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381. [Article] Studies toward the synthesis of coibamide A and analogues
Coibamide A is a highly methylated cyclic depsipeptide isolated from Panamanian marine filamentous cyanobacteria as part of an International Cooperative Biodiversity Groups (ICBG) program based in Panama. ...Citation Citation
- Title:
- Studies toward the synthesis of coibamide A and analogues
- Author:
- Li, Dong
Coibamide A is a highly methylated cyclic depsipeptide isolated from Panamanian marine filamentous cyanobacteria as part of an International Cooperative Biodiversity Groups (ICBG) program based in Panama. This structurally unique agent exhibits potent cancer cell toxicity with an unprecedented selectivity profile in the National Cancer Institute (NCI) 60 cell line panel, possibly through a novel mechanism as suggested by "COMPARE negative" results. Therefore, it is considered a promising lead agent in cancer drug discovery. Although field recollections have provided a few milligrams of coibamide A, the amount obtained is still insufficient for extensive biological testing. The producing strain has recently been cultured, but coibamide yields are very low and the growth rate is slow. Chemical synthesis of coibamide A is central to further biological testing and potential clinical development, and has become the major focus of my work. A macrocycle-side chain strategy was originally proposed for the synthesis of coibamide A. It was unsuccessful, however, due to the difficulties trying to couple the macrocycle and side chain together at the last step. To solve this problem, a modified macrocycle – side chain stragety was proposed. Coibamide A was disconnected into two other subunits: the N-MeLeu-macrocycle and the "tripeptide" side chain. The reason for this modification was that the secondary amine of N-MeLeu, with some distance from the bulky macrocycle, should be spatially more availalbe for the final step to couple with the side chain "tripeptide". This new strategy was able to generate "synthetic coibamide" in a moderate yield, this compound, however, was not the natural product coibamide A according to HPLC, 1H NMR and activity test. By Marfey's analysis, we found that in this synthetic coibamide A, no N,O-diMe L-Ser was detected and only its D-counterpart was present, which indicated an unusual L-to-D inversion during coupling reactions. Because it was very difficult to overcome this unexpected inversion during this strategy, a third scheme, the Y-Strategy, was proposed. For the Y-strategy, instead of building the macrocycle first, we coupled the side chain with a macrocycle tripeptide first to afford a linear heptapeptide. Then the ester bond between the hydroxy of N-MeThr and carboxy of N-MeAla (of a tetrapeptide) was built to generate the full-size "Y-structure", which is then deprotected and cyclized to produce the target molecule coibamide A. While the heptapeptide was synthesized sucessfully, the ester bond formation reaction to generate the Y-structure did not happen. Although the Y-strategy did not eventually yield coibamide, it is the most convergent and efficient strategy so far. Because the pharmacological data for coibamide A suggest a unique mechanism and no natural coibamide analogues were separated from the field collections or cultures, the synthesis of coibamide analogues is also extremely valueable for activity and mechanism studies and becomes part of our synthetic effort. The analogues should reasonably resemble the structure of coibamide A, and be easier to be achieved synthetically compared to coibamide A itself. Two families of analogues were designed: the N-desmethyl coibamide family (most or all of the N-methylated amino acid components were replaced by regular amino acids) and the N-MeSer coibamide family (the junction N-MeThr was changed to N-MeSer). Per-N-desmethyl coibamide and several other analogues from the first family were synthesized by the modified macrocycle - side chain strategy, however, none of them exhibits any activity against the testing cell lines. Attempt to per-methylate these compounds also failed due to decomposition of substrates under basic conditions. N-MeSer-coibamide was successfully synthesized through the Y-strategy and purified by HPLC. Cell toxicity has been observed in the activity test, although the potency was several hundred times lower than the natural coibamide A. The synthetic process of N-MeSer coibamide should be optimized for better yields and easier purification as the focus of next stage.
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Riparian ecosystems play numerous and essential roles related to the quality and flow of water, and food/habitat for fish, and varieties of wildlife. Due to lateral and linear linkages throughout the landscape, ...
Citation Citation
- Title:
- The ecology of riparian ecosystems of Northeast Oregon : shrub recovery at Meadow Creek and the structure and biomass of headwater Upper Grande Ronde ecosystems
- Author:
- Case, Richard L.
