bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small mammals in new farm woodlands
Authors: MOORE N. P. , ASKEW N. , BISHOP J. D. 
Published: December 2004

ABSTRACTA number of recently planted farm woodlands, along with adjacent agricultural land and hedgerows were surveyed using live traps to compare their importance for small mammals. Small mammal numbers were far higher in newly planted woodlands than in both hedgerows and agricultural land. Seven species were trapped in farm woods compared with five in hedgerows and two in agricultural land. The most frequently trapped species in the establishing woodlands was the harvest mouse Micromys minutus, followed by the wood mouse Apodemus sylvaticus. The potential importance of newly planted farm woodlands for small mammals is discussed.
The decline of Steller sea lionsEumetopias jubatusin Alaska: a review of the nutritional stress hypothesis
Authors: TRITES A. W. , DONNELLY C. P. 
Published: December 2004

ABSTRACT1. The decline of Steller sea lionsEumetopias jubatusin the Gulf of Alaska and Aleutian Islands between the late 1970s and 1990s may have been related to reduced availability of suitable prey. Many studies have shown that pinnipeds and other mammals suffering from nutritional stress typically exhibit reduced body size, reduced productivity, high mortality of pups and juveniles, altered blood chemistry and specific behavioural modifications.2. Morphometric measurements of Steller sea lions through the 1970s and 1980s in Alaska indicate reduced body size. Reduced numbers of pups born and an apparent increase in juvenile mortality rates also appear to be nutritionally based. Blood chemistry analyses have further shown that Steller sea lions in the Gulf of Alaska and Aleutian Islands area exhibited signs of an acute phase reaction, or immune reaction, in response to unidentified physical and/or environmental stress. Behavioural studies during the 1990s have not noted any changes that are indicative of an overall shortage in the quantity of prey available to lactating female sea lions.3. The data collected in Alaska are consistent with the hypothesis that Steller sea lions in the declining regions were nutritionally compromised because of the relative quality of prey available to them (chronic nutritional stress), rather than because of the overall quantity of fishper se(acute nutritional stress). This is further supported by captive studies that indicate the overall quality of prey that has been available to Steller sea lions in the declining population could compromise the health of Steller sea lions and hinder their recovery.
Cryptic species, cryptic endosymbionts, and geographical variation in chemical defences in the bryozoan Bugula neritina
Authors: Mcgovern Tamara M. , Hellberg Michael E. 
Published: December 2004

AbstractMolecular markers often offer the only means to discriminate between species and to elucidate the specificity of many community interactions, both of which are key to the understanding of ecological patterns. Western Atlantic populations of the bryozoan Bugula neritina vary in the palatability of their larvae to predators: individuals south of Cape Hatteras produce chemical deterrents to fish predators that are absent in more northern individuals. We use mitochondrial cytochrome oxidase c subunit I (COI) sequences to show that the differences in palatability between populations correlate with the geographical distributions of two cryptic species within B. neritina. Furthermore, these cryptic species differ in their associations with bacteria that may confer chemical resistance to predation. Small subunit rRNA primers specific to a subset of γ‐proteobacteria amplified only the bacterium Endobugula sertula from the southern cryptic species. Endobugula sertula produces a family of chemical compounds (bryostatins) that may deter predators of its animal host. In contrast, the same primers amplified an array of γ‐proteobacteria from the unprotected northern cryptic bryozoan species, but never E. sertula. In combination, these findings suggest that the geographical variation in palatability observed in the larvae of B. neritina is not the result of local adaptation of a single species to regions of differing predation pressure, but rather results from the comparison of cryptic species that differ in the presence or absence of a bacterium that may provide protection against predators. The ability to identify the cryptic Bugula species and their differing relationships with bacterial associates provides an example of the important role molecular techniques may play in addressing ecological questions.
Differential cycles of range contraction and expansion in European high mountain plants during the Late Quaternary: insights from Pritzelago alpina (L.) O. Kuntze (Brassicaceae)
Authors: Kropf Matthias , Kadereit Joachim W. , Comes Hans Peter 
Published: December 2004

