Costa Rican Rain Forest Research Articles

DNA Barcoding—a Windfall for Tropical Biology?

'I AM STANDING IN A COSTA RICAN RAIN FOREST', writes tropical ecologist and conservationist Dan Janzen (2005). 'There are a thou sand species of plants within a long stone's throw. Nearly every one of them is a described species with a proper scientific name, a handle that you can plug into Google and come up with something.... And I cannot identify a single species. Imagine what it would do to any and all aspects of human interactions with wild plants if you could walk up to any plant anywhere-seedling, sapling, 40 m tree, grass, root, pressed leaf, or fallen log-and know in a few seconds its scientific name'. Janzen, one of tropical biology's more ardent advocates, po etically describes the taxonomic impediment that exists today for many ecologists and evolutionary biologists working in the field: determining the correct species identification for any plant sample in a fast and repeatable fashion. In fact Janzen knew when he wrote this passage that a rapid and accurate method is now being devel oped and refined for the quick identification of plant species based on extracting DNA sequence from a tiny tissue sample from any part of a plant. Appropriately called 'DNA barcoding', referring to the coded labels one finds on commercial products, DNA barcodes consist of a standardized short sequence of DNA between 400 and 800 base pairs long that can be easily generated and characterized for all species on the planet (Savolainen et al. 2005). These genetic barcodes will be stored in an open access digital library that can be used to compare the DNA barcode sequence of an unidentified sample from the field, garden, or market by matching it to a known sequence with an associated species name in the data base. DNA barcoding has the potential to greatly advance our access to the col lective knowledge of biodiversity and in turn our understanding of Nature. By harnessing advances in molecular genetics, sequencing technology, and bioinformatics, DNA barcoding will allow users to quickly and cheaply recognize known species and retrieve informa tion about them. It may also speed the discovery of the thousands of species yet to be named. Barcoding, if developed sufficiently, will be a vital new tool for appreciating and managing the Earth's immense and changing biodiversity (Cowan et al. 2006). And most of that diversity is in the tropics. Some of the basic questions about tropical ecosystems that biologists have been attempting to answer over the last century re quire an estimate of species diversity. Why do tropical biomes have greater species diversity than temperate zone habitats? How is this species richness maintained in time and space? What are the ecolog ical and evolutionary processes that influence species composition in tropical forests? Answers to some of these broad questions ini tially require accurate assessments of the level of species diversity in a particular habitat. These assessments must have accurate species identifications and, ideally, a uniform species definition. As tropical biologists, we all know how difficult it is to obtain accurate identifi cation of organisms in species-rich tropical forests. DNA barcoding will provide a new tool that will supplement traditional methods and allow us to more independently assess this overwhelming species diversity.

No short-term change in soil properties following four-fold litter addition in a Costa Rican rain forest

We experimentally manipulated forest floor litter to investigate the influence of litter quality and quantity on soil properties over the short-term (weeks to months) in a wet tropical forest in NE Costa Rica. The study included old growth forest on high fertility soils, old growth forest on low fertility soils, and secondary forest on intermediate fertility soils. Forest floor litter was removed from a 16 m 2 area and added to an adjacent 4 m 2 area in March 2003, resulting in a one to four-fold increase in the annual litter input to the forest floor. We created three addition, three removal and three control plots per forest type. We measured treatment effects on variation in soil moisture, temperature, pH, and Bray-1 P (plant available) over a 5-month period that captured the dry-wet season transition. Litter manipulation had no effect on any of the soil properties measured during the 5-month study period. Significant variability through time and a similar temporal pattern across the three forest stands suggest that climatic variability is driving short-term patterns in these soil properties rather than seasonal inputs of litter. In general, soils were warmer, drier and more basic with higher available P during dry season months. Even in wet tropical forests, small variability in climate can play an important role in soil dynamics over periods of weeks to months. Although litter manipulation did not influence soil properties over the 5-month study period, a longer lag may exist between the timing of litter inputs and the influence of that litter on soil properties, especially plant available P.