Riparian ecosystems play numerous and essential roles related to the quality and flow of water, and food/habitat for fish, and varieties of wildlife. Due to lateral and linear linkages throughout the landscape, these zones influence the integrity of the terrestrial as well as the entire aquatic-riverine ecosystem. Since Euro-American settlement in the West, the structure and condition of many riparian ecosystems has been significantly altered. To provide tools and an ecological perspective related to riparian restoration and management, and to document late 20th century headwater riparian structure and biomass in the Upper Grande Ronde Basin, this research project was undertaken. At Meadow Creek, the response of riparian hardwood species to the termination of livestock grazing was quantified. Regression equations were developed to predict shrub biomass. Permanently marked hardwood plants were measured annually to quantify parameters of growth (height, crown area, mainstem diameter, number of stems, biomass). Permanent belt transects on gravel bars were utilized to quantify rates of shrub establishment. Elk/deer-proof exclosures allowed the quantification of the browsing influence of wild ungulates. In 1991, initial shrub heights and densities reflected decades of grazing pressure. Mean heights of515 woody plants (14 species) was 47 cm and densities on gravel bars averaged 10.7 plants/100m². After two seasons without livestock grazing, mean crown volumes of willows (Salix spp.) increased 550% inside of wild ungulate exclosures and 195% outside, black cottonwood (Populus trichocarpa) 773% inside and 808% outside, and thin-leaf alder (Almis incana) 1046% inside and 198% outside, respectively. Willows were significantly impeded (p<0.Ol) mule deer and Rocky Mountain elk, alder samples were too small to statistically test, and cottonwood was not significantly impeded. However, impacts by deer and elk may be exaggerated due to high densities and the ungulate density-dynamics unique within the 77 km² Starkey Experimental Forest big-game enclosure surrounding the study site. Establishment rates are low at this time, i.e., only 10% of previously suppressed willows produced catkins. Although in transects densities increased by 5 new woody plants/lOOm² (50m of streambank). Other non-anthropogenic factors influencing the recovery of shrubs, included beaver which removed mainstems from 20% of willows, 11% of thin-leaf alder, and 4% of black cottonwood, and active insect defoliation which was noted on 16% of willows, 7% of thin-leaf alder, and 0% of black cottonwood. Crude protein levels measured in willow and alder leaves was relatively high (16.1 to 16.3%) helping to explain their palatability and use by wild and domestic herbivores. Few studies have quantified biomass, structure and composition of headwater riparian ecosystems. Data such as this are important given their dominant roles in ecosystem biodiversity, and aquatic function. To document relatively intact forested headwater ripanan conditions in the Upper Grande Ronde Basin, the biomass, structure and composition along six headwater reaches was quantified. Sampling was done using a nested belt transect/plot arrangement along 500 meter reaches. Total aboveground biomass (TAGB) ranged from 203 to 261 Mg/ha, with overstory conifers contributing 101 to 177 Mg/ha. Living understory components (saplings, seedlings, shrubs, and herbs) comprised 5 to 18 Mg/ha (2 to 9% of TAGB), while forest floor detrital accumulations comprised 65 to 101 Mg/ha (29 to 42% of TAGB). Average shade per day for July, 1993 ranged between 53% and 75%, reducing the unshaded solar energy potential of 2390 Mj/day to between 680 and 1280 Mj/day striking each m² of stream surface. This baseline reference information can serve in multi-disciplined research, as well as, be a basis for long term studies of natural systems responding to changing climate and different resource management scenarios.
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383. [Article] Genomic Investigations of Diversity within the Milkweed Genus Asclepias, at Multiple Scales
At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more ...Citation Citation
- Title:
- Genomic Investigations of Diversity within the Milkweed Genus Asclepias, at Multiple Scales
- Author:
- Weitemier, Kevin Allen
At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more efficiently and precisely. The studies in this dissertation investigate genomic diversity within the milkweed genus, Asclepias, at multiple scales, including diversity found within a single individual, diversity within and among populations in a species, and diversity across the entire genus. These investigations contribute to our understanding of the genomic content and architecture within Asclepias and the Gentianales, patterns of population diversification in the western United States, and the evolutionary history of select loci within Asclepias, with implications across flowering plants. Chapter 2 investigates patterns of polymorphisms among paralogous copies of nuclear ribosomal DNA (nrDNA) within individual genomes, and presents a bioinformatic pipeline for characterizing polymorphisms