The isolation, characterization, and application of WRKY genes as useful molecular markers in tropical trees

The improvement of tropical tree crops using conventional breeding methods faces challenges due to the length of time involved. Thus, like most crops, there is an effort to utilize molecular genetic markers in breeding programs to select for desirable agronomic traits. Known as marker assisted breeding or marker assisted selection, genetic markers associated with a phenotype of interest are used to screen and select material reducing the time necessary to evaluate candidates. As the focus of this research was improving disease resistance in tropical trees, the usefulness of the WRKY gene superfamily was investigated as candidates for generating useful molecular genetic markers. WRKY genes encode plant-specific transcriptional factors associated with regulating plants' responses to both biotic and abiotic stress. ^ One pair of degenerate primers amplified 48 WRKY gene fragments from three taxonomically distinct, economically important, tropical tree crop species: 18 from Theobroma cacao L., 21 from Cocos nucifera L. and 9 from Persea americana Mill. Several loci from each species were polymorphic because of single nucleotide substitutions present within a putative non-coding region of the loci. Capillary array electrophoresis-single strand conformational polymorphism (CAE-SSCP) mapped four WRKY loci onto a genetic linkage map of a T. cacao F2 population segregating for resistance to witches' broom disease. Additionally, PCR primers specific for four T. cacao loci successfully amplified WRKY loci from 15 members of the Byttneriae tribe. A method was devised to allow the reliable discrimination of alleles by CAE-SSCP using only the mobility assigned to the sample peaks. Once this method was validated, the diversity of three WRKY loci was evaluated in a germplasm collection of T. cacao . One locus displayed high diversity in the collection, with at least 18 alleles detected from mobility differences of the product peaks. The number of WRKY loci available within the genome, ease of isolation by degenerate PCR, codominant segregation demonstrated in the F2 population, and usefulness for screening germplasm collections and closely related wild species demonstrates that the WRKY superfamily of genes are excellent candidates for developing a number of genetic molecular markers for breeding purposes in tropical trees. ^

Wayside Trees of Tropical Florida : a guide to the native and exotic trees and palms of Miami and tropical south Florida

Wayside Trees is an beautifully illustrated guide to Florida trees growing south of Lake Okeechobee. It covers both native and exotic species in the areas of Miami to Palm Beach on the east coast, and Naples to Fort Meyers on the west. The introduction describes environmental, cultural and economic importance of trees, while a non-technical key provides a means for even non-specialists to identify the 167 most common species. The bulk of the book consists of illustrated descriptions of the trees, arranged by plant family, and includes ecological and cultural information on each species. Lavishly illustrated with over 1200 color photographs and diagrams, the book is designed to serve homeowners, gardeners, teachers and students, as well as environmental professionals. It is also a useful guide to urban tropical trees growing outside south Florida. The authors, a botanist and a graphic artist, have 70 collective years of experience living, working, and loving the trees of south Florida.

Carbon isotopic composition of cypress trees from South Florida and changing hydrologic condition

δ13C values were determined from cypresstree rings from two different study areas in SouthFlorida. One site is located in the Southeastern Everglades Marsh, where pond cypress (Taxodium ascendens) was sampled from tree islands (annual tree rings from 1970 to 2000). Bald cypress (Taxodium distichum) trees were sampled at the other site, located along the Loxahatchee River in a coastal wetland (decadal tree rings from 1830 to 1990). The isotopic time series from both sites display different, location-specific information. The pond cypressisotopic time series has a positive correlation with the total amount of annual precipitation, while the bald cypress data from the Loxahatchee River study area had two different records dependent on the level of saltwater stress. In general, for terrestrial trees growing in a temperate environment, water stress causes an increase in water-use efficiency (WUE) resulting in a relative 13C enrichment. Yet, trees growing in wetland settings in some cases do not respond in the same manner. We propose a conceptual model based on changes in carbon assimilation and isotopic fractionation as controlled by differences in stomatal resistance (water stress) and mesophyll resistance (biochemical and nutrient related) to explain the isotopic records from both sites. With further work and a longer time series, our approach may be tested, and used to reconstruct change in hydroperiods further back in time, and potentially provide a baseline for wetland restoration.