Tropical tree species composition affects the oxidation of dissolved organic matter from litter

Plant species effects on soil nutrient availability are relatively well documented, but the effects of species differences in litter chemistry on soil carbon cycling are less well understood, especially in the species-rich tropics. In many wet tropical forest ecosystems, leaching of dissolved organic matter (DOM) from the litter layer accounts for a significant proportion of litter mass loss during decomposition. Here we investigated how tree species differences in soluble dissolved organic C (DOC) and nutrients affected soil CO2 fluxes in laboratory incubations. We leached DOM from freshly fallen litter of six canopy tree species collected from a tropical rain forest in Costa Rica and measured C-mineralization. We found significant differences in litter solubility and nutrient availability. Following DOM additions to soil, rates of heterotrophic respiration varied by as much as an order of magnitude between species, and overall differences in total soil CO2 efflux varied by more than four-fold. Variation in the carbon: phosphorus ratio accounted for 51% of the variation in total CO2 flux between species. These results suggest that tropical tree species composition may influence soil C storage and mineralization via inter-specific variation in plant litter chemistry.

Of Birds, People (and Coffee): Research and Conservation in Costa Rica

I am a wildlife veterinarian and currently a doctoral candidate at the University of Georgia’s (UGA) Odum School of Ecology. Years ago, I was fortunate enough to collaborate with an ecologist on a study on tapirs (Tapirus bairdii) in a stretch of lowland rainforest in Costa Rica. That opened up a world for me and set me on a path towards my current professional passion: to merge veterinary medicine with an ecological perspective, in particular towards applied conservation. However, I felt I was missing the tools to truly take the host-pathogen interactions I had learned in veterinary school to the population, community, or landscape level, which an advanced ecology degree could offer. The general theme of my dissertation work revolves around how human-altered landscapes affect disease dynamics. In specific, I am investigating how shade-grown coffee plantations influence the biodiversity, abundance, and health of wild birds. Shadegrown coffee (or ‘‘bird-friendly’’ coffee) is a method by which forest either is never cleared and coffee bushes are planted in between existing trees or previously cleared coffee plots are replanted with native trees. Traditional coffee plantations are monoculture operations that clear large areas of forest and replace them with coffee. This requires generous amounts of fertilizers and pesticides, because coffee is originally an understory, shade-loving plant, heavily stressed under the sun; however, it makes harvesting a lot easier. Shade-grown coffee works well in small plantations, and studies have shown that avian biodiversity is much improved in these operations, which is important in areas in Central America where neotropical migrants are running out of available habitat. These plantations also act as points of contact between forest birds and humans and their domestic animals (including free-roaming chickens), and I am particularly interested in the balance of benefits and potential problems these plantations create for wild birds. I have worked as an exotic animal and zoo veterinarian and have been an avid bird-watcher all my life, but working with wild birds in the field has given me the opportunity to really see them in their element and appreciate the issues that threaten free-ranging birds worldwide.

Foliar and ecosystem respiration in an old‐growth tropical rain forest

Foliar respiration is a major component of ecosystem respiration, yet extrapolations are often uncertain in tropical forests because of indirect estimates of leaf area index (LAI). A portable tower was used to directly measure LAI and night-time foliar respiration from 52 vertical transects throughout an old-growth tropical rain forest in Costa Rica. In this study, we (1) explored the effects of structural, functional and environmental variables on foliar respiration; (2) extrapolated foliar respiration to the ecosystem; and (3) estimated ecosystem respiration. Foliar respiration temperature response was constant within plant functional group, and foliar morphology drove much of the within-canopy variability in respiration and foliar nutrients. Foliar respiration per unit ground area was 3.5 +/- 0.2 micromol CO2 m(-2) s(-1), and ecosystem respiration was 9.4 +/- 0.5 micromol CO2 m(-2) s(-1)[soil = 41%; foliage = 37%; woody = 14%; coarse woody debris (CWD) = 7%]. When modelled with El Niño Southern Oscillation (ENSO) year temperatures, foliar respiration was 9% greater than when modelled with temperatures from a normal year, which is in the range of carbon sink versus source behaviour for this forest. Our ecosystem respiration estimate from component fluxes was 33% greater than night-time net ecosystem exchange for the same forest, suggesting that studies reporting a large carbon sink for tropical rain forests based solely on eddy flux measurements may be in error.

Differences in the degree of environmental control on large and small tropical plants: just a sampling effect?