among copies of a high-copy locus. Results are presented for intragenomic nrDNA polymorphisms across Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom Perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). Most nrDNA positions (91%) were polymorphic in at least one individual, with polymorphic sites being less frequent in subunit regions and loops. Highly polymorphic sites existed in each individual, with highest abundance in the “noncoding” ITS regions. Phylogenetic signal was present in the distribution of intragenomic polymorphisms across the genus. Intragenomic polymorphisms in nrDNA are common in Asclepias, being found at higher frequency than any other study to date. The high and variable frequency of polymorphisms across species highlights concerns that phylogenetic applications of nrDNA may be error-prone. The new analytical approach provided in this chapter is applicable to other taxa and other high-copy regions characterized by low coverage genome sequencing (genome skimming). Chapter 3 presents Hyb-Seq, a new method combining target enrichment and genome skimming to allow simultaneous data collection for low-copy nuclear genes and high-copy genomic targets for plant systematics and evolution studies. A program is presented that takes genome and transcriptome assemblies and locates loci likely to be low copy and phylogenetically informative, to be used for probe development and enrichment in sequence libraries. A workflow is presented for processing data, from raw sequence reads to assembled exons and reconstructed trees. Genome and transcriptome assemblies for Asclepias syriaca were used to design enrichment probes for 3385 exons from 768 genes (>1.6 Mbp) followed by Illumina sequencing of enriched libraries. Hyb-Seq of 12 individuals (10 Asclepias species and two related genera) resulted in at least partial assembly of 92.6% of exons and 99.7% of genes and an average assembly length >2 Mbp. Importantly, complete plastomes and nrDNA cistrons were assembled using off-target reads. Phylogenomic analyses demonstrated signal conflict between genomes. The Hyb-Seq approach enables targeted sequencing of thousands of low-copy nuclear exons and flanking regions, as well as genome skimming of high-copy repeats and organellar genomes, to efficiently produce genome-scale data sets for phylogenomics. Chapter 4 presents an assembly of the genome of the common milkweed, Asclepias syriaca. It uses principles from Chapter 3 to target SNPs and reconstruct linkage groups, enabling an analysis of chromosomal evolution within Gentianales, the order containing Asclepias. Asclepias syriaca is the first species in Apocynaceae with reconstructions of the nuclear, chloroplast, and mitochondrial genomes, and the first to have linkage group information incorporated into the nuclear assembly. The final assembly of Asclepias syriaca contains 54,266 scaffolds ≥1 kbp, with N50 = 3415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. Scaffolds ≥200 bp sum to 229.7 Mbp, with N50 = 1904 bp. A total of 14,474 protein coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated based on genes from Coffea canephora and Catharanthus rosea. A large proportion of gene space is represented in the assembly, with 96.7% of Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Analyses were performed for three gene families, involved in rubber production, light sensing, and cardenolide production, with the finding that the cardenolide related progesterone 5β-reductase gene family is likely reduced in Asclepias relative to other Apocynaceae. Scaffolds covering 75 Mbp of the Asclepias assembly were grouped into eleven linkage groups. Comparisons of these groups with pseudochromosomes in Coffea found that six chromosome show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. Finally, in Chapter 5, diversity within a species across its entire range is investigated with a phylogeographic study of the jewel milkweed, Asclepias cryptoceras. This study applies the SNP targets developed from Chapter 4 to populations of A. cryptoceras, asking whether two recognized subspecies are genetically distinct, and searching for the origin of populations that are morphologically intermediate between the two. A total of 54,673 SNPs were found on 7372 contigs, across 96 individuals from ten populations. Principal component analysis and measures of allelic differentiation indicate a clear disjunction between subspecies cryptoceras and davisii (F[subscript ST] = 0.092 between geographic regions). For intermediate populations, estimates of hybrid index below 0.25 and measures of allelic diversity and private alleles, argue against a hybrid origin due to secondary contact, and instead support their origin as stepping stone populations during expansion along a southern corridor from east to west.
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Reintroduction of wolves to Yellowstone National Park (YNP) in 1995-96 provided a rare opportunity to observe the response of an ecosystem to the return of a top predator, including possible reversal of ...
Citation Citation
- Title:
- Trophic cascades and large mammals in the Yellowstone ecosystem
- Author:
- Painter, Luke E.