Factors Affecting Current and Future Treeline Locations and Dynamics in the Peruvian Andes

The elevational distributions of tropical treelines are thought to be determined by temperature, and are predicted to shift upslope in response to global warming. In contrast to this hypothesis, global-scale studies have shown that only half of all studied treelines are shifting upslope. Understanding how treelines will respond to climate change has important implications for global biodiversity, especially in the tropics, because tropical treelines generally represent the upper-elevation distribution limit of the hyper-diverse cloudforest ecosystem. In Chapter 1, I introduce the idea that grasslands found above tropical treelines may represent a potential grass ceiling which forest species cannot cross or invade. I use an extensive literature review to outline potential mechanisms which may be acting to stabilize treeline and prevent forest expansion into high-elevation grasslands. In Chapters 2-4, I begin to explore these potential mechanisms through the use of observational and experimental methods. In Chapter 2, I show that there are significant numbers of seedlings occurring just outside of the treeline in the open grasslands and that seed rain is unlikely to limit seedling recruitment above treeline. I also show that microclimates outside of the closed-canopy cloudforest are highly variable and that mean temperatures are likely a poor explanation of tropical treeline elevations. In Chapter 3, I show that juvenile trees maintain freezing resistances similar to adults, but nighttime radiative cooling near the ground in the open grassland results in lower cold temperatures relative to the free atmosphere, exposing seedlings of some species growing above treeline to lethal frost events. In Chapter 4, I use a large-scale seedling transplant experiment to test the effects of mean temperature, absolute low temperature and shade on transplanted seedling survival. I find that increasing mean temperature negatively affects seedling survival of two treeline species while benefiting another. In addition, low temperature extremes and the presence of shade also appear to be important factors affecting seedling survival above tropical treelines. This work demonstrates that mean temperature is a poor predictor of tropical treelines and that temperature extremes, especially low temperatures, and non-climatic variables should be included in predictions of current and future tropical treeline dynamics.

Deadly Night Shade, women rock group

General note: Title and date provided by Bettye Lane.

Deadly Night Shade, women rock group

General note: Title and date provided by Bettye Lane.

Predicting Forest Responses to Changing Environmental Conditions

Forests change with changes in their environment based on the physiological responses of individual trees. These short-term reactions have cumulative impacts on long-term demographic performance. For a tree in a forest community, success depends on biomass growth to capture above- and belowground resources and reproductive output to establish future generations. Here we examine aspects of how forests respond to changes in moisture and light availability and how these responses are related to tree demography and physiology.

First we address the long-term pattern of tree decline before death and its connection with drought. Increasing drought stress and chronic morbidity could have pervasive impacts on forest composition in many regions. We use long-term, whole-stand inventory data from southeastern U.S. forests to show that trees exposed to drought experience multiyear declines in growth prior to mortality. Following a severe, multiyear drought, 72% of trees that did not recover their pre-drought growth rates died within 10 years. This pattern was mediated by local moisture availability. As an index of morbidity prior to death, we calculated the difference in cumulative growth after drought relative to surviving conspecifics. The strength of drought-induced morbidity varied among species and was correlated with species drought tolerance.

Next, we investigate differences among tree species in reproductive output relative to biomass growth with changes in light availability. Previous studies reach conflicting conclusions about the constraints on reproductive allocation relative to growth and how they vary through time, across species, and between environments. We test the hypothesis that canopy exposure to light, a critical resource, limits reproductive allocation by comparing long-term relationships between reproduction and growth for trees from 21 species in forests throughout the southeastern U.S. We found that species had divergent responses to light availability, with shade-intolerant species experiencing an alleviation of trade-offs between growth and reproduction at high light. Shade-tolerant species showed no changes in reproductive output across light environments.

Given that the above patterns depend on the maintenance of transpiration, we next developed an approach for predicting whole-tree water use from sap flux observations. Accurately scaling these observations to tree- or stand-levels requires accounting for variation in sap flux between wood types and with depth into the tree. We compared different models with sap flux data to test the hypotheses that radial sap flux profiles differ by wood type and tree size. We show that radial variation in sap flux is dependent on wood type but independent of tree size for a range of temperate trees. The best-fitting model predicted out-of-sample sap flux observations and independent estimates of sapwood area with small errors, suggesting robustness in new settings. We outline a method for predicting whole-tree water use with this model and include computer code for simple implementation in other studies.

