most plant phylogenetic inference has used DNA sequence data from the plastid genome. This genome represents a single genealogical sample with no recombination among genes, potentially limiting the resolution of evolutionary relationships in some contexts. In contrast, nuclear DNA is inherently more difficult to employ for phylogeny reconstruction because major mutational events in the genome, including polyploidization, gene duplication, and gene extinction can result in homologous gene copies that are difficult to identify as orthologs or paralogs. Gene tree parsimony (GTP) can be used to infer the rooted species tree by fitting gene genealogies to species trees while simultaneously minimizing the estimated number of duplications needed to reconcile conflicts among them. Here, we use GTP for five nuclear gene families and a previously published plastid data set to reconstruct the phylogenetic backbone of the aquatic plant family Pontederiaceae. Plastid-based phylogenetic studies strongly supported extensive paraphyly of Eichhornia (one of the four major genera) but also depicted considerable ambiguity concerning the true root placement for the family. Our results indicate that species trees inferred from the nuclear genes (alone and in combination with the plastid data) are highly congruent with gene trees inferred from plastid data alone. Consideration of optimal and suboptimal gene tree reconciliations place the root of the family at (or near) a branch leading to the rare and locally restricted E. meyeri. We also explore methods to incorporate uncertainty in individual gene trees during reconciliation by considering their individual bootstrap profiles and relate inferred excesses of gene duplication events on individual branches to whole-genome duplication events inferred for the same branches. Our study improves understanding of the phylogenetic history of Pontederiaceae and also demonstrates the utility of GTP for phylogenetic analysis.
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Inferring the higher-order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set.
Am. J. Bot.
PUBLISHED: 05-27-2011
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Investigating the early diversification of major clades requires well-corroborated and accurate phylogenetic inferences. We examined the performance of a large set of plastid genes for inferring the broad phylogenetic backbone of mosses-the second largest major clade of land plants-and their nearest relatives.
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Bryophyte-specific primers for retrieving plastid genes suitable for phylogenetic inference.
Am. J. Bot.
PUBLISHED: 05-27-2011
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We present here new bryophyte-specific primers that permit retrieval of 17 slowly evolving plastid genes and their associated introns and intergenic spacers. These regions were chosen to facilitate accurate phylogenetic inference across a broad range of mosses and other bryophytes.
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Innate immune performance and steroid hormone profiles of pregnant versus nonpregnant cottonmouth snakes (Agkistrodon piscivorus).
Gen. Comp. Endocrinol.
PUBLISHED: 04-25-2011
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Squamates (lizards and snakes) have independently evolved viviparity over 100 times, and exhibit a wide range of maternal investment in developing embryos from the extremes of lecithotrophic oviparity to matrotrophic viviparity. This group therefore provides excellent comparative opportunities for studying endocrine and immune involvement during pregnancy, and their possible interactions. We studied the cottonmouth (Agkistrodon piscivorus), since they exhibit limited placentation (e.g., ovoviviparity), allowing comparison with squamate species hypothesized to require considerable maternal immune modulation due to the presence of a more extensive placental connection. Furthermore, the cottonmouths biennial reproductive cycle provides an opportunity for simultaneously comparing pregnant and non-pregnant females in the wild. We document significantly elevated concentrations of progesterone (P4) and significantly lower concentrations of estradiol (E2) in pregnant females relative to non-pregnant females. Pregnant females had lower plasma bacteria lysis capacity relative to non-pregnant females. This functional measure of innate immunity is a proxy for complement performance, and we also determined significant correlations between P4 and decreased complement performance in pregnant females. These findings are consistent with studies that have determined P4s role in complement modulation during pregnancy in mammals, and thus this study joins a growing number of studies that have demonstrated convergent and/or conserved physiological mechanisms regulating viviparous reproduction in vertebrates.
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Choosing and using a plant DNA barcode.
PLoS ONE
PUBLISHED: 03-24-2011
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The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.
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Host reproductive phenology drives seasonal patterns of host use in mosquitoes.
PLoS ONE
PUBLISHED: 02-08-2011
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Seasonal shifts in host use by mosquitoes from birds to mammals drive the timing and intensity of annual epidemics of mosquito-borne viruses, such as West Nile virus, in North America. The biological mechanism underlying these shifts has been a matter of debate, with hypotheses falling into two camps: (1) the shift is driven by changes in host abundance, or (2) the shift is driven by seasonal changes in the foraging behavior of mosquitoes. Here we explored the idea that seasonal changes in host use by mosquitoes are driven by temporal patterns of host reproduction. We investigated the relationship between seasonal patterns of host use by mosquitoes and host reproductive phenology by examining a seven-year dataset of blood meal identifications from a site in Tuskegee National Forest, Alabama USA and data on reproduction from the most commonly utilized endothermic (white-tailed deer, great blue heron, yellow-crowned night heron) and ectothermic (frogs) hosts. Our analysis revealed that feeding on each host peaked during periods of reproductive activity. Specifically, mosquitoes utilized herons in the spring and early summer, during periods of peak nest occupancy, whereas deer were fed upon most during the late summer and fall, the period corresponding to the peak in births for deer. For frogs, however, feeding on early- and late-season breeders paralleled peaks in male vocalization. We demonstrate for the first time that seasonal patterns of host use by mosquitoes track the reproductive phenology of the hosts. Peaks in relative mosquito feeding on each host during reproductive phases are likely the result of increased tolerance and decreased vigilance to attacking mosquitoes by nestlings and brooding adults (avian hosts), quiescent young (avian and mammalian hosts), and mate-seeking males (frogs).