Reintroduction of wolves to Yellowstone National Park (YNP) in 1995-96 provided a rare opportunity to observe the response of an ecosystem to the return of a top predator, including possible reversal of decades of decline of aspen, cottonwood, and tall willows suppressed by intensive herbivory on elk winter ranges. To investigate changes in aspen stands in northern Yellowstone since the return of wolves, I compared browsing intensity and heights of young aspen in 87 randomly selected stands in 2012 to similar data collected in the same stands in 1997-98. I also measured the spatial density of elk and bison scat piles as an index to relative population densities, and used annual counts of elk to calculate trends in elk density. In 1998, browsing rates averaged 88%, heights were suppressed, and no tall saplings (≥200 cm) were found in sampling plots. In 2012, browsing rates in 2012 were much lower averaging 44%, and 28% of plots had at least one sapling ≥200 cm, tall enough to escape browsing and therefore more likely to survive to replace dying overstory trees. Heights of young aspen were inversely related to browsing intensity, but not significantly related to leader length, suggesting that differences in height were primarily due to differences in browsing, not factors related to productivity. Aspen recovery was patchy, possibly due in part to locally high elk or bison densities in some parts of the winter range. These results of reduced browsing with increased sapling recruitment were consistent with a trophic cascade from wolves to elk to aspen resulting in a widespread and spatially variable recovery of aspen stands. There was wide variation in browsing intensity and aspen height between sectors of the Yellowstone northern ungulate winter range (northern range). The east sector generally had lower rates of browsing and more stands with tall saplings than the central and west sectors, a pattern that matched recent trends in elk population densities. Only a small minority of stands in the west sector had tall saplings, consistent with higher elk densities in the west. Densities of elk in winter on the northern range recently have been highest in the northwest sector outside the park boundary, where elk benefit from lower wolf densities and milder winters. Aspen stands did not recover at a comparable range-wide elk density when elk were culled in the park in the 1950s and 1960s, suggesting that the influence of wolves may be an important factor in the recent redistribution and reduction of herbivory impacts by elk. To examine the relationship between elk and aspen outside of YNP, I assessed browsing intensity and sapling recruitment in 43 aspen stands in the Shoshone National Forest east of the park, compared to data collected in the same stands in 1997-98. As in northern YNP, results were consistent with a trophic cascade with reduced browsing and increased recruitment of aspen saplings, but aspen recovery was patchy. Elk densities were moderate to high in most of the area, suggesting that the partial aspen recovery may involve a behavioral response to predation or other factors resulting in local variation in browsing impacts. Livestock may also have limited aspen recruitment. Recovery of some aspen stands in the Shoshone National Forest may provide some of the first evidence of a trophic cascade from wolves to elk to aspen outside of a national park, a trophic cascade possibly weakened by the influence of another large herbivore (cattle). Like cattle, bison in northern Yellowstone may have an effect on woody browse plants. Bison have increased in number and may prevent recovery of some aspen stands in places of high bison density. I also examined browsing impacts of bison on willow and cottonwood in the Lamar Valley. To distinguish the effects of bison from those of elk, I compared browsing at different heights on tall willows, below and above the reach of bison. Because elk were absent from the area in summer when bison were present at high density, I also measured browsing that occurred in the summer. I found high rates of summer browsing, and growth of willows and cottonwoods was suppressed in the Lamar Valley. Above the reach of bison (>100 cm), growth was not suppressed and browsing rates were low, suggesting that these plant species have been released from suppression by elk but bison have compensated for some of the reduction in elk browsing. This study provided the first evidence of significant herbivory by bison of woody browse plants in Yellowstone, and revealed some of the complexity of the Yellowstone food web. In summary, these research results support the hypothesis of a trophic cascade resulting from large carnivore restoration and subsequent changes in elk population densities and distribution. The return of wolves may have combined with other factors such as changes in hunting and land ownership, and increased predation by bears, to result in large-scale shifts in the distribution of elk in northern Yellowstone and greatly reduced elk densities in some areas. If these trends continue, the result may be a new alternative state with lower elk densities, and potential for enhanced biodiversity through reduced herbivory of woody browse species.
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Offshore renewable energy development (ORED) could induce local ecological changes, negatively affecting species of conservation interest. If well planned and coordinated, on the other hand, ORED could ...