Summary Tropical rain forest tree species are commonly perceived to have more generalized habitat distributions than understorey species. However, the correspondence between floristic patterns in large trees and smaller understorey plants in relation to environmental differences has rarely been investigated. Comparative analyses are complicated by the fact that tree data are often much more noisy, with higher overall species richness and poorer spatial and temporal representation of species composition within sampling plots. Using data on trees and pteridophytes collected in 1125 plots located within 6 km2 of lowland rain forest in Costa Rica, we asked: (i) Is there evidence that trees are more generalized in their edaphic and topographic distributions than pteridophytes, and (ii) How much might differences in sampling efficiency affect the results? We ran community‐level analyses using Mantel tests, and for the five most frequent tree and pteridophyte species we ran logistic regression analyses of species occurrence. To investigate the influence of differing sampling efficiency, the analyses were repeated with four rarefied pteridophyte data sets approximating key structural features of the tree data set. Differences in community composition in trees and in all pteridophyte data sets were most strongly correlated with environmental differences in the same five soil variables. The most frequent species in both plant groups had non‐random edaphic and topographic distributions. Both Mantel correlations and the predictive performance of single species models (AUC values) were higher for the full pteridophyte data set than for trees, but these differences were much reduced after pteridophyte rarefaction. The performance of the species occurrence models calibrated with rarefied pteridophyte data appeared poor when tested on rarefied data. However, their performance in predicting occurrences in the full data set was usually moderate (AUC > 0.70). This suggests that the tree species models may also predict species’ potential habitat distributions better than is apparent from their AUC values. Synthesis. Our results indicate that rain forest trees and pteridophytes may respond to mesoscale environmental variation in qualitatively similar ways, but that trees will appear much more generalized in their response to the environment unless differences in sampling efficiency are taken into account.

Conventional and genetic measures of seed dispersal for Dipteryx panamensis (Fabaceae) in continuous and fragmented Costa Rican rain forest

The effects of habitat fragmentation on seed dispersal can strongly influence the evolutionary potential of tropical forest plant communities. Few studies have combined traditional methods and molecular tools for the analysis of dispersal in fragmented landscapes. Here seed dispersal distances were documented for the tree Dipteryx panamensis in continuous forest and two forest fragments in Costa Rica, Central America. Distance matrices were calculated between adult trees (n = 283) and the locations of seeds (n = 3016) encountered along 100 × 4-m transects (n = 77). There was no significant difference in the density of seeds dispersed > 25 m from the nearest adult (n = 253) among sites. There was a strong correlation between the locations of dispersed seeds and the locations of overstorey palms favoured as bat feeding roosts in continuous forest and both fragments. Exact dispersal distances were determined for a subset of seeds (n = 14) from which maternal endocarp DNA could be extracted and matched to maternal trees using microsatellite analysis. Dispersal within fragments and from pasture trees into adjacent fragments was documented, at a maximum distance of 853 m. Results show no evidence of a fragmentation effect on D. panamensis seed dispersal in this landscape and strongly suggest bat-mediated dispersal at all sites.

Using image processing to detect and classify narrow-band cricket and frog calls

An automatic call recognition (ACR) process is described that uses image processing techniques on spectrogram images to detect and classify constant-frequency cricket and frog calls recorded amidst a background of evening sounds found in a lowland Costa Rican rainforest. This process involves using image blur filters along with thresholding filters to isolate likely calling events. Features of these events, notably the event's central frequency, duration and bandwidth, along with the type of blur filter applied, are used with a Bayesian classifier to make identifications of the different calls. Of the 22 distinct sonotypes (calls presumed to be species-specific) recorded in the study site, 17 of them were recorded in high enough numbers to both train and test the classifier. The classifier approaches 100% true-positive accuracy for these 17 sonotypes, but also has a high false-negative rate (over 50% for 4 sonotypes). The very high true-positive accuracy of this process enables its use for monitoring singing crickets (and some frog species) in tropical forests.