AbstractNuclear DNA sequence variation of the internal transcribed spacer (ITS) and amplified fragment length polymorphisms (AFLPs) were used to illuminate the evolutionary history of Pritzelago alpina, a herbaceous perennial of (sub)alpine to nival habitats of the European high mountains. Maximum likelihood analysis of ITS sequences of P. alpina, Hornungia petraea and Hymenolobus procumbens (the ‘Pritzelago alliance’) resolved P. alpina and H. petraea as sister taxa. ITS divergence estimates support an origin for P. alpina in the Late Tertiary, while intraspecific diversification started in the Late Quaternary (0.4–0.9 million years ago). AFLP analysis of 76 individuals of P. alpina, representing 24 localities across its entire west–east distribution, identified four mountain lineages in Cantabria, the Pyrenees, (south‐) western Alps, and northeastern Alps/Tatras/Carpathians. In an analysis of molecular variance (amova), 14.3% of the total variation derived from this separation. However, relationships among these lineages remained unresolved in neighbour‐joining and principal co‐ordinates analyses, suggesting a population history of near simultaneous vicariance. Comparison with our previous ITS/AFLP study of Anthyllis montana (Fabaceae) indicates that the two co‐distributed but altitudinally differentiated plant species exhibit temporally concordant but spatially discordant patterns of genetic variation. Moreover, levels of AFLP divergence were significantly lower in P. alpina than in the submediterranean, lower‐elevation A. montana. Together, these data are consistent with a ‘displacement refugia model’, which predicts that European mountain plant species associated with lower‐ and upper‐elevation habitats had a different cycle of range contraction into (long‐term) glacial and (short‐term) interglacial refugia, respectively.
Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars
Authors: Cooper Dawn , Cory Jenny S. , Myers Judith H. 
Published: December 2004

AbstractThe cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.
Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province
Authors: Calsbeek Ryan , Thompson John N. , Richardson James E. 
Published: December 2004

AbstractThe California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2–10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts.
Testing Pleistocene refugia theory: phylogeographical analysis of Desmognathus wrighti, a high‐elevation salamander in the southern Appalachians
Authors: Crespi Erica J. , Rissler Leslie J. , Browne Robert A. 
Published: December 2004

AbstractDuring the colder climates of the Pleistocene, the ranges of high‐elevation species in unglaciated areas may have expanded, leading to increased gene flow among previously isolated populations. The phylogeography of the pygmy salamander, Desmognathus wrighti, an endemic species restricted to the highest mountain peaks of the southern Appalachians, was examined to test the hypothesis that the range of D. wrighti expanded along with other codistributed taxa during the Pleistocene. Analyses of genetic variation at 14 allozymic loci and of the 12S rRNA gene in the mtDNA genome was conducted on individuals sampled from 14 population isolates throughout the range of D. wrighti. In contrast to the genetic patterns of many other high‐elevation animals and plants, genetic distances derived from both molecular markers showed significant isolation by distance and genetic structuring of populations, suggesting long‐term isolation of populations. Phylogeographical analyses revealed four genetically distinct population clusters that probably remained fragmented during the Pleistocene, although there was also evidence supporting recent gene flow among some population groups. Support for isolation by distance is rare among high‐elevation species in unglaciated areas of North and Middle America, although not uncommon among Plethodontid Salamanders, and this pattern suggests that populations of D. wrighti did not expand entirely into suitable habitat during the Pleistocene. We propose that intrinsic barriers to dispersal, such as species interactions with other southern Appalachian plethodontid salamanders, persisted during the Pleistocene to maintain the fragmented distribution of D. wrighti and allow for significant genetic divergence of populations by restricting gene flow.
Diverging patterns of mitochondrial and nuclear DNA diversity in subarctic black spruce: imprint of a founder effect associated with postglacial colonization
Authors: Gamache Isabelle , Jaramillo‐Correa Juan Pablo , Payette Serge , Bousquet Jean 
Published: December 2004

