bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐lasting effects on nitrogen cycling 12 years after treatments cease despite minimal long‐term nitrogen retention
Authors: CLARK CHRISTOPHER M. , HOBBIE SARAH E. , VENTEREA RODNEY , TILMAN DAVID 
Published: November 2008

AbstractAtmospheric deposition of biologically active nitrogen (N) has increased dramatically over the past 60 years, with far‐reaching impacts on the structure and function of many ecosystems. Much research has examined the initial impacts of N enrichment; however, few studies have been multidecadal, and even fewer long‐term studies have examined the longevity of N‐induced impacts on N cycling after inputs cease. Here, we address this gap by reporting the state of key N pools and fluxes in a Minnesota grassland for plots that received N addition for 10 years and then none for 12 years, in comparison with plots that received annual N treatment for the entire 22 years. We found weak evidence for long‐term N retention in plots that ceased receiving treatment; and in plots that continued to receive N over the 22‐year period, retention that was high after 12 years (50–100% of inputs) was greatly reduced after 22 years (to 15%). In spite of this, net N mineralization rates remained elevated in plots that ceased receiving treatment 12 years prior, likely because N‐rich litter maintained higher N‐cycling rates. These results suggest (1) some systems do not retain much deposited N, with potentially large impacts on downstream habitats; (2) the previously reported high retention efficiencies for this and many other terrestrial ecosystems may be relatively short‐lived as N sinks become saturated over time; and (3) the effects of even small amounts of retained N in N‐limited environments may be particularly long‐lasting. In total, these findings highlight the importance of long‐term studies in evaluating the impacts of chronic N deposition to ecosystems, and urge additional research examining dynamics following N cessation to evaluate the reversibility of these impacts.
Comparison of the impacts of consumers, ambient UV, and future UVB irradiance on mid‐latitudinal macroepibenthic assemblages
Authors: MOLIS MARKUS , WAHL MARTIN 
Published: November 2008

AbstractFuture levels in ultraviolet‐B (UVB) radiation are expected to increase directly due to stratospheric ozone depletion and under water indirectly by, for example, global warming effects on DOC concentrations, altered trophic interactions in the plankton, or reduced eutrophication. While detrimental UV effects have been reported at the cellular level, little to nothing is known about community‐wide effects of ambient and future UVB radiation. In a 4‐month field experiment, the ambient UV regime was (i) reduced by cut‐off filters which removed either UVB or total UV from the solar spectrum or (ii) increased to predicted future levels by UVB lamps. To allow relating the effects of present and future UV regimes to another important ecological control of community structure and diversity in subtidal marine habitats, consumer effects were quantified by an exclusion treatment under ambient light regimes. Ambient UV regimes did not affect community structure, biomass accrual, and diversity. In contrast, under enhanced UVB levels, the dominance of the competitively superior blue mussels increased and species richness and biomass accrual decreased. Species composition of the assemblages differed between the two UV regimes. Effects of enhanced UVB radiation and of consumption on biomass accrual, diversity, and structure of the community were comparable in magnitude and timing, but of opposite direction. In contrast, the effects of enhanced UVB radiation on growth and abundance of mussels were in the same direction, but shorter and weaker than consumer effects. Most UV effects were transitory and vanished within the first 2 months of succession. Our results indicate that present and future UVB levels may be of limited importance and not stronger in effect size than other ecological controls in structuring the shallow‐water low‐diversity macrobenthic communities in temperate regions.
The land–atmosphere water flux in the tropics
Authors: FISHER JOSHUA B. , MALHI YADVINDER , BONAL DAMIEN , DA ROCHA HUMBERTO R. , DE ARAÚJO ALESSANDRO C. , GAMO MINORU , GOULDEN MICHAEL L. , HIRANO TAKASHI , HUETE ALFREDO R. , KONDO HIROAKI , KUMAGAI TOMO'OMI , LOESCHER HENRY W. , MILLER SCOTT , NOBRE ANTONIO D. , NOUVELLON YANN , OBERBAUER STEVEN F. , PANUTHAI SAMREONG , ROUPSARD OLIVIER , SALESKA SCOTT , TANAKA KATSUNORI , TANAKA NOBUAKI , TU KEVIN P. , VON RANDOW CELSO 
Published: November 2008