Wood CO2 efflux in a primary tropical rain forest

AbstractThe balance between photosynthesis and plant respiration in tropical forests may substantially affect the global carbon cycle. Woody tissue CO2 efflux is a major component of total plant respiration, but estimates of ecosystem‐scale rates are uncertain because of poor sampling in the upper canopy and across landscapes. To overcome these problems, we used a portable scaffolding tower to measure woody tissue CO2 efflux from ground level to the canopy top across a range of sites of varying slope and soil phosphorus content in a primary tropical rain forest in Costa Rica. The objectives of this study were to: (1) determine whether to use surface area, volume, or biomass for modeling and extrapolating wood CO2 efflux, (2) determine if wood CO2 efflux varied seasonally, (3) identify if wood CO2 efflux varied by functional group, height in canopy, soil fertility, or slope, and (4) extrapolate wood CO2 efflux to the forest. CO2 efflux from small diameter woody tissue (<10 cm) was related to surface area, while CO2 efflux from stems >10 cm was related to both surface area and volume. Wood CO2 efflux showed no evidence of seasonality over 2 years. CO2 efflux per unit wood surface area at 25° (FA) was highest for the N‐fixing dominant tree species Pentaclethra macroloba, followed by other tree species, lianas, then palms. Small diameter FA increased steeply with increasing height, and large diameter FA increased with diameter. Soil phosphorus and slope had slight, but complex effects on FA. Wood CO2 efflux per unit ground area was 1.34±0.36 μmol m−2 s−1, or 508±135 g C m−2 yr−1. Small diameter wood, only 15% of total woody biomass, accounted for 70% of total woody tissue CO2 efflux from the forest; while lianas, only 3% of total woody biomass, contributed one‐fourth of the total wood CO2 efflux.

Two new ascomycetes from rainforest litter in Costa Rica

Two new ascomycetes, Boerlagiomyces costaricensis (Pleosporales) and Scopinella musciformis (Sordariales sensu lato), from litter samples collected in rainforests of Costa Rica, are described and illustrated. Boerlagiomyces costaricensis has globose, ostiolate ascomata covered by numerous setae-like hairs; cylindrical, fissitunicate asci without apical structures; and large, fusiform, muriform, hyaline to pale brown ascospores. Scopinella musciformis is characterized by ostiolate ascomata with a few compact clusters of hypha-like hairs distributed on the peridial surface and a long neck; ovate to ellipsoidal unitunicate asci; and small quadrangular ascospores with diagonal germ slits.

Two new ascomycetes from rainforest litter in Costa Rica

Two new ascomycetes, Boerlagiomyces costaricensis (Pleosporales) and Scopinella musciformis (Sordariales sensu lato), from litter samples collected in rainforests of Costa Rica, are described and illustrated. Boerlagiomyces costaricensis has globose, ostiolate ascomata covered by numerous setae-like hairs; cylindrical, fissitunicate asci without apical structures; and large, fusiform, muriform, hyaline to pale brown ascospores. Scopinella musciformis is characterized by ostiolate ascomata with a few compact clusters of hypha-like hairs distributed on the peridial surface and a long neck; ovate to ellipsoidal unitunicate asci; and small quadrangular ascospores with diagonal germ slits.

Determinants of Leaf Litter Nutrient Cycling in a Tropical Rain Forest: Soil Fertility Versus Topography

We investigated the influence of landscape-level variation in soil fertility and topographic position on leaf litter nutrient dynamics in a tropical rain forest in Costa Rica. We sampled across the three main edaphic conditions (ultisol slope, ultisol plateau, and inceptisol) to determine the effect of soil nutrients on leaf litter nutrient concentrations while controlling for topography, and to examine topographic effects while controlling for soil nutrients. Both leaf litter macronutrient [phosphorus (P), nitrogen (N), sulfur (S), calcium (Ca), potassium (K), magnesium (Mg)] and micronutrient concentrations were quantified throughout a 4-year period. Leaf litter [P], [N] and [K] varied significantly among soil types. The variation in [P], [N], and [K] was explained by soil fertility alone. Leaf litter [S], [Ca], and [Mg] did not vary among the three soil types. Macronutrient (P, K, Mg, S, Ca) concentrations in the leaf litter were much less variable than those of Fe and Al. Lower variability in essential plant nutrients suggests a great deal of plant control over the amount of nutrients resorbed before senescense. Leaf litter macronutrient concentrations varied significantly over the 4-year period, but the temporal variation did not differ among the three edaphic types as anticipated. Hence, although the magnitude of nutrient fluxes may be controlled by local factors such as soil fertility, temporal patterns are likely regulated by a common environmental variable such as precipitation or temperature.