AbstractHigh‐latitude ecotonal populations at the species margins may exhibit altered patterns of genetic diversity, resulting from more or less recent founder events and from bottleneck effects in response to climate oscillations. Patterns of genetic diversity were investigated in nine populations of the conifer black spruce (Picea mariana[Mill.] BSP.) in northwestern Québec, Canada, using seed‐dispersed mitochondrial (mt) DNA and nuclear (nc) DNA. mtDNA diversity (mitotypes) was assessed at three loci, and ncDNA diversity was estimated for nine expressed sequence tag polymorphism (ESTP) loci. Sampling included populations from the boreal forest and the southern and northern subzones of the subarctic forest‐tundra, a fire‐born ecotone. For ncDNA, populations from all three vegetation zones were highly diverse with little population differentiation (θN = 0.014); even the northernmost populations showed no loss of rare alleles. Patterns of mitotype diversity were strikingly different: within‐population diversity and population differentiation were high for boreal forest populations [expected heterozygosity per locus (HE) = 0.58 and θM = 0.529], but all subarctic populations were fixed for a single mitotype (HE = 0). This lack of variation suggests a founder event caused by long‐distance seed establishment during postglacial colonization, consistent with palaeoecological data. The estimated movement of seeds alone (effective number of migrants per generation, NmM < 2) was much restricted compared to that estimated from nuclear variants, which including pollen movement (NmN > 17). This could account for the conservation of a founder imprint in the mtDNA of subarctic black spruce. After reduction, presumably in the early Holocene, the diversity in ncDNA would have been replenished rapidly by pollen‐mediated gene flow, and maintained subsequently through vegetative layering during the current cooler period covering the last 3000 years.
Negative cross‐talk between salicylate‐ and jasmonate‐mediated pathways in the Wassilewskija ecotype of Arabidopsis thaliana
Authors: Traw M. B. , Kim J. , Enright S. , Cipollini D. F. , Bergelson J. 
Published: December 2004

AbstractPlants often respond to attack by insect herbivores and necrotrophic pathogens with induction of jasmonate‐dependent resistance traits, but respond to attack by biotrophic pathogens with induction of salicylate‐dependent resistance traits. To assess the degree to which the jasmonate‐ and salicylate‐dependent pathways interact, we compared pathogenesis‐related protein activity and bacterial performance in four mutant Arabidopsis thaliana lines relative to their wild‐type backgrounds. We found that two salicylate‐dependent pathway mutants (cep1, nim1‐1) exhibited strong effects on the growth of the generalist biotrophic pathogen, Pseudomonas syringae pv. tomato, whereas two jasmonate‐dependent pathway mutants (fad3‐2fad7‐2fad8, jar1‐1) did not. Leaf peroxidase and exochitinase activity were negatively correlated with bacterial growth, whereas leaf polyphenol oxidase activity and trypsin inhibitor concentration were not. Interestingly, leaf total glucosinolate concentration was positively correlated with bacterial growth. In the same experiment, we also found that application of jasmonic acid generally increased leaf peroxidase activity and trypsin inhibitor concentration in the mutant lines. However, the cep1 mutant, shown previously to overexpress salicylic acid, exhibited no detectable biological or chemical responses to jasmonic acid, suggesting that high levels of salicylic acid may have inhibited a plant response. In a second experiment, we compared the effect of jasmonic acid and/or salicylic acid on two ecotypes of A. thaliana. Application of salicylic acid to the Wassilewskija ecotype decreased bacterial growth. However, this effect was not observed when both salicylic acid and jasmonic acid were applied, suggesting that jasmonic acid negated the beneficial effect of salicylic acid. Collectively, our results confirm that the salicylate‐dependent pathway is more important than the jasmonate‐dependent pathway in determining growth of P. syringae pv. tomato in A. thaliana, and suggest important negative interactions between these two major defensive pathways in the Wassilewskija ecotype. In contrast, the Columbia ecotype exhibited little evidence of negative interactions between the two pathways, suggesting intraspecific variability in how these pathways interact in A. thaliana.
Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris
Authors: García‐Gil M. R. , Mikkonen M. , Savolainen O. 
Published: December 2004

