When You and I Were Young, Maggie

VERSE 1I wandered today to the hill, Maggie,To watch the scene below;The creek and the creaking old mill, Maggie,As we used to long ago,The green grove is gone from the hill, Maggie,Where first the daisies sprung;The creaking old mill is still, Maggie,Since you and I were young. CHORUSAnd now we are aged and gray, Maggie,And the trials of life nearly done;Let us sing of the days that are gone, Maggie,When you and I were young.Let us sing, VERSE 2A city so silent and lone, Maggie,Where the young and the gay and the best,In polished white mansions of stone, Maggie,Have each found a place of rest,Is built were the birds used to play, Maggie,And join in the songs that were sung:For we sang as gay as they. Maggie,When you and I were young. CHORUS VERSE 3They say I am feeble with age, MaggieMy steps are less sprightly than then,My face is a well-written page, Maggie,But time alone was the pen.They say we are aged and gray, Maggie,As sprays by the white breakers flung;But to me you’re as fair as you were, MaggieWhen you and I were young. CHORU

When You And I Were Young, Maggie.

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Cytonuclear discordance in the Florida Everglades invasive Burmese python (Python bivittatus) population reveals possible hybridization with the Indian python (P. molurus)

The invasive Burmese python (Python bivittatus) has been reproducing in the Florida Everglades since the 1980s. These giant constrictor snakes have caused a precipitous decline in small mammal populations in southern Florida following escapes or releases from the commercial pet trade. To better understand the invasion pathway and genetic composition of the population, two mitochondrial (mtDNA) loci across 1,398 base pairs were sequenced on 426 snakes and 22 microsatellites were assessed on 389 snakes. Concatenated mtDNA sequences produced six haplotypes with an average nucleotide and haplotype diversity of π = 0.002 and h = 0.097, respectively. Samples collected in Florida from morphologically identified P. bivittatus snakes were similar to published cytochrome oxidase 1 and cytochrome b sequences from both P. bivittatus and Python molurus and were highly divergent (genetic distances of 5.4% and 4.3%, respectively). The average number of microsatellite alleles and expected heterozygosity were NA = 5.50 and HE = 0.60, respectively. Nuclear Bayesian assignment tests supported two genetically distinct groups and an admixed group, not geographically differentiated. The effective population size (NE = 315.1) was lower than expected for a population this large, but reflected the low genetic diversity overall. The patterns of genetic diversity between mtDNA and microsatellites were disparate, indicating nuclear introgression of separate mtDNA lineages corresponding to cytonuclear discordance. The introgression likely occurred prior to the invasion, but genetic information on the native range and commercial trade is needed for verification. Our finding that the Florida python population is comprised of distinct lineages suggests greater standing variation for adaptation and the potential for broader areas of suitable habitat in the invaded range

Sulfide geochronology along the Endeavour Segment of the Juan de Fuca Ridge

Forty-nine hydrothermal sulfide-sulfate rock samples from the Endeavour Segment of the Juan de Fuca Ridge, northeastern Pacific Ocean, were dated by measuring the decay of 226Ra (half-life of 1600 years) in hydrothermal barite to provide a history of hydrothermal venting at the site over the past 6000 years. This dating method is effective for samples ranging in age from ∼200 to 20,000 years old and effectively bridges an age gap between shorter- and longer-lived U-series dating techniques for hydrothermal deposits. Results show that hydrothermal venting at the active High Rise, Sasquatch, and Main Endeavour fields began at least 850, 1450, and 2300 years ago, respectively. Barite ages of other inactive deposits on the axial valley floor are between ∼1200 and ∼2200 years old, indicating past widespread hydrothermal venting outside of the currently active vent fields. Samples from the half-graben on the eastern slope of the axial valley range in age from ∼1700 to ∼2925 years, and a single sample from outside the axial valley, near the westernmost valley fault scarp is ∼5850 ± 205 years old. The spatial relationship between hydrothermal venting and normal faulting suggests a temporal relationship, with progressive younging of sulfide deposits from the edges of the axial valley toward the center of the rift. These relationships are consistent with the inward migration of normal faulting toward the center of the valley over time and a minimum age of onset of hydrothermal activity in this region of 5850 years

Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): G04016, doi:10.1029/2005JG000097.The presence, diversity, and distribution of a key group of subseafloor archaea, the Thermococcales, was examined in multiple diffuse flow hydrothermal vents at Axial Seamount, an active deep-sea volcano located in the northeast Pacific Ocean. A polymerase chain reaction (PCR) approach was used to determine if this group of subseafloor indicator organisms showed any phylogenetic distribution that may indicate distinct subseafloor communities at vents with different physical and chemical characteristics. Targeted primers for the Thermococcales 16S rRNA (small subunit ribosomal RNA) gene and intergenic transcribed spacer (ITS) region were designed and applied to organisms filtered in-situ directly from a variety of diffuse flow vents. Thermococcales were amplified from 9 of 11 samples examined, and it was determined that the ITS region is a better phylogenetic marker than the 16S rRNA in defining consistent groups of closely related sequences. Results show a relationship between environmental clone distribution and source vent chemistry. The most highly diluted vents with elevated iron and alkalinity contained a distinct group of Thermococcales as defined by the ITS region, suggesting separate subseafloor Thermococcales populations at diffuse vents within the Axial caldera.This work was supported by Washington Sea Grant (NA76RG0119), National Science Foundation (OCE 9816491), NSF IGERT (DGE- 9870713), NASA Astrobiology Institute through the Carnegie Geophysical Institute, the NOAA/PMEL Vents Program, NOAA West Coast and Polar Undersea Research Center, and by the Joint Institute for the Study of the Atmosphere and Ocean under NOAA Cooperative Agreement No. NA117RJ1232

Seismic structure of the Endeavour Segment, Juan de Fuca Ridge : correlations with seismicity and hydrothermal activity

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 112 (2007): B02401, doi:10.1029/2005JB004210.Multichannel seismic reflection data collected in July 2002 at the Endeavour Segment, Juan de Fuca Ridge, show a midcrustal reflector underlying all of the known high-temperature hydrothermal vent fields in this area. On the basis of the character and geometry of this reflection, its similarity to events at other spreading centers, and its polarity, we identify this as a reflection from one or more crustal magma bodies rather than from a hydrothermal cracking front interface. The Endeavour magma chamber reflector is found under the central, topographically shallow section of the segment at two-way traveltime (TWTT) values of 0.9–1.4 s (∼2.1–3.3 km) below the seafloor. It extends approximately 24 km along axis and is shallowest beneath the center of the segment and deepens toward the segment ends. On cross-axis lines the axial magma chamber (AMC) reflector is only 0.4–1.2 km wide and appears to dip 8–36° to the east. While a magma chamber underlies all known Endeavour high-temperature hydrothermal vent fields, AMC depth is not a dominant factor in determining vent fluid properties. The stacked and migrated seismic lines also show a strong layer 2a event at TWTT values of 0.30 ± 0.09 s (380 ± 120 m) below the seafloor on the along-axis line and 0.38 ± 0.09 s (500 ± 110 m) on the cross-axis lines. A weak Moho reflection is observed in a few locations at TWTT values of 1.9–2.4 s below the seafloor. By projecting hypocenters of well-located microseismicity in this region onto the seismic sections, we find that most axial earthquakes are concentrated just above the magma chamber and distributed diffusely within this zone, indicating thermal-related cracking. The presence of a partially molten crustal magma chamber argues against prior hypotheses that hydrothermal heat extraction at this intermediate spreading ridge is primarily driven by propagation of a cracking front down into a frozen magma chamber and indicates that magmatic heat plays a significant role in the hydrothermal system. Morphological and hydrothermal differences between the intermediate spreading Endeavour and fast spreading ridges are attributable to the greater depth of the Endeavour AMC and the corresponding possibility of axial faulting.E.V.A. was supported by a National Science Foundation Graduate Research Fellowship, the WHOI-MIT Joint Program, and the WHOI Deep Ocean Exploration Institute. This work was also supported by OCE-0002551 to the Woods Hole Oceanographic Institution, OCE-0002488 to Lamont-Doherty Earth Observatory, and OCE-0002600 to Scripps Institution of Oceanography

Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

BACKGROUND: The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss). RESULTS: We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84%) of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome) also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins), Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value < 1e-10). We identified multigenic families that appeared larger in spruce than in the Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. CONCLUSION: This report illustrates specific approaches for large-scale gene discovery and annotation in an organism that is very distantly related to any of the fully sequenced genomes. The ArboreaSet sequences and cDNA clones represent a valuable resource for investigations ranging from plant comparative genomics to applied conifer genetics

Hydrothermal venting at Vailulu'u Seamount : the smoking end of the Samoan chain

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 5 (2004): Q02003, doi:10.1029/2003GC000626.The summit crater of Vailulu'u Seamount, the youngest volcano in the Samoan chain, hosts an active hydrothermal system with profound impact on the ocean water column inside and around its crater (2 km wide and 407 m deep at a 593 m summit depth). The turbidity of the ocean water reaches 1.4 NTU, values that are higher than in any other submarine hydrothermal system. The water is enriched in hydrothermal Mn (3.8 ppb) and 3He (1 × 10−11 cc/g) and we measured water temperature anomalies near the crater floor up to 0.2°C. The hydrothermal system shows complex interactions with the ocean currents around Vailulu'u that include tidally-modulated vertical motions of about 40–50 m, and replenishment of waters into the crater through breaches in the upper half of the crater wall. Inside and outside potential density gradients suggest that hydrothermal venting exports substantial amounts of water from the crater (1.3 ± 0.2 × 108 m3/day), which is in good agreement with fluxes obtained from a tracer release experiment inside the crater of Vailulu'u (0.8 × 108 m3/day [Hart et al., 2003]). This mass flux, in combination with the differences in the inside and outside crater temperature, yields a power output of around 760 megawatts, the equivalent of 20–100 MOR black smokers. The Mn output of 300 kg/day is approximately ten times the output of a single black smoker

Regeneration niche differentiates functional strategies of desert woody plant species

Plant communities vary dramatically in the number and relative abundance of species that exhibit facilitative interactions, which contributes substantially to variation in community structure and dynamics. Predicting species’ responses to neighbors based on readily measurable functional traits would provide important insight into the factors that structure plant communities. We measured a suite of functional traits on seedlings of 20 species and mature plants of 54 species of shrubs from three arid biogeographic regions. We hypothesized that species with different regeneration niches—those that require nurse plants for establishment (beneficiaries) versus those that do not (colonizers)—are functionally different. Indeed, seedlings of beneficiary species had lower relative growth rates, larger seeds and final biomass, allocated biomass toward roots and height at a cost to leaf mass fraction, and constructed costly, dense leaf and root tissues relative to colonizers. Likewise at maturity, beneficiaries had larger overall size and denser leaves coupled with greater water use efficiency than colonizers. In contrast to current hypotheses that suggest beneficiaries are less “stress-tolerant” than colonizers, beneficiaries exhibited conservative functional strategies suited to persistently dry, low light conditions beneath canopies, whereas colonizers exhibited opportunistic strategies that may be advantageous in fluctuating, open microenvironments. In addition, the signature of the regeneration niche at maturity indicates that facilitation expands the range of functional diversity within plant communities at all ontogenetic stages. This study demonstrates the utility of specific functional traits for predicting species’ regeneration niches in hot deserts, and provides a framework for studying facilitation in other severe environments

TRY plant trait database - enhanced coverage and open access

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives