Improving Parameterization of Scalar Transport through Vegetation in a Coupled Ecosystem-Atmosphere Model

Link P.A., Improving Parameterization of Scalar Transport through Vegetation in a Coupled Ecosystem-Atmosphere Model. PhD Thesis, VU University, Amsterdam, The Netherlands.

Several regional-scale ecosystem models currently parameterize subcanopy scalar transport using a rough-wall boundary eddy diffusivity formulation. This formulation predicts unreasonably high soil evaporation beneath tall, dense forests and low soil evaporation beneath short, sparse grass. This study investigates alternative formulations by reviewing literature on flow and scalar transport in canopies, taking field measurements of subcanopy latent heat flux, and testing alternative model formulations in constrained numerical experiments. A field campaign was conducted in a dense rainforest in Luquillo National Forest, Puerto Rico, to measure wind and fluxes with eddy covariance devices. Wind velocities and fluxes of latent heat, sensible heat, and momentum were found to be much smaller below the canopy than above it. Modeling experiments tested a mixing-layer-based formulation of eddy diffusivity and a soil evaporation cutoff based on vortex penetration depth. The vortex penetration cutoff was found to be the most physically accurate and computationally simple option, and this study recommends that ecosystem and land-surface models adopt this formulation for subcanopy scalar transport.

Twelve testable hypotheses on the Geobiology of weathering

Brantley S.L., Megonigal J.P., Scatena F.N. et al 2010. Twelve testable hypotheses on the Geobiology of weathering. Geobiology. DOI: 10.1111/j.1472-4669.2010.00264.x

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earth’s surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby controlling the location and extent of biological weathering. (2) Biological stoichiometry drives changes in mineral stoichiometry and distribution through weathering. (3) On landscapes experiencing little erosion, biology drives weathering during initial succession, whereas weathering drives biology over the long term.(4) In eroding landscapes, weathering-front advance at depth is coupled to surface denudation via biotic processes.(5) Biology shapes the topography of the Critical Zone.(6) The impact of climate forcing on denudation rates in natural systems can be predicted from models incorporating biogeochemical reaction rates and geomorphological transport laws.(7) Rising global temperatures will increase carbon losses from the Critical Zone.(8) Rising atmospheric PCO2 will increase rates and extents of mineral weathering in soils.(9) Riverine solute fluxes will respond to changes in climate primarily due to changes in water fluxes and secondarily through changes in biologically mediated weathering.(10) Land use change will impact Critical Zone processes and exports more than climate change. (11) In many severely altered settings, restoration of hydrological processes is possible in decades or less, whereas restoration of biodiversity and biogeochemical processes requires longer timescales.(12) Biogeochemical properties impart thresholds or tipping points beyond which rapid and irreversible losses of ecosystem health, function, and services can occur.

Long-term influence of deforestation on tree species composition and litter dynamics of a tropical rain forest in Puerto Rico

Zou X, Zucca CP, Waide RB & McDowell WH (1995)
Long-term influence of deforestation on tree species composition
and litter dynamics of a tropical rain forest in
Puerto Rico. Forest Ecology and Management 78:

Understanding the long-term impact of deforestation on ecosystem structure and function of tropical forests may aid in designing future conservation programs to preserve biodiversity and sustain ecosystem productivity. We examined forest structure, tree species composition, litterfall rate, and leaf litter decomposition in a mid-successional forest (MSF) and an adjacent mature tabonuco forest (MTF) in the Luquillo Experimental Forest of Puerto Rico. Whereas the MTF site received limited human disturbance, the MSF site had been cleared for timber production by the beginning of this century and was abandoned after hurricanes struck the Luquillo Mountains in the 1920s and 1930s. We found that the MSF was dominated by successional tree species 50 years after secondary succession, and did not differ in tree basal area and litterfall rate from the MTF. Leaf decomposition rate in the MSF was higher than in the MTF, but this differencew as small.O ur resultss how that deforestation has long-term (over 50 years) influence on tree species composition and that recovery of leaf decomposition processes in secondary forest is relatively faster than that of tree species composition.

Water, Sediment, and Nutrient Discharge Characteristics of Rivers in Puerto Rico, andtheir Potential Influence on Coral Reefs

Warne, A.G., Webb, R.M.T., and Larsen, M.C., 2005, Water, Sediment, and Nutrient Discharge Characteristics of Rivers in Puerto Rico, and their Potential Influence on Coral Reefs: U.S. Geological Survey Scientific Investigations Report
2005-5206, 58 p.