Citation Citation
- Title:
- Effects of Altered Habitats and Fishing Practices in Wind and Wave Farms
- Author:
- Wilhelmsson, Dan
Offshore renewable energy development (ORED) could induce local ecological changes, negatively affecting species of conservation interest. If well planned and coordinated, on the other hand, ORED could be beneficial to the marine environment in the region of device deployment in several respects. Because of the current scale and pace of offshore renewable energy development, interest is growing in the opportunities offered by the changes in fishing patterns that could result. Trawling, one of the most severe threats to the marine environment, particularly to fish and benthic invertebrate assemblages, will be prohibited or limited inside wind and wave farms. Areas of several square kilometres may therefore, in some important respects, resemble Marine Protected Areas; for areas that were previously trawled this exclusion could lead to average increases in biomass of motile organisms. Primary data from wind and wave farms are still scarce, but results to date from surveys targeting fish assemblages within offshore wind farms in Denmark, the Netherlands, and Sweden basically indicate either increased abundance of some fish species (e.g., sand eels (Ammodytidae), cod (Gadus morhua), whiting (Merlangius merlangus), sole (Solea solea)) or no effect compared to conditions before construction of the wind farm. Effects are likely to be most prominent for species that had been heavily exploited in the area prior to the wind or wave farm establishment. It is believed that a relatively large area of exclusion is required to enhance biodiversity and generate spill-over effects. Construction and deployment of artificial reefs (AR) in coastal waters is practiced worldwide to manage fisheries, mitigate damage to the environment, protect (i.e., from trawling) and facilitate the rehabilitation of certain habitats (e.g., spawning sites) or water bodies, or to increase the recreational value of an area (e.g., by providing opportunities for recreational diving and fishing). Unless animals are deterred by potential disturbances, such as noise, maintenance work, and electromagnetic fields from turbines, it is reasonable to expect offshore wind energy structures, and also foundations of some types of wave energy devices, to function as artificial reef modules and enhance local abundance of marine organisms, including commercially important fish and crustaceans. However, taxon- and age-specific responses of fishes to ARs vary greatly with AR design and position as well as by region and latitude. It can therefore be difficult to predict the structure of fish and crustacean assemblages associated with the submerged parts of wind and wave energy devices, as well as the radius of influence. Nevertheless, relatively recent studies targeting the potential for wind turbines and wave energy foundations to aggregate fish and motile invertebrates in Sweden, the Netherlands, Belgium, and Denmark suggest that densities of a number of fish and decapod species increase with proximity to these structures. Another category of artificial habitat is a Fish Aggregation Device (FAD), a floating structure deliberately placed on the surface or suspended in the water column to attract fish and enhance fishing efficiency. FADs are widely used in Asia and the western Indian Ocean. It has been suggested that floating offshore energy devices may function as FADs for pelagic fish, which could provide additional opportunities for fisheries management. Both ARs and FADs can have negative environmental and social effects if not properly planned and/or used. If ARs only aggregate fish from surrounding areas and do not contribute to added production, enhanced fishing efficiency in the AR area may aggravate overfishing if the new circumstances are not managed with caution. Similarly, increasing catchability, the main purpose of an FAD, may exacerbate the problem of overfishing on commercial species that are already at risk. ARs can also give rise to conflicts over user rights among fisher groups, and between recreational divers and fishers. Further, densities of benthic prey items have been shown to decrease with proximity to ARs due to predation by fish residing on the structures. FADs have been suggested as potential “ecological traps,” meaning that their presence could lure fish into remaining near the structures under non-optimal local feeding conditions, affecting physical condition and growth. Artificial structures may also provide habitats suitable for establishment of non-indigenous species; deployment of clusters of artificial structures may facilitate the establishment of new taxa in the recipient region by providing “beach heads” and stepping-stones. Non-indigenous sessile invertebrates have already been recorded at wind farms in the North Sea and the Baltic Sea. A range of design and location factors may influence the fish community structure on artificial reefs, such as height, size, inclination, protuberance, surface structure, void space and number of interior hollows, shade effects, distance between modules, isolation, and composition of the surrounding seabed. Research is underway to evaluate species-specific habitat preferences in the design of offshore energy foundations to optimize biomass of desired species, or alternatively, minimize artificial reef effects where desired. For example, in an experiment with wave energy foundations on the west coast of Sweden the potential for enhancing the abundance of associated fish and crustaceans through low-cost manipulations of the structural complexity of foundations was examined. Additional experiments will provide further guidance on the influence of different designs of foundations on commercially important fish and shellfish. This presentation will focus on the potential influence of offshore wind and wave farms on fish and commercially important crustaceans. The uncertainties with regard to positive and negative effects of on benthic and pelagic assemblages and specific species will also be discussed. The presentation will draw on results from a number of field studies and experiments conducted in offshore wind and wave farms, as well as on secondary literature on the influence of differently designed artificial habitats on benthic fauna.
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Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new ...
Citation Citation
- Title:
- Forest macro-arthropods as potential indicators of ecosystem conditions in Western Idaho : an analysis of community composition, biological diversity, and community structure
- Author:
- Ruby, Margaret E.
Adaptive ecosystem management is a new paradigm for managing federal forests which requires regular monitoring of ecosystem function and diversity to measure the effects of management. Managers need new strategies and tools to help them assess their progress in maintaining healthy, productive and biologically diverse forests. Biomonitoring of select forest macro-arthropod species can provide useful information on the effects of management on forest biodiversity and ecosystem function. The purpose of this study was threefold: (1) to inventory the macro-arthropod community and important environmental variables in the Bear Creek and Indian Creek study area within the Payette National Forest (PNF) in Western Idaho; (2) to compare measures of community composition, diversity, and structure in forest macro-arthropod communities between patches of different sizes and treatment; and (3) to assist PNF managers in their ecosystem management efforts by providing principles to guide the use of macro-arthropods as indicators of changing forest conditions. Transects with pitfall traps were used to collect macro-arthropods at 22 sites in the Bear Creek and Indian Creek study area during the summer of 1994. Five forest patch types in Abies grandis habitat types were sampled. Intact forest patches of 100 or more hectares, and large patches of 50-100 hectares, ranged in age between 50 and 250 years old with multistoried structure. Small patches up to 10 hectares were remnants or fragments of formerly intact forest isolated by logging. A plantation patch was 15 years old with patchy understory and forb cover. Clearcut patches had little or no overstory, and variable understory, and forb layers. At each transect, soil samples were collected and six environmental descriptor variables were analyzed according to patch treatment and patch size. These site descriptors were: basal area (ft²/acre); percent canopy cover for the overstory, understory; and forb layers; litter depth (cm), and percent soil moisture content. Differences detected using an ANOVA and T-tests are discussed in the Results section. Arthropod community composition, diversity, and structure were described according to relative abundance, and four measures of diversity. They were also described by membership in seventeen orders and/or super-families; ten functional groups; two disperser classes (long or short distance); and three species indicator classes. A total of 5455 macro-arthropod individuals, representing 17 orders and/or super-families and 219 species were collected in the Bear Creek and Indian Creek study area. While macro-arthropod fauna relative abundance did not vary significantly by treatment (ANOVA p<0.3), it did vary significantly by patch size (ANOVA p<0.03). Fauna relative abundance was 35% greater in clearcut patches than in large patches (T-test p<0.09). Fauna relative abundance in small patches was twice that of intact (T-test p<0.03) and large (T-test p<0.02) patches. Taxonomic diversity (number of genera/taxa) of beetle, ant, and bug taxa differed significantly according to treatment type(each ANOVA p<0.05). For the top four taxa (beetles, ants, spiders, and bugs), taxonomic diversity was highest in the plantation and clearcut patches. Ants and bugs had their highest taxonomic diversity in the plantation patch (separate T-tests p<0.05) while the taxonomic diversity of beetles was highest in clear-cut patches (T-test p<0.05). Beetle and ant taxonomic diversity varied significantly by patch size (each ANOVA p<0.05). For beetles and bugs, small patches were twice as diverse as intact patches (separate T-tests p<0.04) and 1.5 times that of large patches. Ant diversity was similarly distributed amongst the patch sizes, with significant differences between small and intact and between small and large patches (separate T-tests p<0.05). Of the four species diversity measures employed, only two, [alpha] and JK1 (both measures of richness), were found to vary significantly by patch treatment and size. Evenness (E) and the Shannon Diversity Index (H') failed to detect differences in the majority of tests. Fauna [alpha] and JK1 differed significantly by treatment type (each ANOVA p<0.05). Richness in clearcut patches was nearly twice in intact and large patches, followed by plantation and large patches. Fauna [alpha] and JKl also differed significantly by patch size (each ANOVA p <0.001), with small patch fauna twice as rich as that in large and intact patches (separate T-tests p <0.01). Of the top four functional groups, predators were the most abundant and had the highest taxonomic diversity (number of genera/functional group), followed by herbivores, fungivores and parasites. Predators and herbivores showed increasing taxonomic diversity with decreasing patch size, from intact to large to small (ANOVA p< 0.05). Similarly, predators and herbivores exhibited increasing taxonomic diversity with increasing levels of management: from intact and large to plantation and clear-cuts (ANOVA p< 0.05). Predators and herbivores were most numerous in the managed and small patches. Fungivore taxonomic diversity was also highest in the small and managed patches, though neither patch size nor treatment differences were significant (ANOVA p<0.85). Parasite taxonomic diversity differed by patch size with highest generic diversity in the small patches (ANOVA p<0.l) and by treatment type with generic diversity highest in plantations and clearcuts followed in order by large and intact patches (ANOVA p<0.l). Twice as many genera were long distance dispersers as were short distance dispersers. Relative abundance of long distance dispersers varied significantly by patch treatment and patch size (each ANOVA p<0.0l). Long distance dispersers were most numerous in clear-cut patches, followed in order by plantation, small, large, and intact patches. Relative abundance of short distance dispersers was not significantly different between treatment types (ANOVA p<0.20) but was significantly different between patch sizes (ANOVA p<0.0l). Short distance dispersers were most numerous in small patches followed by plantation, large, and intact and least numerous in clearcut patches. An indicator species analysis of 121 Bear Creek and Indian Creek genera (Dufrene and Legendre 1997), revealed sub-groups of species with 75 to 100 percent "perfect indication" or affiliation for specific patch types. When intact and large patches were pooled and analyzed against all treated patches (plantation and clearcut patches), a list of 36 genera with 75 to 100 percent "perfect affiliation" for intact or large patches was produced (MRPP p<0.05). Small patches had 42 indicators with 75 to 100 percent "perfect indication" when compared with the pooled intact and large patches (MRPP p<0.l). Conclusions Macro-arthropod community composition, diversity and structure did vary, usually significantly, by patch treatment and size. Useful measures of generic diversity include richness estimators [alpha], [beta], and JK1. Examination of taxonomic diversity was also useful, especially for the more mobile arthropods. Pitfall traps provided copious data on the structure of the community in regards to predators and herbivores. Pitfalls, however, did not provide much information about the status of fungivores and parasites in the various different patches. Another trapping method such as the berlaise funnel, would likely provide more information about those functional groups which are likely operating at a finer scale of resolution than that tested by the pitfall trap. Employing both methods would provide a much better assessment of the community of arthropods living on the forest floor. The indicator species analysis program also provided very useful lists of species which are affiliated with particular patch conditions. Taken together, these measures could be adopted for use by forest managers to allow them to assess and monitor the effects of a management regime on the structure and composition of macro-arthropod communities as part of a comprehensive adaptive management plan.
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The forest alpine tundra ecotone (FTE, also known as alpine treeline or subalpine parkland), is a conspicuous feature of mountain landscapes throughout the world. Climate change-driven increases in temperature ...
Citation Citation
- Title:
- Patterns of tree establishment and vegetation composition in relation to climate and topography of a subalpine meadow landscape, Jefferson Park, Oregon, USA
- Author:
- Zald, Harold Samuel James
The forest alpine tundra ecotone (FTE, also known as alpine treeline or subalpine parkland), is a conspicuous feature of mountain landscapes throughout the world. Climate change-driven increases in temperature are believed to result in FTE movement and tree invasion of subalpine meadows, which have been documented throughout the Northern Hemisphere across a wide range of geographic locations, climatic regimes, forest types, land use histories, and disturbance regimes. Climate-driven FTE movement may have numerous ecological effects such as: positive temperature feedbacks, increased net primary productivity and carbon storage, and declines of plant populations and species. The magnitude of these ecological effects is highly uncertain, but will be largely determined by the rates and spatial extent of FTE movement and meadow invasion. FTE movement and meadow invasion are often considered at global or regional spatial scales in relation to climate, yet they are fundamentally driven by tree regeneration processes that are influenced by a variety of climatic and biophysical factors at micro site, landscape, and regional scales. Much of the research on the FTE has not taken a landscape approach incorporating multi-scale processes. For example, species distribution models used to project climate change effects on future species distributions and plant biodiversity in mountainous landscapes rely on species distribution data that is often sparse and incomplete across FTE landscapes. This dissertation attempts to overcome many of the limitations in FTE research by taking a landscape approach to develop a greater understanding of past spatiotemporal patterns of tree invasion, current spatial patterns of vegetation composition and structure, and potential future patterns of climate-driven tree invasion in the FTE. The setting for this research is Jefferson Park, a 260 ha subalpine parkland landscape in the Oregon High Cascades, USA. This study uses field plots, remotely sensed imagery, airborne Light Detection and Ranging (LiDAR), and simulation modeling to: 1) predictively map current fine-scale species distributions, vegetation structure, and tree ages; 2) reconstruct patterns of tree invasion over the last fifty years in subalpine meadows in relation to climatic conditions, landforms, microtopography, and seed dispersal limitations; and 3) develop a statistical model that projects future patterns of tree invasion into subalpine meadows under different climate scenarios in Jefferson Park. In chapter two, I generated fine-scale spatially-explicit predictions of current vegetation composition, structure, and tree ages in the Jefferson Park study area. Objectives of this chapter were threefold: 1) to characterize spatial patterns of tree ages, vegetation composition, and vegetation structure in a FTE landscape in the Oregon Cascades using predictive mapping; 2) determine how vegetation composition and structure were associated with gradients of environmental factors derived from multispectral satellite imagery and Light Detection and Ranging (LiDAR) data; and 3) determine if predictive mapping characterizations of tree age, vegetation composition, and vegetation structure were improved by the inclusion of LiDAR