1. WALLACE RESOURCE LIBRARY
Module 04 – Ecosystems – Tropical Rainforests:
D01 – Assessing bird point count data from a Honduran cloud forest

2. Why Survey Biodiversity?
Global decline in biodiversity
But how do we know?
In order to assess biodiversity we must apply appropriate survey techniques
This provides the information we need to understand what is happening to biodiversity on a local as well as a global scale
We are all familiar with the notion that global biodiversity is at increasing risk of extinction due to a variety of reasons. These reasons include, but are not limited to; habitat destruction and degradation, environmental pollution, over-harvesting of wildlife for human consumption, wildlife diseases and climate change. But how do we know that biodiversity is threatened on a global scale?
In order to understand fully what is happening to global biodiversity, we must find sensible ways of monitoring it. How we go about this enormous task depends very much firstly on at what level we are trying to assess biodiversity levels. It is impossible to look at all biological diversity at the same time so we must break it down into more manageable sections in some way.
The survey techniques that we use will depend on the size of the area that we are interested in studying. For example, satellite images can be taken of large areas of forest to calculate the proportion of forested, degraded or deforested areas, whereas a microscope might be necessary to study the diversity of the invertebrate community living on a single tree within that same forest. So the first thing that we have to do is identify our study area.
The next decision to make is are we interested in all biological diversity in that area, or are we actually only interested in a small number of key species? Normally researchers are only interested in a small proportion of the overall diversity present, because even within a small area it can be very difficult to survey and identify everything present. This is why it is common to have different researchers working in the same location all carrying out different survey techniques in order to monitor the particular species or communities that they are interested in. We can then combine this information to get a clearer picture of the biodiversity contained within the study area.
However, it is impractical to survey and identify 100% of species within any given area. Therefore, we often monitor species that are easier to detect and then use information on these species to provide us with information on what is happening within the ecosystem in general.

3. Why Survey Biodiversity?
IUNC Red list of Threatened Species
Extinct (EX)
Extinct in the Wild (EW)
Critically Endangered (CR)
Endangered (EN)
Vulnerable (VU)
Near Threatened (NT)
Least Concern (LC)
Perhaps the most well known way that biodiversity survey data is used is for the classification of species under the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. This system categorises species into the above levels of conservation concern based on all of the data that is available. Although many species have been assessed under the IUCN Red List, there are still a very large number of species that have not yet been formally classified due to a lack of data. These species currently fall into another category called “Data Deficient (DD)” and yet many other species have not even been assessed at all (they fall into a Not Evaluated category).
Therefore, one very important use of survey data is to identify which species are of the highest conservation concern. The IUCN red list provides a mechanism for doing this on a global scale, but many other databases exist that assess the conservation status of species on a national or local level.
It is the collection of this important data that allows us to piece together the puzzle of what is actually happening to wildlife populations around the globe.

4. How do we Survey Biodiversity?
Global or National scale
- Satellite images
Local scale
Capture-Mark-Recapture
Transect and Distance sampling
Passive trapping
Camera trapping
Direct counts e.g. Helicopter surveys
We can get a broad understanding of the rate of loss of biological diversity and even predict its future decline by looking at satellite images and measuring habitat change in particular ecosystems. However, satellites are only useful if we first have an idea of the amount of biodiversity contained within that ecosystem. In order to get that information we need researchers to actually study those systems using a variety of different survey techniques.
The methods that we use will depend on what we want to know. For example we may simply be interested in the number of different species present in a given area. Alternatively, we might want to know the population size for a particular species within that area, or perhaps we may want to know the population size of all large mammal species in that area.
As conservationists we have a wide variety of survey techniques available to us and which one we use will depend on the question we want to answer. Below are some examples of common techniques used (there are many more). How we actually carry out these techniques will depend on the species we are trying to survey:
Capture-Mark-Recapture – suitable for estimating the population size of locally abundant species or intensively studied populations
Transect sampling - suitable for estimating species diversity and relative abundance
Distance sampling – suitable for estimating population size of multiple species encountered along a transect
Passive trapping – suitable for assessing local species diversity and estimating local abundance
Camera trapping - suitable for assessing local species diversity and estimating local abundance of elusive animals such as large mammals
Direct counts e.g. Helicopter surveys – suitable for obtaining accurate population data for large animals in open areas such as large mammals in Africa