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Spatial patterns of plant diversity below-ground as revealed by DNA barcoding.
Mol. Ecol.
PUBLISHED: 01-22-2011
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Our understanding of the spatial organization of root diversity in plant communities and of the mechanisms of community assembly has been limited by our ability to identify plants based on root tissue, especially in diverse communities. Here, we test the effectiveness of the plastid gene rbcL, a core plant DNA barcoding marker, for investigating spatial patterns of root diversity, and relate observed patterns to above-ground community structure. We collected 3800 root fragments from four randomly positioned, 1-m-deep soil profiles (two vertical transects per plot), located in an old-field community in southern Ontario, Canada, and extracted and sequenced DNA from 1531 subsampled fragments. We identified species by comparing sequences with a DNA barcode reference library developed previously for the local flora. Nearly 85% of sampled root fragments were successfully sequenced and identified as belonging to 29 plant species or species groups. Root abundance and species richness varied in horizontal space and were negatively correlated with soil depth. The relative abundance of taxa below-ground was correlated with their frequency above-ground (r = 0.73, P = 0.0001), but several species detected in root tissue were not observed in above-ground quadrats. Multivariate analyses indicated that diversity was highly structured below-ground, and associated with depth, root morphology, soil chemistry and soil texture, whereas little structure was evident above-ground. Furthermore, analyses of species co-occurrence indicates strong species segregation overall but random co-occurrence among confamilials. Our results provide insights into the role of environmental filtering and competitive interactions in the organization of plant diversity below-ground, and also demonstrate the utility of barcoding for the identification of plant roots.
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Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes).
Am. J. Bot.
PUBLISHED: 08-26-2010
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• Premise of the Study: The monilophytes (ferns and relatives)-the third largest group of land plants-exhibit a diverse array of vegetative and reproductive morphologies. Investigations into their early ecological and life-history diversification require accurate, well-corroborated phylogenetic estimates. We examined the utility of a large plastid-based data set in inferring backbone relationships for monilophytes. • Methods: We recovered 17 plastid genes for exemplar taxa using published and new primers. We compared results from maximum-likelihood and parsimony analyses, assessed the effects of removing rapidly evolving characters, and examined the extent to which our data corroborate or contradict the results of other studies, or resolve current ambiguities. • Key Results: Considering multifamily clades, we found bootstrap support comparable to or better than that in published studies that used fewer genes from fewer or more taxa. We firmly establish filmy ferns (Hymenophyllales) as the sister group of all leptosporangiates except Osmundaceae, resolving the second deepest split in leptosporangiate-fern phylogeny. A clade comprising Ophioglossaceae and Psilotaceae is currently accepted as the sister group of other monilophytes, but we recover Equisetum in this position. We also recover marattioid and leptosporangiate ferns as sister groups. Maximum-likelihood rate-class estimates are somewhat skewed when a long-branch lineage (Selaginella) is included, negatively affecting bootstrap support for early branches. • Conclusions: Our findings support the utility of this gene set in corroborating relationships found in previous studies, improving support, and resolving uncertainties in monilophyte phylogeny. Despite these advances, our results also underline the need for continued work on resolving the very earliest splits in monilophyte phylogeny.
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Nestedness of ectoparasite-vertebrate host networks.
PLoS ONE
PUBLISHED: 08-10-2009
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Determining the structure of ectoparasite-host networks will enable disease ecologists to better understand and predict the spread of vector-borne diseases. If these networks have consistent properties, then studying the structure of well-understood networks could lead to extrapolation of these properties to others, including those that support emerging pathogens. Borrowing a quantitative measure of network structure from studies of mutualistic relationships between plants and their pollinators, we analyzed 29 ectoparasite-vertebrate host networks--including three derived from molecular bloodmeal analysis of mosquito feeding patterns--using measures of nestedness to identify non-random interactions among species. We found significant nestedness in ectoparasite-vertebrate host lists for habitats ranging from tropical rainforests to polar environments. These networks showed non-random patterns of nesting, and did not differ significantly from published estimates of nestedness from mutualistic networks. Mutualistic and antagonistic networks appear to be organized similarly, with generalized ectoparasites interacting with hosts that attract many ectoparasites and more specialized ectoparasites usually interacting with these same "generalized" hosts. This finding has implications for understanding the network dynamics of vector-born pathogens. We suggest that nestedness (rather than random ectoparasite-host associations) can allow rapid transfer of pathogens throughout a network, and expand upon such concepts as the dilution effect, bridge vectors, and host switching in the context of nested ectoparasite-vertebrate host networks.