Data from 29 streamflow-gaging stations, including 9 stations with daily suspended-sediment concentration, and data from 24 water-quality stations were compiled and analyzed to investigate the potential effects of river sediment and nutrient discharges on the coral reefs of Puerto Rico. The largely mountainous watersheds of the 8,711-square-kilometer island of Puerto Rico are small, channel gradients are steep, stream valleys tend to be well-incised and narrow, and major storms tend to be intense but brief; hence flooding is rapid with peak discharges several orders of magnitude above base discharge, and flood waters recede quickly. Storm runoff transports a substantial part of fluvial suspended sediment from uplands to the coast, as indicated by sediment data from a set of nine streamflow-gaging stations representative of runoff from watersheds considered typical of conditions in Puerto Rico. For example, the highest recorded daily sediment discharge is 1 to 3.6 times the annual suspended-sediment discharge, and runoff from major storms induces sediment transport 1 to 32 times the median annual sediment load. Precipitation associated with Hurricane Georges in September 1998 is estimated to have averaged 300 millimeters across the island, which is equivalent to a volume of about 2.6 billion cubic meters. Analysis of runoff and sediment yield from Hurricane Georges indicates that more than 1.0 billion cubic meters of water and at least 2.4 million metric tonnes of sediment (and as much as 5 to 10 million metric tonnes), were discharged to the coast and shelf as a result of this major storm. Because of their relatively small size, dams and reservoirs of Puerto Rico have relatively little effect on total discharge of water and sediment to the coastal marine waters during major storms. The presence of reservoirs, however, may be detrimental to coral reefs for two reasons: (1) coarse sediments deposited in the reservoir can be replaced by finer sediments scoured, if available, from the river channels and flood plains below the dam; and (2) the loads of phosphorus and ammonia reaching the coastal waters may increase as organic matter decomposes in the anoxic bottom waters of the reservoir. Rainfall, water discharge, sediment discharge, and sediment yield vary across the island. Mean annual runoff for the island is estimated to be 910 millimeters, about 57 percent of mean annual precipitation (1,600 millimeters). Mean annual suspended-sediment discharge from Puerto Rico into surrounding coastal waters is estimated to range from 2.7 to 9.0 million metric tonnes. Hydrologic and sediment data associated with Hurricane Georges indicate that sediment yield is generally proportional to the depth of storm runoff. Discharge and sediment-concentration data indicate that during this storm, river water and sediment that discharged into the marine environment generally formed hypopycnal plumes (buoyant suspension layers). Generally, hyperpycnal (density) plumes can develop in areas with high discharges and sediment concentrations. Both hypopycnal and hyperpycnal plumes distribute suspended sediment over broad areas of the Puerto Rico shelf and shelf slope. Comparison of long-term suspended-sediment discharge and watershed characteristics for Puerto Rico with those of other river systems around the world indicates that Puerto Rico rivers are similar to temperate and tropical upland river systems.

Land Transitions in the Tropics: Going Beyond the Case Studies

Uriarte, M., Schneider, L. and Rudel, T. K. (2010), Land Transitions in the Tropics: Going Beyond the Case Studies. Biotropica, 42: 1–2. doi: 10.1111/j.1744-7429.2009.00580.x

Estimates of the percent of Earth’s land surface that has either been transformed or degraded by human activity range between 39 and 50 percent, with agriculture accounting for the vast majority of these changes. Although much of the focus of research on land use and cover change in the tropics has been on deforestation, ongoing socioeconomic changes both locally and globally have made land transitions in the tropics extremely fluid. In addition, feedbacks between land cover change and human behavior constrain the extent and trajectories of land transitions. The sustainability of land use systems in the tropics depends on an understanding of coupled human–natural systems that can lead to general frameworks for management and prediction. The unprecedented availability of land use/cover data together with ecological data collected at large spatial scales offer exciting opportunities for advancing our understanding of socioecological systems. We rely on six studies of land transitions in the tropics to illustrate some promising approaches and pose critical questions to guide this body of research.

A comparison of current and historical fish assemblages in a Caribbean island estuary: conservation value of historical data

Smith, K. L., Corujo Flores, I. and Pringle, C. M. (2008), A comparison of current and historical fish assemblages in a Caribbean island estuary: conservation value of historical data. Aquatic Conservation: Marine and Freshwater Ecosystems, 18: 993–1004. doi: 10.1002/aqc.920

1. Historical data are often one of the only resources available for documenting and assessing causes of environmental change, particularly in developing regions where funding for ecological studies is limited. In this paper, previously unpublished data from a 1977 year-long study of the fish community of the Espiritu Santo estuary are presented. This dataset is among the oldest and most extensive surveys of a Caribbean island estuarine fish community. 2. A comparison of these historical data with data collected in June and July 2004 using identical sampling methods allowed description of potential long-term changes in the fish community, identification of vulnerable species, and assessment of potential drivers of change. 3. Results strongly suggest a decline in species richness and abundance in the Espiritu Santo estuarine fish community, with greater declines in freshwater-tolerant than marine or euryhaline species. Declines in freshwater inflow to the estuary, due to large-scale upstream water abstractions for municipal use, have increased since the initial 1977 survey. 4. This is the first study to examine long-term change in the fish community of a tropical island estuary. Results indicate that additional research and conservation efforts are needed to understand mechanisms of change and to protect Caribbean island estuarine fish communities.

