Honduras forest dissertation/thesis topics

There are a wide range of possible dissertations that can be done within Cusuco National Park. Some of the topic areas involve data collected as part of the general monitoring effort. In such cases (which are indicated below), the data-collection sites and methods are fixed, and the range of possible research questions is therefore limited. However, it also means that the likely sample size of the data collected is large, and that compatible data on a wide range of other taxonomic groups will be available (including information on the vegetation structure, habitat type, altitude, etc), allowing a variety of research questions to be addressed using the data. Other subject areas, which are not part of the general monitoring effort, allow a much larger range of possible research questions and flexibility in the planning of the work. The main constraints for these projects are logistical (equipment, safety, etc), so be sure to contact Operation Wallacea with your research ideas well before you come out, to check feasibility and the likely fitness level required. The computers at Base Camp have standard statistical and multivariate software (including Pisces Conservation's Community Analysis Package, ECOM and Species, Diversity and Richness, which allow ordination, canonical correspondence analysis, cluster analysis, TWINSPAN, numerous species richness estimators and beta diversity measures, etc); some statistical advice is available and there is a small field DNA lab. All research topics coded HM will operate from Base Camp where the senior scientist is based, but researchers on these topics will be dispersed around the various forest sites for much of their stay, depending on the requirements of the research project. The HL project is based in the lowland Manacal site and the HS project will be part of a mobile team moving between the mountain villages.

HM201 Barcoding the diversity of Cusuco cloud forest (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology and HM003 DNA extraction course)

So many taxonomists have worked in the Cusuco Park now as part of the Opwall teams that substantial species lists have been obtained for many taxa. The next stage is to complete genetic barcoding for these species and submit these data to GenBank. This is an ideal project for dissertation students who can isolate and amplify the cytochrome C oxidase subunit 1 (COI) gene sequence for taxa such as dung beetles, jewel scarab beetles, amphibians, small mammals or bats to determine whether or not the genetic data matches the morphometric data or whether there are previously undescribed species. There are 6 endemic species of amphibian in the Park none of which have been sequenced and there are suspected cryptic species of dung beetle, frog and small mammal that have yet to be fully analysed and described. The project could compare the species identified from the gene sequencing with the morphometric data, potentially describe cryptic species and compare the sequences of species found in Cusuco that have been deposited in public databases. Generally it will be expected that you collect your samples from at least three camps, and work with the appropriate biodiversity team. Students working on this project will be isolating and amplifying the relevant section of the COI gene and testing that there is viable DNA using agarose electrophoresis. The DNA samples will then be returned to the home institutions on FTA Whatman cards so that sequencing can be done. DNA sequencing cannot be done in the field, and students wanting to do projects of this type will need to ensure that they or their institution can cover the cost of the sequencing (approx $6 per sample).

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HM202 Landscape genetics of amphibian species (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology and HM003 DNA extraction course)

A new field in population genetics, Landscape Genetics investigates population structure and connectivity in the context of barriers and facilitators within the environment. The detailed satellite imagery and habitat mapping which exists within Cusuco allows a particularly fine-grained analysis of gene flow among populations of species within the park. With the Chytrid fungus widespread within Cususco, many species of amphibian endemic to cloud forests have suffered declines. Determining how these species move through the landscape and how populations are connected is extremely important for directing conservation effort. Polymorphic microsatellite markers are used to genotype amphibian samples at multiple loci and patterns of gene flow are resolved using software such as BAYESASS and GENELAND. Using least cost movement paths developed using ARC GIS, the correlation between genetic and geographic distance can be investigated and features in the landscape that act as facilitators or barriers can be resolved. Opwall is funding a PhD student to complete the preliminary stage which will involve the development of a library of polymorphic microsatellite loci with which to genotype multiple species of amphibian. This will take place through the cross-species characterisation of existing amphibian loci and if required, the identification of new loci and the development of primers. During this stage a target of at least 13 loci per species will be resolved with which to conduct population genetic studies. The study will aim to develop a set of loci which are polymorphic in a variety of species, however if this is not possible, a species specific set of loci will be used. The primers will be fluorescently labelled and divided into multiplexes to reduce time and cost in genotyping. Optimisation of the PCR conditions necessary to amplify microsatellite loci in multiplexes will enable the procedure to then be conducted in the field lab at Base Camp, Cusuco. Note dissertation students doing this project will need access to GENEMAPPER software. The DNA extraction and PCR work can be done in the field lab.