data. Predictive mapping of vegetation attributes was accomplished using gradient analysis with nearest neighbor imputation; integrating field plots, multispectral SPOT 5 satellite imagery, and LiDAR data. Vegetation composition was best described by SPOT 5 imagery and LiDAR-derived topography, while vegetation structure was best described by LiDAR-derived vegetation heights. Predictions of species occurrence were most accurate for tree species, moderate for shrub species and vegetation groups, and highly variable for graminoid species. Tree age, which was the most accurately predicted vegetation structure variable, indicates the study area was largely un-forested in 1600, gradually invaded by trees from 1600 to the 1920's, and rapidly invaded from the 1920's to 1980. Predictive mapping of vegetation structure variables such as basal area and stand density were subject to large amounts of error, possibly resulting from scale incompatibilities between vegetation patterns and plot size, and/or heterogeneous FTE landscapes where forest structure does not develop along consistent trajectories with stand age. This study suggests integrating multispectral satellite imagery, LiDAR data, and field plots can accurately predict fine-scale spatial characterizations of species distributions and tree invasion in the FTE. This study also indicates that sample design can influence spatial patterns of model uncertainty, which needs to be considered if predictive mapping of vegetation and sensitive ecosystems is a component of inventory and monitoring programs. In chapter three, I focused on quantifying spatiotemporal patterns of subalpine parkland tree invasion in Jefferson Park over the past five decades in relation multi-scale climatic and biophysical controls. LiDAR data provided previously unavailable fine-scale spatial characterizations of microtopography and vegetation structure. I utilized LiDAR, georeferenced field plots, and tree establishment reconstructions to quantify spatiotemporal patterns of tree invasion in relation to late season snow persistence, landform types, fine-scale topographic variability, distances from potential seed sources, and climate variation within 130 ha of the subalpine parkland landscape of Jefferson Park. Tree occurrence (i.e. tree presence in 2 m plots and grid cells) occurred in 7.75% of study area meadows in 1950 and increased to 34.7% in 2007. Landform types and finer-scale patterns of topography and vegetation structure influenced summer snow depth, which influenced temporal and spatial patterns of tree establishment. Tree invasion rates were higher on debris flow landforms, which had lower summer snow depth than glacial landforms, suggesting potentially rapid treeline responses to disturbance events. Tree invasion rates were strongly associated with reduced annual snow fall on glacial landforms, but not on debris flows. Tree establishment was spatially constrained to micro sites with high topographic positions and close proximity to overstory canopy, site conditions associated with low summer snow depth. Seed source limitations placed an additional species-specific spatial constraint on where trees invaded meadows. Climate and topography had an interactive effect, with trees establishing on higher topographic positions during both high snow/low temperature and low snow/high temperature periods, but had greater than expected establishment on lower topographic positions during low snow/high temperature periods. Within the context of larger landform types, topography and proximity to overstory trees constrained where trees established in the meadows, even during climate periods with higher temperatures and lower snowfall. Results of this study suggest large scale climate-driven models of vegetation change may overestimate treeline movement and meadow invasion, because they do not account for biophysical controls limiting tree establishment at multiple spatial scales. In chapter four, I used field data and analyses from chapter 3 to parameterize a spatially and temporally explicit statistical model of fine-scale tree invasion within 130 ha of the Jefferson Park study area. The model incorporated both the climatic and biophysical controls found in chapter 3 to influence tree invasion. The model was used in two ways: (1) to spatially project patterns of tree invasion from 1950 to 2007 in response to historical climate; and (2) to project future tree invasion of the study area from 2007 to 2064 under six different annual snowfall scenarios. Modeling addressed the following questions: (1) Can fine-scale (2 m pixel size) patterns of historical tree invasion be accurately predicted? (2) How sensitive is future tree invasion (and therefore meadow persistence) to different future snowfall scenarios? (3) Are non-climatic factors such as landforms and biotic interactions associated with different spatial patterns of tree invasion? From 1950 to 2007, simulated historical meadow area declined from 82% to 65% of the study area. Model outputs of historical area, spatial distributions, and spatial clustering of tree invasion generally agreed with independent validation, and suggest biotic interactions due to young tree establishment facilitation are important on glacial landforms but not debris flows. Simulations of future scenarios indicated meadow declined to 36 to 43% of the study area by 2064. Projected meadow area declined with reduced annual snow fall, but not under prolonged high and low snow fall periods. Meadows persisted under all future scenarios in 2064. This model suggests subalpine meadows may significantly decline under climate warming, but will still persist in 2064. Micro sites and recruitment limitation may be equally or more important factors than climate change in influencing subalpine landscape change, suggesting local high-elevation persistence of subalpine meadows under future climate warming.