AbstractTropical vegetation is a major source of global land surface evapotranspiration, and can thus play a major role in global hydrological cycles and global atmospheric circulation. Accurate prediction of tropical evapotranspiration is critical to our understanding of these processes under changing climate. We examined the controls on evapotranspiration in tropical vegetation at 21 pan‐tropical eddy covariance sites, conducted a comprehensive and systematic evaluation of 13 evapotranspiration models at these sites, and assessed the ability to scale up model estimates of evapotranspiration for the test region of Amazonia. Net radiation was the strongest determinant of evapotranspiration (mean evaporative fraction was 0.72) and explained 87% of the variance in monthly evapotranspiration across the sites. Vapor pressure deficit was the strongest residual predictor (14%), followed by normalized difference vegetation index (9%), precipitation (6%) and wind speed (4%). The radiation‐based evapotranspiration models performed best overall for three reasons: (1) the vegetation was largely decoupled from atmospheric turbulent transfer (calculated from Ω decoupling factor), especially at the wetter sites; (2) the resistance‐based models were hindered by difficulty in consistently characterizing canopy (and stomatal) resistance in the highly diverse vegetation; (3) the temperature‐based models inadequately captured the variability in tropical evapotranspiration. We evaluated the potential to predict regional evapotranspiration for one test region: Amazonia. We estimated an Amazonia‐wide evapotranspiration of 1370 mm yr−1, but this value is dependent on assumptions about energy balance closure for the tropical eddy covariance sites; a lower value (1096 mm yr−1) is considered in discussion on the use of flux data to validate and interpolate models.
Geostatistical genetic analysis for inferring the dispersal pattern of a partially clonal species: example of the chestnut blight fungus
Authors: DUTECH C. , ROSSI J.‐P. , FABREGUETTES O. , ROBIN C. 
Published: November 2008

AbstractSpatial genetic analyses can be used to infer dispersal processes in natural populations. For partially clonal species with alternating sexual and asexual reproduction, the repetition of genotypes must be taken into account in analyses. The methods currently employed to evaluate the relevance of the spatial scale used for the estimation of gene flow are not suitable for these species. We investigated recently developed methods for taking into account repeated genotypes and for determining whether the sampling scale is large enough to capture all the spatial genetic structure existing within a population. We applied these methods to a fungal plant pathogen species,Cryphonectria parasitica,which has caused the death of many American and European chestnut trees since its introduction from Asia at the beginning of the 20th century. These methods were found to be useful for unravelling the effects of clonality and historical gene flow on the spatial genetic structure, and indicated that dispersal processes have probably occurred over a larger spatial scale than previously assumed.
Mating system, pollen and propagule dispersal, and spatial genetic structure in a high‐density population of the mangrove tree Kandelia candel
Authors: GENG QIFANG , LIAN CHUNLAN , GOTO SUSUMU , TAO JIANMIN , KIMURA MEGUMI , ISLAM MD SAJEDUL , HOGETSU TAIZO 
Published: November 2008

AbstractMangrove tree species form ecologically and economically important forests along the tropical and subtropical coastlines of the world. Although low intrapopulation genetic diversity and high interpopulation genetic differentiation have been detected in most mangrove tree species, no direct investigation of pollen and propagule dispersal through paternity and/or parentage analysis and spatial genetic structure within populations has been conducted. We surveyed the mating system, pollen and propagule dispersal, and spatial genetic structure in a natural population of Kandelia candel, one of the typical viviparous mangrove tree species, using nuclear and chloroplast microsatellite markers. High diversity and outcrossing rates were observed. Paternity and parentage analysis and modelling estimations revealed the presence of an extremely short‐distance component of pollen and propagule dispersal (pollen: 15.2 ± 14.9 m (SD) by paternity analysis and 34.4 m by modelling; propagule: 9.4 ± 13.8 m (SD) by parentage analysis, and 18.6 m by modelling). Genetic structure was significant at short distances, and a clumped distribution of chloroplast microsatellite genotypes was seen in K. candel adults. We conclude that the K. candel population was initiated by limited propagule founders from outside by long‐distance dispersal followed by limited propagule dispersal from the founders, resulting in a half‐sib family structure.
Host range expansion of an introduced insect pest through multiple colonizations of specialized clones
Authors: PECCOUD J. , FIGUEROA C. C. , SILVA A. X. , RAMIREZ C. C. , MIEUZET L. , BONHOMME J. , STOECKEL S. , PLANTEGENEST M. , SIMON J.‐C. 
Published: November 2008