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HM203 The effect of altitude, rainfall and temperature on leaf structure (Weeks 4-8: Training - need to have completed HM001 Jungle Training and Neo-tropical Forest Ecology)

This project is designed to investigate the factors that affect leaf size, thickness and shape in trees. It is known that these leaf variables change with altitude but the main environmental driving force behind this change has long puzzled ecologists. The forest here allows samples to be taken in areas of quite different rainfall and temperature and so provide a unique opportunity of teasing apart this puzzle. Samples will be collected at a number of different camps using standard techniques to measure leaf area, thickness, shape,dry weight and dry weight per unit area of the samples. It will also possible to look at stomatal density, the presence of drip-tips, degree of herbivory and a number of other factors which link into the overall question. There are also data available from previous projects that can be used to help gain a bigger picture.

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HM204 Factors affecting freshwater invertebrate communities (Weeks 2-8; Training - need to have completed HM001 jungle training and Neo-tropical forest ecology)

The high-altitude forest reserves in Honduras were initially given legal protection as National Parks in order to protect the water supply downstream. However, water quality monitoring in the San Pedro Sula valley below Cusuco Park is done only via infrequent chemical testing. Because chemical monitoring can easily miss intermittent pollution episodes, in many European countries monitoring of aquatic macro-invertebrate communities is done on a 3-monthly basis to assess water quality. This works well because different species have different tolerances to pollution. The macro-invertebrate communities reflect the worst conditions that have occurred over the previous few months and are therefore useful for picking up episodic pollution events. Over the next 3 years Operation Wallacea is developing a biotic water quality index that can be used for water quality monitoring in the Merendon mountains (which include Cusuco NP), building on pilot work done in 2008. Aquatic macro-invertebrate communities will be sampled and water quality will be assessed in a range of stream orders and habitats, in different catchments all over the park. These data can be used for dissertations/theses to examine the effect of specific factors such as stream order, flow rates, habitat, forest cover, geology etc, on the invertebrate communities.

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Some colonies of leaf cutter ants have more than a million workers and their massive underground nests house a fungus that the ants actively farm for food. To nurture their fungal crop the ants must forage for fresh leaf material, which they convert into "mulch" on which the fungus grows. The vast amount of leaf pieces needed to maintain the nest make these ants the dominant "herbivore" in the new world tropics. Understanding how these ants forage and how we can stop them foraging on valuable crop plants is likely to be important for their control. Projects could focus on using ant waste (and component thereof) and trail disruption to control ants and their foraging in the field. The work will involve a mix of observation and manipulation of nests of different sizes and will likely involve night-time work in the forest. Other projects, relating to foraging ecology and behaviour (especially with respect to parasites and disease) may also be developed.

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HM206 Diversity and niche separation in tarantula species in Cusuco Park (Weeks 4-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

In general the arachnofauna (spiders and their allies) of Honduras is very poorly known and there are only 3 described tarantulas from Honduras, two of which Brachypelma albopilosum and Aphonopelma seemanni were actually described from Costa Rica though seemingly do occur also in Honduras. The third Honduran tarantula, Mygalarachne brevipes is the only known endemic, but only exists in our knowledge as a single old museum specimen, collected before1871 from an unknown location in Honduras. In Costa Rica, there are at least 34 well-described tarantula species in a much smaller geographic area than Honduras (and about 25 more potential tarantula species, several pending description) so it is highly likely that there are many tarantula species still waiting to be discovered in Honduras. Of the 3 species listed from Honduras, 1 of those (A. seemanni) is widely collected in Honduras for the commercial pet-trade market. A key issue is that A. seemanni was originally described from Costa Rica, so any trade identification as 'A.seemanni' may be dubious, and multiple similar species may be being exported under this erroneous name.. Such pet-trade collections of Mexican tarantulas in the early 1990s led to the blanket protection of the genus Brachypelma under CITES and the trade in Mexican tarantulas has become tightly monitored by national wildlife authorities. The current trade in tarantulas cannot be easily regulated in Honduras yet due to poor current scientific understanding, and lack of even basic biological studies. But, protection is likely to be required, and local-captive breeding of tarantulas for pet-trade export could be a useful source of revenue. This topic could be developed into a series of different research questions. For example how many species of tarantulas are present Cusuco and how do they niche partition? Pitfall traps adjacent to spider burrows could be used to determine prey types and observational data gathered on the area used by each species to collect prey. What differences in prey types exist between tarantula species, and does prey choice varies over lifespan of each species? Are there any signs of parasitic wasps (fm. Pompilidae) preying on tarantulas? Note funding is available to complete genetic bar coding on the Honduran tarantulas so this would make an interesting dissertation topic.