Nutrient additions to a tropical rain forest drive substantial soil carbon dioxide losses to the atmosphere

Terrestrial biosphere-atmosphere carbon dioxide (CO(2)) exchange is dominated by tropical forests, where photosynthetic carbon (C) uptake is thought to be phosphorus (P)-limited. In P-poor tropical forests, P may also limit organic matter decomposition and soil C losses. We conducted a field-fertilization experiment to show that P fertilization stimulates soil respiration in a lowland tropical rain forest in Costa Rica. In the early wet season, when soluble organic matter inputs to soil are high, P fertilization drove large increases in soil respiration. Although the P-stimulated increase in soil respiration was largely confined to the dry-to-wet season transition, the seasonal increase was sufficient to drive an 18% annual increase in CO(2) efflux from the P-fertilized plots. Nitrogen (N) fertilization caused similar responses, and the net increases in soil respiration in response to the additions of N and P approached annual soil C fluxes in mid-latitude forests. Human activities are altering natural patterns of tropical soil N and P availability by land conversion and enhanced atmospheric deposition. Although our data suggest that the mechanisms driving the observed respiratory responses to increased N and P may be different, the large CO(2) losses stimulated by N and P fertilization suggest that knowledge of such patterns and their effects on soil CO(2) efflux is critical for understanding the role of tropical forests in a rapidly changing global C cycle.

A Comparison of Manual and Automatic Moth Sampling Methods (Lepidoptera: Arctiidae, Geometridae) in a Rain Forest in Costa Rica

Abstract Sampling with UV fluorescent light tubes is a commonly used technique both in applied and basic insect studies. Our study compares the performance of two such methods: manual sampling (light towers) and automatic sampling (funnel light traps). The abundance, diversity, and body size of moths representing two species-rich families (Lepidoptera: Arctiidae, Geometridae) were analyzed in a lowland rain forest in Costa Rica (La Selva Biological Station, 10.4° N, 84.0° W) during 2003 and 2004. Light towers were equipped with two 15-W UV fluorescent tubes and were operated for 3 h in 16 nights. Traps equipped with single 8-W fluorescent tubes were run throughout 20 nights in the understory of the forest. In addition, parallel trap sampling was carried out in the canopy. A total of 1,238 arctiid moths representing 162 species and 1,769 geometrid moths representing 196 species were collected. In Geometridae, tower samples were significantly larger than trap samples. Towers also attracted a higher overall ...

Automatic call recognition of cricket songs using image processing

An automatic call recognition (ACR) process is described that uses image processing techniques on spectrogram images to detect constant-frequency cricket calls recorded amidst a background of evening sounds found in a lowland Costa Rican rainforest. This process involves using image blur filters along with binary filters to isolate calling events. The binary filters are used to isolate potential calls from background noise, and the blur filters are used to unite discrete call fragments as a single continuous call. Features of these events, notably the events central frequency, duration, and bandwidth, along with the type of blur filter applied, are used with a Bayesian classifier to make identifications of the different calls. Of the 22 distinct sonotypes (calls presumed to be species specific) recorded in the study site, 17 of them are recorded in high enough numbers to both train and test the classifier. The classifier approaches 100% true-positive accuracy for these 17 sonotypes. The high true-positive accuracy of this process enables its use for monitoring singing crickets in tropical forests.

Contrasting patterns of vertical stratification in two moth families in a Costa Rican lowland rain forest

Summary The vertical stratification of two species-rich moth families (Lepidoptera: Arctiidae, Geometridae) was analysed in a lowland rain forest in Costa Rica. Moths were trapped with automatic 8 W ultraviolet light traps at three sites in the understorey and canopy of a primary forest at the La Selva Biological Station (10.4° N, 84.0° W). A total of 846 arctiid moths (148 species) and 946 geometrid moths (140 species) were analysed. Species richness and diversity of arctiid moths was significantly lower in the understorey than in the canopy (Fisher's alpha: 24 vs. 49) whereas geometrid moths showed an inverse pattern (Fisher's alpha: 44 vs. 27). This resulted in an overall increase in the proportion of conspicuously coloured species towards the canopy. Moth ensembles were clearly separated in multidimensional scaling ordinations, and differed significantly in their faunal composition and dominance between the strata. The available host plant data suggest that the flight height of moths was determined by larval resource availability. Examples include understorey flyers such as the geometrid genus Eois feeding on Piper , and canopy flyers such as the arctiid moth genera Aclytia , Macrocneme and Poliopastea which feed on lianas.