AbstractAsexuality confers demographic advantages to invasive taxa, but generally limits adaptive potential for colonizing of new habitats. Therefore, pre‐existing adaptations and habitat tolerance are essential in the success of asexual invaders. We investigated these key factors of invasiveness by assessing reproductive modes and host‐plant adaptations in the pea aphid, Acyrthosiphon pisum, a pest recently introduced into Chile. The pea aphid encompasses lineages differing in their reproductive mode, ranging from obligatory cyclical parthenogenesis to fully asexual reproduction. This species also shows variation in host use, with distinct biotypes specialized on different species of legumes as well as more polyphagous populations. In central Chile, microsatellite genotyping of pea aphids sampled on five crops and wild legumes revealed three main clonal genotypes, which showed striking associations with particular host plants rather than sampling locations. Phenotypic analyses confirmed their strong host specialization and demonstrated parthenogenesis as their sole reproductive mode. The genetic relatedness of these clonal genotypes with corresponding host‐specialized populations from the Old World indicated that each clone descended from a particular Eurasian biotype, which involved at least three successful introduction events followed by spread on different crops. This study illustrates that multiple introductions of highly specialized clones, rather than local evolution in resource use and/or selection of generalist genotypes, can explain the demographic success of a strictly asexual invader.
Fine‐scale genetic structure of a long‐lived reptile reflects recent habitat modification
Authors: MOORE J. A. , MILLER H. C. , DAUGHERTY C. H. , NELSON N. J. 
Published: November 2008

AbstractAnthropogenic habitat fragmentation — ubiquitous in modern ecosystems — has strong impacts on gene flow and genetic population structure. Reptiles may be particularly susceptible to the effects of fragmentation because of their extreme sensitivity to environmental conditions and limited dispersal. We investigate fine‐scale spatial genetic structure, individual relatedness, and sex‐biased dispersal in a large population of a long‐lived reptile (tuatara, Sphenodon punctatus) on a recently fragmented island. We genotyped individuals from remnant forest, regenerating forest, and grassland pasture sites at seven microsatellite loci and found significant genetic structuring (RST = 0.012) across small distances (< 500 m). Isolation by distance was not evident, but rather, genetic distance was weakly correlated with habitat similarity. Only individuals in forest fragments were correctly assignable to their site of origin, and individual pairwise relatedness in one fragment was significantly higher than expected. We did not detect sex‐biased dispersal, but natural dispersal patterns may be confounded by fragmentation. Assignment tests showed that reforestation appears to have provided refuges for tuatara from disturbed areas. Our results suggest that fine‐scale genetic structuring is driven by recent habitat modification and compounded by the sedentary lifestyle of these long‐lived reptiles. Extreme longevity, large population size, simple social structure and random dispersal are not strong enough to counteract the genetic structure caused by a sedentary lifestyle. We suspect that fine‐scale spatial genetic structuring could occur in any sedentary species with limited dispersal, making them more susceptible to the effects of fragmentation.
Landscape genetic structure of coastal tailed frogs (Ascaphus truei) in protected vs. managed forests
Authors: SPEAR STEPHEN F. , STORFER ANDREW 
Published: November 2008