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HM207 Factors affecting dung beetle and sphingid moth communities (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

This topic takes advantage of the existing, fixed-method sampling programme of light trapping for sphingid moths and jewel scarab beetles at each of the 28 main sites, and of pit traps for dung beetles at all 150 sites, as well as the taxonomic expertise on site to help with identifications. Students on this project will participate in the main data collection effort. The moth data sets can be analysed by grouping sites with similar altitudes and levels of disturbance and determining the effects of these variables. Data from each of the 150 dung beetle data sets can be analysed in relation to the habitat structure measurements. Given that jewel scarab beetles are extremely attractive and highly valued by collectors, a project using mark-recapture analysis of trapped jewel scarab beetles to estimate population size and other parameters to inform sustainable exploitation of the beetles would also be useful. It is also possible to collect morphometric data from dung beetles, which could be used to explore hypotheses relating morphology to habitat structure. Alternatively, a project could use live trapping of dung beetles to assess how far they travel to their food source, via mark-recapture methods. Dung beetles play a vital role in decomposition in the forest and in seed dispersal and the effectiveness of these roles could be tested using various experimental designs.

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HM208 Developing strategies for protecting the threatened amphibian fauna of the Cusuco cloud forests (Weeks 2-8; Training - need to have completed HM001 jungle training and Neo-tropical forest ecology)

The single most important reason for the need for effective conservation of the Cusuco National Park is the importance of this cloud forest for amphibians. There are 6 species of amphibians found only in the Cusuco Park comprising two tree frogs (Plectrohyla exquisita & Plectrohyla dasypus), one bromeliad frog (Isthmohyla melacaena), two arboreal salamanders (Bolitoglossa diaphora & Cryptotriton nasalis) and one ground dwelling salamander (Oedipina thomasi ). In addition there are another 10 species that are found in Cusuco but which are endangered under the IUCN categories. Of these, two tree frogs (Duellmanohyla soralia & Bromeliohyla bromeliacea) have their largest remaining populations in Cusuco, two tree frogs(Craugastor coffeus & Ecinimiohyla salvaje) and one salamander (Nototriton barbouri) are known from only one other site other than Cusuco. To add even greater urgency these small populations are now under threat of infection from amphibian chytrid fungus (Batrachochytrium dendrobatidis) which is causing catastrophic amphibian population declines throughout Mesoamerica. Chytrid fungus appears to have reached the Park at least 15 years ago and has caused significant declines in these isolated mountain top amphibians. Topic scan be developed in a number of directions. For example how is chytrid fungus transmitted? Studies are being done to look at air and water dispersal mechanisms and to radiotrack arboreal frogs to see how far they move. Data are urgently required on the population sizes and distributions of each of the cloud forest amphibian species and the catchments in which each occur. This involves trekking up rivers to survey frog and salamander species in a range of remote sites to obtain as complete a coverage of the Park as possible. Day time surveys for tadpoles are supplemented by night time river treks to complete spotlight surveys and to listen for calls. The position of trees with bromeliad frogs calling will be marked and the Canopy Access team organised to climb the trees to recover bromeliad frogs. All frogs sampled will be swabbed for the presence of chytrid fungus. In addition genetic samples will be taken for bar coding. Another project could complete a bar coding study on these endemic amphibians (see HM201) or look at gene flow between apparently isolated populations (HM202).

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HM209 Factors affecting bird communities (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

This topic takes advantage of the existing, fixed-method point count survey work being undertaken for birds at each of the 150 survey sites, as well as the forest structure and other data gathered at each of these sites. In addition, some sites around the park are sampled via mist netting, yielding morphometric measurements and allowing identification of elusive species not sampled by point counts. Experienced ornithologists will help train the dissertation students in the identification of the bird species from both calls and sightings. Aspects of these data sets can then be analysed to study a whole range of impacts on bird communities. For example, selected species can be studied and the data analysed to identify the main environmental variables affecting their distribution. Sites with similar altitudes and forest types can be grouped to assess the effects of these variables on the bird communities. Similarly, bird communities may be compared between the core and buffer zones of the park. Or the data could be used to investigate ecological interactions between bird species. A more derived possibility could be to test whether the size of the eye relative to the head size determines the order in which each bird species joins the dawn chorus.