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Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?
Mol Ecol Resour
PUBLISHED: 05-01-2009
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The ability to discriminate between species using barcoding loci has proved more difficult in plants than animals, raising the possibility that plant species boundaries are less well defined. Here, we review a selection of published barcoding data sets to compare species discrimination in plants vs. animals. Although the use of different genetic markers, analytical methods and depths of taxon sampling may complicate comparisons, our results using common metrics demonstrate that the number of species supported as monophyletic using barcoding markers is higher in animals (> 90%) than plants (~70%), even after controlling for the amount of parsimony-informative information per species. This suggests that more than a simple lack of variability limits species discrimination in plants. Both animal and plant species pairs have variable size gaps between intra- and interspecific genetic distances, but animal species tend to have larger gaps than plants, even in relatively densely sampled genera. An analysis of 12 plant genera suggests that hybridization contributes significantly to variation in genetic discontinuity in plants. Barcoding success may be improved in some plant groups by careful choice of markers and appropriate sampling; however, overall fine-scale species discrimination in plants relative to animals may be inherently more difficult because of greater levels of gene-tree paraphyly.
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Phylogeography of the Brownback Salamander reveals patterns of local endemism in Southern Appalachian springs.
Mol. Phylogenet. Evol.
PUBLISHED: 02-26-2009
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The Appalachian Mountains of eastern North America are characterized by high faunal diversity and many endemic species, especially in the unglaciated southern latitudes where lineages have been accumulating for tens of millions of years. The Brownback Salamander, Eurycea aquatica, is an enigmatic species that dwells in isolated springs in southeastern North America. Eurycea aquatica have often been dismissed as simply robust spring-adapted ecomorphs of the widespread and more gracile species Eurycea cirrigera. We sequenced the mitochondrial gene encoding NADH dehydrogenase subunit-2 (ND2; 753 bp) and the nuclear recombination activating gene-1 (Rag1; 1201 bp) for E. aquatica (ND2 n = 72; Rag1 n = 17) from across their presumed distribution and compared them to E. cirrigera (ND2 n = 23; Rag1 n = 10) from nearby populations. Using phylogenetic and morphological analyses we explicitly test if E. aquatica in the Southern Appalachians is simply a local spring-adapted ecomorph of E. cirrigera or a single lineage that resulted from fragmentation of (or dispersal to) spring habitats. We found that E. aquatica from isolated springs form a well-supported monophyletic group that is nested among E. cirrigera, E. wilderae, and E. junaluska. Furthermore, we uncovered three very divergent lineages of E. aquatica that we estimate have been isolated from each another since the early Pliocene to late Miocene (2.5-6.1 Myr) and may each represent distinct species. The distribution of these lineages is coincident with the distribution of other endemic spring-dwelling vertebrates, and suggests that this region may be a relictual habitat for an unexpected diversity of unrecognized endemics.
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Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny.
Am. J. Bot.
PUBLISHED: 01-01-2009
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We examined multiple plastid genes from a diversity of gymnosperm lineages to explore the consistency of signal among different outgroups for rooting flowering plant phylogeny. For maximum parsimony (MP), most outgroups attach on a branch of the underlying ingroup tree that leads to Amborella. Maximum likelihood (ML) analyses either root angiosperms on a nearby branch or find split support for these neighboring root placements, depending on the outgroup. The inclusion of two species of Hydatellaceae, recently recognized as an ancient line of angiosperms, does not aid in inference of the root. Cost profiles for placing the root in suboptimal locations are highly correlated across most outgroup comparisons, even comparing MP and ML profiles. Those for Gnetales are the most deviant of all those considered. This divergent outgroup either attaches on a long eudicot branch with moderate bootstrap support in MP analyses or supports no particular root location in ML analysis. Removing the most rapidly evolving sites in rate classifications based on two divergent angiosperm root placements with Gnetales yields strongly conflicting root placements in MP analysis, despite substantial overlap in the estimated sets of conservative sites. However, the generally high consistency in rooting signal among distantly related gymnosperm clades suggests that the long branch connecting angiosperms to their extant relatives may not interfere substantially with inference of the angiosperm root.
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Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes.