Finally, we estimated tree water balances during drought with a statistical time-series analysis. Moisture limitation in forest stands comes predominantly from water use by the trees themselves, a drought-stand feedback. We show that drought impacts on tree fitness and forest composition can be predicted by tracking the moisture reservoir available to each tree in a mass balance. We apply this model to multiple seasonal droughts in a temperate forest with measurements of tree water use to demonstrate how species and size differences modulate moisture availability across landscapes. As trees deplete their soil moisture reservoir during droughts, a transpiration deficit develops, leading to reduced biomass growth and reproductive output.

This dissertation draws connections between the physiological condition of individual trees and their behavior in crowded, diverse, and continually-changing forest stands. The analyses take advantage of growing data sets on both the physiology and demography of trees as well as novel statistical techniques that allow us to link these observations to realistic quantitative models. The results can be used to scale up tree measurements to entire stands and address questions about the future composition of forests and the land’s balance of water and carbon.

Left to right: Gustavo Rubio and Melissa Romigh measuring diameter at breast height (DBH) of mangrove trees at SRS-6, Shark River Slough

This material is based upon work supported by the National Science Foundation through the Florida Coastal Everglades Long-Term Ecological Research program under Cooperative Agreements #DBI-0620409 and #DEB-9910514. This image is made available for non-commercial or educational use only.

Mortality and climatic/environmental correlates of Widdringtonia cedargensis trees in the Cederberg, South Africa

Background: Conifer populations appear disproportionately threatened by global change. Most examples are, however, drawn from the northern hemisphere and long-term rates of population decline are not well documented as historical data are often lacking. We use a large and long-term (1931-2013) repeat photography dataset together with environmental data and fire records to account for the decline of the critically endangered Widdringtonia cedarbergensis. Eighty-seven historical and repeat photo-pairs were analysed to establish 20th century changes in W. cedarbergensis demography. A generalized linear mixed-effects model was fitted to determine the relative importance of environmental factors and fire-return interval on mortality for the species. Results: From an initial total of 1313 live trees in historical photographs, 74% had died and only 44 (3.4%) had recruited in the repeat photographs, leaving 387 live individuals. Juveniles (mature adults) had decreased (increased) from 27% (73%) to 8% (92%) over the intervening period. Our model demonstrates that mortality is related to greater fire frequency, higher temperatures, lower elevations, less rocky habitats and aspect (i.e. east-facing slopes had the least mortality). Conclusions: Our results show that W. cedarbergensis populations have declined significantly over the recorded period, with a pronounced decline in the last 30 years. Individuals that established in open habitats at lower, hotter elevations and experienced a greater fire frequency appear to be more vulnerable to mortality than individuals growing within protected, rocky environments at higher, cooler locations with less frequent fires. Climate models predict increasing temperatures for our study area (and likely increases in wildfires). If these predictions are realised, further declines in the species can be expected. Urgent management interventions, including seedling out-planting in fire-protected high elevation sites, reducing fire frequency in higher elevation populations, and assisted migration, should be considered.

Sampling information, length measurements, DNA alignments, models and phylogenetics trees for Oithona similis s.l.

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24 %, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level. Molecular clock application revealed that the evolutionary history of O. similis s.l. is possibly closely associated with the reorganization of the ocean circulation in the mid Miocene and may be an example of allopatric speciation in the pelagic zone.

Policy and Design Guidelines for Trees in a Growing Seattle

Thesis (Master's)--University of Washington, 2016-08

Crescimento e desenvolvimento de Plinia cauliflora de acordo com a intensidade luminosa em clima subtropical