AbstractHabitat loss and fragmentation are the leading causes of species’ declines and extinctions. A key component of studying population response to habitat alteration is to understand how fragmentation affects population connectivity in disturbed landscapes. We used landscape genetic analyses to determine how habitat fragmentation due to timber harvest affects genetic population connectivity of the coastal tailed frog (Ascaphus truei), a forest‐dwelling, stream‐breeding amphibian. We compared rates of gene flow across old‐growth (Olympic National Park) and logged landscapes (Olympic National Forest) and used spatial autoregression to estimate the effect of landscape variables on genetic structure. We detected higher overall genetic connectivity across the managed forest, although this was likely a historical signature of continuous forest before timber harvest began. Gene flow also occurred terrestrially, as connectivity was high across unconnected river basins. Autoregressive models demonstrated that closed forest and low solar radiation were correlated with increased gene flow. In addition, there was evidence for a temporal lag in the correlation of decreased gene flow with harvest, suggesting that the full genetic impact may not appear for several generations. Furthermore, we detected genetic evidence of population bottlenecks across the Olympic National Forest, including at sites that were within old‐growth forest but surrounded by harvested patches. Collectively, this research suggests that absence of forest (whether due to natural or anthropogenic changes) is a key restrictor of genetic connectivity and that intact forested patches in the surrounding environment are necessary for continued gene flow and population connectivity.
Genetic evidence of intercontinental movement of avian influenza in a migratory bird: the northern pintail (Anas acuta)
Authors: KOEHLER ANSON V. , PEARCE JOHN M. , FLINT PAUL L. , FRANSON J. CHRISTIAN , IP HON S. 
Published: November 2008

AbstractThe role of migratory birds in the movement of the highly pathogenic (HP) avian influenza H5N1 remains a subject of debate. Testing hypotheses regarding intercontinental movement of low pathogenic avian influenza (LPAI) viruses will help evaluate the potential that wild birds could carry Asian‐origin strains of HP avian influenza to North America during migration. Previous North American assessments of LPAI genetic variation have found few Asian reassortment events. Here, we present results from whole‐genome analyses of LPAI isolates collected in Alaska from the northern pintail (Anas acuta), a species that migrates between North America and Asia. Phylogenetic analyses confirmed the genetic divergence between Asian and North American strains of LPAI, but also suggested inter‐continental virus exchange and at a higher frequency than previously documented. In 38 isolates from Alaska, nearly half (44.7%) had at least one gene segment more closely related to Asian than to North American strains of LPAI. Additionally, sequences of several Asian LPAI isolates from GenBank clustered more closely with North American northern pintail isolates than with other Asian origin viruses. Our data support the role of wild birds in the intercontinental transfer of influenza viruses, and reveal a higher degree of transfer in Alaska than elsewhere in North America.
Comparative genomics and the study of evolution by natural selection
Authors: ELLEGREN HANS 
Published: November 2008

AbstractGenomics profoundly affects most areas of biology, including ecology and evolutionary biology. By examining genome sequences from multiple species, comparative genomics offers new insight into genome evolution and the way natural selection moulds DNA sequence evolution. Functional divergence, as manifested in the accumulation of nonsynonymous substitutions in protein‐coding genes, differs among lineages in a manner seemingly related to population size. For example, the ratio of nonsynonymous to synonymous substitution (dN/dS) is higher in apes than in rodents, compatible with Ohta's nearly neutral theory of molecular evolution, which suggests that the fixation of slightly deleterious mutations contributes to protein evolution at an extent negatively correlated with effective population size. While this supports the idea that functional evolution is not necessarily adaptive, comparative genomics is uncovering a role for positive Darwinian selection in 10–40% of all genes in different lineages, estimates that are likely to increase when the addition of more genomes gives increased power. Again, population size seems to matter also in this context, with a higher proportion of fixed amino acid changes representing advantageous mutations in large populations. Genes that are particularly prone to be driven by positive selection include those involved with reproduction, immune response, sensory perception and apoptosis. Genetic innovations are also frequently obtained by the gain or loss of complete gene sequences. Moreover, it is increasingly realized, from comparative genomics, that purifying selection conserves much more than just the protein‐coding part of the genome, and this points at an important role for regulatory elements in trait evolution. Finally, genome sequencing using outbred or multiple individuals has provided a wealth of polymorphism data that gives information on population history, demography and marker evolution.
Conditional neutrality at two adjacent NBS‐LRR disease resistance loci in natural populations of Arabidopsis lyrata
Authors: GOS GESSECA , WRIGHT STEPHEN I 
Published: November 2008