PLoS ONE
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Next-generation sequencing plays a central role in the characterization and quantification of transcriptomes. Although numerous metrics are purported to quantify the quality of RNA, there have been no large-scale empirical evaluations of the major determinants of sequencing success. We used a combination of existing and newly developed methods to isolate total RNA from 1115 samples from 695 plant species in 324 families, which represents >900 million years of phylogenetic diversity from green algae through flowering plants, including many plants of economic importance. We then sequenced 629 of these samples on Illumina GAIIx and HiSeq platforms and performed a large comparative analysis to identify predictors of RNA quality and the diversity of putative genes (scaffolds) expressed within samples. Tissue types (e.g., leaf vs. flower) varied in RNA quality, sequencing depth and the number of scaffolds. Tissue age also influenced RNA quality but not the number of scaffolds ? 1000 bp. Overall, 36% of the variation in the number of scaffolds was explained by metrics of RNA integrity (RIN score), RNA purity (OD 260/230), sequencing platform (GAIIx vs HiSeq) and the amount of total RNA used for sequencing. However, our results show that the most commonly used measures of RNA quality (e.g., RIN) are weak predictors of the number of scaffolds because Illumina sequencing is robust to variation in RNA quality. These results provide novel insight into the methods that are most important in isolating high quality RNA for sequencing and assembling plant transcriptomes. The methods and recommendations provided here could increase the efficiency and decrease the cost of RNA sequencing for individual labs and genome centers.
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Detection of eastern equine encephalomyelitis virus RNA in North American snakes.
Am. J. Trop. Med. Hyg.
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The role of non-avian vertebrates in the ecology of eastern equine encephalomyelitis virus (EEEV) is unresolved, but mounting evidence supports a potential role for snakes in the EEEV transmission cycle, especially as over-wintering hosts. To determine rates of exposure and infection, we examined serum samples from wild snakes at a focus of EEEV in Alabama for viral RNA using quantitative reverse transcription polymerase chain reaction. Two species of vipers, the copperhead (Agkistrodon contortrix) and the cottonmouth (Agkistrodon piscivorus), were found to be positive for EEEV RNA using this assay. Prevalence of EEEV RNA was more frequent in seropositive snakes than seronegative snakes. Positivity for the quantitative reverse transcription polymerase chain reaction in cottonmouths peaked in April and September. Body size and sex ratios were not significantly different between infected and uninfected snakes. These results support the hypothesis that snakes are involved in the ecology of EEEV in North America, possibly as over-wintering hosts for the virus.
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Corticosterone-immune interactions during captive stress in invading Australian cane toads (Rhinella marina).
Horm Behav
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Vertebrates cope with physiological challenges using two major mechanisms: the immune system and the hypothalamic pituitary-adrenal axis (e.g., the glucocorticoid stress response). Because the two systems are tightly integrated, we need simultaneous studies of both systems, in a range of species, to understand how vertebrates respond to novel challenges. To clarify how glucocorticoids modulate the amphibian immune system, we measured three immune parameters and plasma corticosterone (CORT), before and after inflicting a stressor (capture and captive confinement) on introduced cane toads (Rhinella marina) near their invasion front in Australia. Stress increased CORT levels, decreased complement lysis capacity, increased leukocyte oxidative burst, and did not change heterologous erythrocyte agglutination. The strength of the CORT response was positively correlated with leukocyte oxidative burst, and morphological features associated with invasiveness in cane toads (relative leg length) were correlated with stress responsiveness. No immune parameter that we measured was affected by a toads infection by a parasitic nematode (Rhabdias pseudosphaerocephala), but the CORT response was muted in infected versus uninfected toads. These results illustrate the complex immune-stress interactions in wild populations of a non-traditional model vertebrate species, and describe immune adaptations of an important invasive species.
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Molecular phylogenetics of Hydatellaceae (Nymphaeales): sexual-system homoplasy and a new sectional classification.
Am. J. Bot.
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Species relationships are unknown in Hydatellaceae, a small family of dwarf aquatics related to water lilies that arose near the base of angiosperm phylogeny. Here we use molecular evidence to infer a species tree for the family and apply this to reconstructing major transitions in morphology and sexual system in this early branch of angiosperms.
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Serosurveillance of eastern equine encephalitis virus in amphibians and reptiles from Alabama, USA.
Am. J. Trop. Med. Hyg.
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Eastern equine encephalitis virus (EEEV) is among the most medically important arboviruses in North America, and studies suggest a role for amphibians and reptiles in its transmission cycle. Serum samples collected from 351 amphibians and reptiles (27 species) from Alabama, USA, were tested for the presence of antibodies against EEEV. Frogs, turtles, and lizards showed little or no seropositivity, and snakes had high seropositivity rates. Most seropositive species were preferred or abundant hosts of Culex spp. mosquitoes at Tuskegee National Forest, that target ectothermic hosts. The cottonmouth, the most abundant ectotherm sampled, displayed a high prevalence of seropositivity, indicating its possible role as an amplification and/or over-wintering reservoir for EEEV.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.