The jabuticaba fruit tree from classified in the Myrtaceae family and Plinia genre. There are about nine species of this fruit tree, that include as most important, Plinia trunciflora (jabuticaba de cabinho), naturally occurring in southwestern Paraná State, Brazil, P. cauliflora (jabuticaba Paulista or Jabuticaba Açu) and P. jaboticaba (Vell) (jabuticaba sabará), with all the over species producing fruit for the industry or fresh consumption. Nevertheless, there aren‟t commercial orchards with this culture, with highest yield part from extractive. This fact can be combined with lack of technical knowledge for the plants produce in the field. As these species are found in the forest, the first point is whether they can adapt to other light intensity conditions. The aim of this work was to identify the adaptive behavior of jabuticaba fruit seedling and tree when they were put in different light intensities and what this can be considered ideal for the growth, as well as, its influence in the leaves secondary compounds production. Two experiments were conducted, with the first involved with the study of the seedlings and the second with plants in the field. The work was carried out at Universidade Tecnológica Federal do Paraná – Câmpus Dois Vizinhos, Paraná State - Brazil. The experimental design was a completely randomized and a block design with four treatments and four replications of 10 seedlings or two plants per plot, according to nursery or orchard conditions, respectively. The treatments were base according to the light intensity. The treatments used were, 1 - full sun, similar the orchard condition, with 0% shading; 2 - side cover with shade cloth and top with transparent plastic, representing a gap forest condition; 3 - side and top cover with shade cloth, representing stage where the forest canopy is closing, focusing only indirect sunlight; 4 - side and top cover with shade cloth, simulating a closed canopy condition, with PPD (photon flux density) of 10% (90% shading); 5 - side and top cover with shade cloth, simulating a more open canopy condition with PPD 65% (35% shading). The growth and development seedling and plant characteristics were evaluated once by month, as also, during time part in the plants the secondary metabolites leaves, soil activity microbiological and the fresh and dry matter root and shoot and, root length from seedlings. For the growth and development of jabuticaba Açú Paulista seedling recommend to use of side cover with shade cloth and top with transparent plastic, representing a gap forest condition. In orchard, for the growth and development of plants jabuticaba Híbrida tree it was recommended the use of side and top cover with shade cloth of some type. For production of secondary metabolites of leaves, the plant must to be full sunlight condition orchard.

Rate of Belowground Carbon Allocation Differs with Successional Habit of Two Afromontane Trees

Background: Anthropogenic disturbance of old-growth tropical forests increases the abundance of early successional tree species at the cost of late successional ones. Quantifying differences in terms of carbon allocation and the proportion of recently fixed carbon in soil CO2 efflux is crucial for addressing the carbon footprint of creeping degradation. Methodology: We compared the carbon allocation pattern of the late successional gymnosperm Podocarpus falcatus (Thunb.) Mirb. and the early successional (gap filling) angiosperm Croton macrostachyus Hochst. es Del. in an Ethiopian Afromontane forest by whole tree (CO2)-C-13 pulse labeling. Over a one-year period we monitored the temporal resolution of the label in the foliage, the phloem sap, the arbuscular mycorrhiza, and in soil-derived CO2. Further, we quantified the overall losses of assimilated C-13 with soil CO2 efflux. Principal Findings: C-13 in leaves of C. macrostachyus declined more rapidly with a larger size of a fast pool (64% vs. 50% of the assimilated carbon), having a shorter mean residence time (14 h vs. 55 h) as in leaves of P. falcatus. Phloem sap velocity was about 4 times higher for C. macrostachyus. Likewise, the label appeared earlier in the arbuscular mycorrhiza of C. macrostachyus and in the soil CO2 efflux as in case of P. falcatus (24 h vs. 72 h). Within one year soil CO2 efflux amounted to a loss of 32% of assimilated carbon for the gap filling tree and to 15% for the late successional one. Conclusions: Our results showed clear differences in carbon allocation patterns between tree species, although we caution that this experiment was unreplicated. A shift in tree species composition of tropical montane forests (e. g., by degradation) accelerates carbon allocation belowground and increases respiratory carbon losses by the autotrophic community. If ongoing disturbance keeps early successional species in dominance, the larger allocation to fast cycling compartments may deplete soil organic carbon in the long run.

Packings and coverings of the complete graph with trees

In this thesis, we define the spectrum problem for packings (coverings) of G to be the problem of finding all graphs H such that a maximum G-packing (minimum G- covering) of the complete graph with the leave (excess) graph H exists. The set of achievable leave (excess) graphs in G-packings (G-coverings) of the complete graph is called the spectrum of leave (excess) graphs for G. Then, we consider this problem for trees with up to five edges. We will prove that for any tree T with up to five edges, if the leave graph in a maximum T-packing of the complete graph Kn has i edges, then the spectrum of leave graphs for T is the set of all simple graphs with i edges. In fact, for these T and i and H any simple graph with i edges, we will construct a maximum T-packing of Kn with the leave graph H. We will also show that for any tree T with k ≤ 5 edges, if the excess graph in a minimum T-covering of the complete graph Kn has i edges, then the spectrum of excess graphs for T is the set of all simple graphs and multigraphs with i edges, except for the case that T is a 5-star, for which the graph formed by four multiple edges is not achievable when n = 12.