AbstractForest tree species provide many examples of well‐studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12–15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; π was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.
Evidence for the adaptive evolution of the carbon fixation generbcLduring diversification in temperature tolerance of a clade of hot spring cyanobacteria
Authors: Miller S. R. 
Published: December 2004

AbstractDetermining the molecular basis of enzyme adaptation is central to understanding the evolution of environmental tolerance but is complicated by the fact that not all amino acid differences between ecologically divergent taxa are adaptive. Analysing patterns of nucleotide sequence evolution can potentially guide the investigation of protein adaptation by identifying candidate codon sites on which diversifying selection has been operating. Here, I test whether there is evidence for molecular adaptation of the carbon fixation generbcLfor a clade of hot spring cyanobacteria in the genusSynechococcusthat has diverged in thermotolerance. Amino acid replacements duringSynechococcusradiation have resulted in an increase in the number of hydrophobic residues in the RbcLs of more thermotolerant strains. A similar increase in hydrophobicity has been observed for many thermostable proteins. Maximum likelihood models which allow for heterogeneity among codon sites in the ratio of nonsynonymous to synonymous nucleotide substitutions estimated a class of amino acid sites as a target of positive selection. Depending on the model, a single amino acid site that interacts with a flexible element involved in the opening and closing of the active site was estimated with either low or moderate support to be a member of this class. Site‐directed mutagenesis approaches are being explored in order to directly test its adaptive significance.
Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history
Authors: Clauss M. J. , Mitchell‐Olds T. 
Published: December 2004

AbstractDuplicated genes are important in the evolution and ecology of plant‐defences because herbivore and pathogen attack can be countered via functional diversification at two levels: among duplicated loci and within loci. We explore molecular sequence variation for two members of a defence‐related gene family, Arabidopsis thaliana trypsin inhibitors (ATTI), in A. thaliana and a closely related species, A. lyrata subspp. petraea. A worldwide sample of the inbreeding annual A. thaliana had less genetic variation at two ATTI loci (πTOTAL ≤ 0.0006) than observed previously at other functional loci. A significant excess of high frequency derived alleles in the signal sequence and 5′ UTR of ATTI2 was consistent with a model of positive selection. However, demographic processes such as population subdivision and expansion, both likely to have occurred in A. thaliana during the last 10 000 years, can also give rise to similar deviations from neutrality. A single population of A. lyrata subspp. petraea in Germany had up to an order of magnitude more standing genetic variation at ATTI loci than the species‐wide sample of A. thaliana. Although the level of variability for ATTI1 and ATTI2 within this single population was similar to, or even greater than, observed species‐wide diversity for other loci in A. lyrata, there was little evidence to reject an equilibrium neutral model. A spatially explicit sample of 87 A. lyrata subspp. petraea individuals detected outbreeding (FIS = −0.16; FIT = −0.15) but little population subdivision (FST = 0.006) in this self‐incompatible perennial herb. Genetic differences between Arabidopsis species were consistent with, but not fully explained by, divergence in ecology and life history. Diversification appears to have occurred in different functional domains for the tandemly duplicated ATTI1 and ATTI2 genes; the majority of fixed replacements in ATTI1 surround the enzyme binding site of the mature protein, whereas in ATTI2 most functional evolutionary change is located in the signal peptide. This pattern is consistent with a hypothesis of subfunctionalization in trypsin inhibitory function.
The phylogeography of human viruses
Authors: Holmes Edward C. 
Published: December 2004

AbstractViruses, especially those with RNA genomes, represent ideal organisms to study the dynamics of microevolutionary change. In particular, their rapid rate of nucleotide substitution means that the epidemiological processes that shape their diversity act on the same time‐scale as mutations are fixed in viral populations. Consequently, the branching structure of virus phylogenies provides a unique insight into spatial and temporal dynamics. Herein, I describe the key processes in virus phylogeography. These are generally associated with the relative rates of dispersal among populations and virus‐host codivergence (vicariance), and the division between acute (short‐term) and persistent (long‐term) infections. These processes will be illustrated by important human viruses — HIV, dengue, rabies, polyomavirus JC and human papillomavirus – which display varying spatial and temporal structures and virus‐host relationships. Key research questions for the future will also be established.