Anisomeridium flavovulcanus, a new corticolous lichen from Costa Rica

A corticolous species, Anisomeridium flavovulcanus, is described. It has so far been found in the Carribean and Pacific lowland rainforests of Costa Rica, where it is a frequent lichen in the understorey. This conspicuous lichen is characterized by large conical conidiomata, which release a yellow conidial mass at the apex. Dimorphic conidia occur in the same conidiomata: 1-septate microconidia and thick walled globose macroconidia. Ascomata were found only twice; the inconspicuous perithecia are hemispherical, semi-emergent with an apical ostiole, the asci are cylindrical with a cruciform ocular chamber and the ascospores are uniseriately arranged.

Reproduction of the Bat Glossophaga commissarisi (Phyllostomidae: Glossophaginae) in the Costa Rican Rain Forest During Frugivorous and Nectarivorous Periods1

ABSTRACTI studied the reproduction of the 9 g nectarivorous bat Glossophaga commissarisi (Phyllostomidae: Glossophaginae) in relation to its food choice in a Costa Rican lowland rain forest over more than 2 yr. Reproduction was bimodal with birth peaks in April/May and October/November. The first birth peak coincided with a period of frugivory, whereas the second occurred during a period of almost exclusive nectarivory. All adult females recaptured in consecutive reproductive periods were reproductively active on both occasions, indicating that individual G. commissarisi females regularly reproduce twice per year at the study site. Throughout the annual cycle the mean testis length of the males correlated best with the proportion of females lactating, suggesting a post partum estrous pattern. Animals became reproductively active at about 1 yr of age. Fecal samples showed that females consumed significantly more insects than males.

Variation in leaf litter nutrients of a Costa Rican rain forest is related to precipitation

By assessing current leaf litter nutrient dynamics, we may be able to predict responses of nutrient cycling in tropical ecosystems to future environmental change. The goal of this study was to assess whether nutrient cycling is related to seasonal variation in rainfall in a wet tropical forest. We examined leaf litter of an old-growth tropical rain forest in N.E. Costa Rica over a 4-year period to explore seasonal and inter-annual changes in leaf litter nutrient concentrations, and to evaluate potential short- and long-term drivers of variation in litter nutrient concentration, particularly that of phosphorus (P) and nitrogen (N). We also examined the temporal dynamics of calcium, potassium, and magnesium in the leaf litter. Leaf litter [P] and %N changed significantly with time, both seasonally and inter-annually. Seasonal changes in leaf litter [P] were strongly positively correlated with rainfall from the previous 2 weeks; cations, however, were inversely related to this measure of current rainfall, while %N was not related to rainfall. We propose that the positive relationship between current rainfall and leaf litter [P] is due to a response by the vegetation to an increase in nutrient availability and uptake. In contrast, given the negative relationship between current rainfall and cation concentrations, leaching from live leaf tissue is a more likely driver of short-term changes in cations. Should global climate change include altered rainfall patterns in this biome, one class of ecosystem-level responses could be significant changes in P and cation cycling.

The larva ofMecistogaster linearis, with notes on its abundance in lowland rainforest of Costa Rica (Odonata: Pseudostigmatidae)

Abstract The larva of Mecistogaster linearis is described and illustrated from specimens collected within or near the Rio Dantas Wildlife Refuge at the north-western border of the Barbilla National Park on the Costa Rican Caribbean slope. Characters of F-0 larvae permit easy separation from Megaloprepus caerulatus, a species coexisting with M. linearis. Diagnostic characters include overall colour, shape of head, prementum and caudal gills. Exuviae may be determined using shape of mandibles. Two types of branched setae are present on tibiae and tarsi. Most are 3-branched but on front tarsi they are instead feather-shaped. It is suggested that these setae are used for eye-cleaning. M. linearis was a relatively rare but regularly occurring species in the study area throughout the 3-year study period.