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HM210 Bat morphology and factors affecting bat communities (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

This topic takes advantage of the existing bat monitoring programme, as well as the taxonomic and bat-handling expertise on site, allowing a wide range of possible projects. For example, previous projects have examined wing morphology and its relationship with habitat affinity or feeding guild: bats living in deep forest environments tend to have different wing shapes compared to those living on the forest edge because manoeuvrability is a key requirement within the forest, whilst on the forest edge speed is more important (to evade predators and catch prey). In 2010 a range of different survey techniques (mist nets, harp traps and sound recording) are being used, allowing greater flexibility for projects and the possibility of a methodological comparison. Other potential projects include examination of environmental effects on bat abundance. One such effect that is much debated in the literature is that of the moon: 'lunar phobia'. This could be studied by simple comparison of bat catches and detection in different phases of the lunar cycle (including using data from past years), both as a community and per species. If bats tend to be caught less during brighter moon conditions then is it because they are foraging less or because they can see the nets better? If you need to use specialist equipment such as a bat detector (e.g. to compare bat passes with bat captures) then be sure to check its availability with the Opwall office in good time and/or check whether your institution can lend you the equipment.

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HM211 Populations of large mammal species in Cusuco National Park (Weeks2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

 Large mammal surveys in Cusuco are focused on the elusive and threatened populations of Baird's Tapir and the 3 primate species present in the park (howler monkeys, white-faced capuchins, and the central American spider monkey). The survey teams will be taking GPS readings and recording tracks, dung, vocalizations and visual encounters, as well as taking samples of scat and spoor for onsite DNA analysis. This, in combination with the fact that previous years' data is available to dissertation students, means that a wide range of potential projects and research themes are available in this area. For example students could examine effects of different habitat variables (e.g. altitude, canopy density, disturbance levels) on large mammal populations. Alternatively, faecal samples could be analysed in order to investigate the role of large mammals in seed dispersion within the park.

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HM212 Trap selectivity effects on estimates of small mammal diversity and abundance (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

Estimating the species diversity and abundance of small mammals in Neotropical rainforests using live trapping programmes is fraught with difficulties owing to surveys being labour intensive, many species being elusive and trapping methods being too species specific. This topic will use a range of traps, setting methods and baits to assess the effect of these variables of capture rate and species diversity within these catches. Ultimately this project will produce a standard methodology for surveying small mammals in Cusuco National Park, that will not only be efficient but will encompass the entire range of small mammal species that inhabit the area.

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HL213 Howler monkey behaviour, habitat use, feeding ecology and vocalisation (Weeks 2-8; Training - need to have completed HM001 - jungle training and Neo-tropical forest ecology course)

Troops of howler monkeys have been habituated in the forest fragments at Rancho Manacal in the lowlands near Cofradia, enabling a wide range of dissertations or senior theses. Average population density for mantled howler monkeys ranges from 30-40 individuals per km2, but at Manacal the density is over 200 individuals per km2. Such high density is likely to have a significant effect on diet and social behaviour, particularly the loud call vocalizations. Normally howler monkeys maintain 200m-2km between troops (mediated by their loud calls), but at Manacal the troops are adjacent, which is likely to affect the frequency and duration of loud calls in addition to affecting behavioural responses to loud calls heard from neighbouring troops. Howler monkeys are usually described as folivores/frugivores that spend a high percentage of their daily activity budget resting. There are two competing theories of inactivity in howler monkeys: howler monkeys rest in order to digest toxin-loaded mature leaves, or howler monkeys conserve energy to accommodate limited access to high quality food sources (which is especially relevant in disturbed habitats where food availability is low). At Manacal, the howler monkeys have exclusive access to all food sources because their natural competitors (spider monkeys and capuchin monkeys) are unable to survive in these disturbed forest fragments. However, home range size and access to food is limited by forest fragmentation. Manacal therefore provides an interesting location to investigate the relationships between diet, home range size, population density, food availability and activity budgets.

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HS214 Rates of deforestation in the buffer and core zone of Cusuco Park (Weeks 2-8; Need to have completed HM002 Spanish language training)

To improve the management and prospects for the Park, data are needed on the ownership and use of the land in the buffer and core zones. Satellite data analysis has shown continued encroachment into the forests by farmers in the buffer zone but this tells only part of the story. Data are needed on farm boundaries and ownership, crop usage and income generation so that these data can be used to design incentive schemes that are likely to be effective in protecting the forests. These studies have been completed on approximately 20% of the buffer zone land adjacent to the core zone and in 2010 the survey teams will be visiting a number of previously un-surveyed mountain communities to gather additional data. A series of conservation management dissertations/theses could be developed from this data collection exercise with questions such as the economic benefits of illegal clearances, differing views between communities of the value of protecting the forests and knowledge of existing rules concerning the Park etc. Students working on these projects will be with a mobile team visiting remote mountain communities with translators.

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