AbstractWe examined patterns of nucleotide diversity at a genomic region containing two linked candidate disease resistance (NBS‐LRR) genes in seven populations of the outcrossing plant Arabidopsis lyrata. In comparison with two adjacent control genes and neutral reference genes across the genome, the NBS‐LRR genes exhibited elevated nonsynonymous variation and a large number of major‐effect polymorphisms causing early stop codons and/or frameshift mutations. In contrast, analysis of synonymous diversity provided no evidence that the region was subject to long‐term balancing selection or recent selective sweeps in any of the seven populations surveyed. Also in contrast with earlier surveys of one of these R genes, there was no evidence that the resistance genes or the major‐effect mutations were subject to elevated differentiation between populations. We suggest that conditional neutrality in the absence of the corresponding pathogen, rather than long‐term balancing selection or local adaptation, may in some circumstances be a significant cause of elevated functional polymorphism at R genes. In contrast with the R genes, analysis of diversity and differentiation at the flanking FERONIA locus showed high population divergence, suggesting local adaptation on this locus controlling male–female signalling during fertilization.
The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes
Authors: SALZBURGER WALTER 
Published: November 2008

AbstractThe question of how genetic variation translates into organismal diversity has puzzled biologists for decades. Despite recent advances in evolutionary and developmental genetics, the mechanisms that underlie adaptation, diversification and evolutionary innovation remain largely unknown. The exceptionally diverse species flocks of cichlid fishes are textbook examples of adaptive radiation and explosive speciation and emerge as powerful model systems to study the genetic basis of animal diversification. East Africa's hundreds of endemic cichlid species are akin to a natural mutagenesis screen and differ greatly not only in ecologically relevant (hence naturally selected) characters such as mouth morphology and body shape, but also in sexually selected traits such as coloration. One of the most fascinating aspects of cichlid evolution is the frequent occurrence of evolutionary parallelisms, which has led to the question whether selection alone is sufficient to produce these parallel morphologies, or whether a developmental or genetic bias has influenced the direction of diversification. Here, I review fitness‐relevant traits that could be responsible for the cichlids’ evolutionary success and assess whether these were shaped by sexual or natural selection. I then focus on the interaction and the relative importance of sexual vs. natural selection in cichlid evolution. Finally, I discuss what is currently known about the genes underlying the morphogenesis of adaptively relevant traits and highlight the importance of the forthcoming cichlid genomes in the quest of the genetic basis of diversification in this group.
A new oxidative sensing and regulation pathway mediated by the MgrA homologue SarZ in Staphylococcus aureus
Authors: Chen Peng R. , Nishida Satoshi , Poor Catherine B. , Cheng Alice , Bae Taeok , Kuechenmeister Lisa , Dunman Paul M. , Missiakas Dominique , He Chuan 
Published: November 2008

SummaryOxidative stress serves as an important host/environmental signal that triggers a wide range of responses from the human pathogen Staphylococcus aureus. Among these, a thiol‐based oxidation sensing pathway through a global regulator MgrA controls the virulence and antibiotic resistance of the bacterium. Herein, we report a new thiol‐based oxidation sensing and regulation system that is mediated through a parallel global regulator SarZ. SarZ is a functional homologue of MgrA and is shown to affect the expression of ∼87 genes in S. aureus. It uses a key Cys residue, Cys‐13, to sense oxidative stress and to co‐ordinate the expression of genes involved in metabolic switching, antibiotic resistance, peroxide stress defence, virulence, and cell wall properties. The discovery of this SarZ‐mediated regulation, mostly independent from the MgrA‐based regulation, fills a missing gap of oxidation sensing and response in S. aureus.