The Forest Types and Ages Cleared for Land Development in Puerto Rico

Kennaway, Todd; Helmer, E. H. 2007. The Forest Types and Ages Cleared for Land Development in Puerto Rico.. GIScience & Remote Sensing, 44, No. 4, :356-382.

On the Caribbean island of Puerto Rico, forest, urban/built-up, and pasture lands have replaced most formerly cultivated lands. The extent and age distribution of each forest type that undergoes land development, however, is unknown. This study assembles a time series of four land cover maps for Puerto Rico. The time series includes two digitized paper maps of land cover in 1951 and 1978 that are based on photo interpretation. The other two maps are of forest type and land cover and are based on decision tree classification of Landsat image mosaics dated 1991 and 2000. With the map time series we quantify land-cover changes from 1951 to 2000; map forest age classes in 1991 and 2000; and quantify the forest that undergoes land development (urban development or surface mining) from 1991 to 2000 by forest type and age. This step relies on intersecting a map of land development from 1991 to 2000 (from the same satellite imagery) with the forest age and type maps. Land cover changes from 1991 to 2000 that continue prior trends include urban expansion and transition of sugar cane, pineapple, and other lowland agriculture to pasture. Forest recovery continues, but it has slowed. Emergent and forested wetland area increased between 1977 and 2000. Sun coffee cultivation appears to have increased slightly. Most of the forests cleared for land development, 55%, were young (1–13 yr). Only 13% of the developed forest was older (41–55+ yr). However, older forest on rugged karst lands that long ago reforested is vulnerable to land development if it is close to an urban center and unprotected.

Diversity and composition of tropical secondary forests recovering from large-scale clearing: results from the 1990 inventory in Puerto Rico

Chinea, J. Danilo; Helmer, Eileen H. 2003. Diversity and composition of tropical secondary forests recovering from large-scale clearing: results from the 1990 inventory in Puerto Rico.. Forest Ecology and Management 180 :227-240.

The extensive recovery from agricultural clearing of Puerto Rican forests over the past half-century provides a good opportunity to study tropical forest recovery on a landscape scale. Using ordination and regression techniques, we analyzed forest inventory data from across Puerto Rico’s moist and wet secondary forests to evaluate their species composition and whether the landscape structure of older forest affected tree species composition of recovering forests at this scale. Our results support conclusions from studies conducted in Puerto Rico at smaller scales and temperate forests at larger scales that timing of abandonment and land use history are of overwhelming importance in determining the species composition of recovering forests. Forest recovery is recent enough in Puerto Rico that previous land use is clearly evident in current species composition, and creates new forest communities. As demonstrated in other work, physical factors such as elevation and substrate co-vary with land use history, so that the species composition of the forest landscape results from the interplay between biophysical and socioeconomic forces over time. Our results also indicate that increasing the distance to the largest forest patches occurring in the landscape 12 years previous had a small negative impact on species richness but not species diversity or community composition.We conclude that land use history has as much influence in species composition as biophysical variables and that, at the scale of this study, there is no large influence of forest landscape structure on species diversity or composition.


The Environmental Quality Board recognizes that water pollution is detrimental to public health and welfare, creates public nuisances, is harmful to wildlife, fish and other aquatic life, and impairs domestic, agricultural, industrial, recreational and other beneficial uses of water. It is the goal of this Board, and this Regulation, to preserve, maintain and enhance the quality of the waters of Puerto Rico in such manner that they be compatible with the social and economic needs of the Commonwealth of Puerto Rico. The purposes of this Regulation are to: (1) designate the uses for which the quality of the waters of Puerto Rico shall be maintained and protected, (2) prescribe the water quality standards required to sustain the designated uses, (3) identify other rules and regulations applicable to sources of pollution that may affect the quality of waters subject to this Regulation and (4) prescribe additional measures necessary for implementing, achieving and maintaining the prescribed water quality. This Regulation is enacted in accordance with Law No. 9 approved on June 18, 1970, as amended known as the Public Policy Environmental Act, and nullifies any previous provision, resolution, agreement or regulation of the Commonwealth of Puerto Rico on the same subject which may contradict this Regulation.

Spatial Patterning in the Dooryard Gardens of Puerto Rico

Spatial Patterning in the Dooryard Gardens of Puerto Rico
Clarissa T. Kimber
Geographical Review
Vol. 63, No. 1 (Jan., 1973), pp. 6-26

Puerto Rican dooryard gardens derive from two old traditions, the vernacular and the high style, which correspond to the rustic and aristocratic ideals. The gardens are classified in six design categories-the jibaro, the traditional, the vernacular, the contemporary ideal, the house-and-garden ideal, and the manor-and can be thought of as being aligned along a continuum that has been modified recently by the introduction of the American suburban ideal. The principal design elements are the dwelling, other buildings, bare earth, and the arrangement of trees, shrubs, herbs, and flowering plants. Of secondary importance is the arrangement of the plants according to intended-use categories. Economic position is changing the relative importance of the different garden design types, though there is no evidence that any are being eliminated. Behavior associated with these garden types suggests that garden design provides a clue to codified cultural patterns.
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