5. How do we Survey Wildlife Disease?
Disease can cause rapid and unpredictable population declines
Conservation managers need to know if disease is present
Often need to capture animals or collect samples
Laboratory testing for disease
Wildlife disease is a major concern for conservation managers. Outbreaks of disease can cause rapid and major population declines in previously ‘healthy’ populations. Perhaps the most alarming and catestrphic population declines that have occurred in recent decades have been caused by the fungus Batrachochytrium dendrobatidis (known as B.d for short).
B.d is a type of fungus that specifically infects the type of keratin that amphibians have in their skin and the mouth parts of their tadpoles. The disease that it causes is called chytridiomycosis (also known as chytrid for short) and it has been linked to the recent extinction of a number of amphibian species and the rapid global population declines of many others.
In order to understand chytrid and how it is affecting amphibian populations, it is important to monitor population size over time, but also the level of infection within the population. In order to do this individual animals must be captured by hand swabbed for chytrid. It is important to wear sterile disposable gloves while handling amphibians to prevent the transmission of chytrid from one animal to the next and also to avoid accidentally contaminating your samples. Swabs are then preserved in ethanol and taken back to the laboratory for analysis.

6. Testing for Chytrid in Cusuco
Field Genetics Lab Cusuco National Park
Can test for Chytrid infection in the field
DNA extraction
PCR
Gel electroporesis
In Cusuco National Park, Operation Wallacea have set up a field genetics laboratory that allows amphibians to be tested for infection with Chytrid. This means that we can get results immediately rather than having to send samples away to an off site laboratory.
Swabs taken from the potentially infected animals are processed in the lab. DNA is extracted and then the Polymerase Chain Reaction (PCR) used to amplify the DNA to detectable levels.
The PCR products are then run on an agarose gel in a process known as gel elctrophoresis and infected individuals are identified by the presence of a bright band when viewed under UV light (as can be seen in the photo above).

7. Two Critically Endangered Tree Frogs
Duellmanohyla soralia
Plectrohyla dasypus
For the purposes of this study we will focus on just two species of tree frog, Plectrohyla dasypus and Duellmanohyla soralia. Both of these species are classified as being critically endangered by the IUCN Red List and so are of exceptionally high conservation concern. Both species are tree frogs and are similar in their morphology and behaviour, however, P. dasypus inhabits higher elevations and is typically encountered between m above sea level, whereas D. soralia inhabits lower elevations and is found between approximately m above sea level. We will look to see if there is a difference in the prevalence of chytrid within populations of these two critically endangered species in Cusuco National Park.

8. Tasks for the data set
You are going to be looking at levels of chytrid infection in D. soralia and P. dasypus
You will compare the proportion of individuals that have tested positive for chytrid for each of the two species
You will then look to see how infection rates change for each species between the different study sites

9. Research questions:
What is the overall proportion of the sample that was infected with chytrid for each species and which species appears to be most negatively affected by chytrid?
How does the proportion of infected individuals vary between each of the survey sites for each of the two species and why might sample size be an important factor to consider when interpreting these results?
In order to answer the questions students will need to complete the data analysis task provided

10. Summary and conclusions
The proportion of the total sample that tested positive for chytrid was 0.1 (or 10%) for Duellmanohyla soralia and 0.37 (or 37%) for Plectrohyla dasypus. This may suggest that P. dasypus more susceptible to chytrid fungus than D. soralia.
The proportion of individuals infected with chytrid was variable between species and between survey sites. The highest proportion of individuals infected with chytrid was found at Base Camp for P.dasypus (100% of 6 individuals tested), whereas 0% of the 18 D. soralia samples collected from Base Camp tested positive for chytrid.
The proportion of the total sample that tested positive for chytrid was 0.1 (or 10%) for Duellmanohyla soralia and 0.37 (or 37%) for Plectrohyla dasypus. From this data it can be said that P. dasypus is more frequently found to be infected with chytrid than D. soralia. This may suggest that P. dasypus more susceptible to chytrid fungus than D. soralia.
The proportion of individuals infected with chytrid was variable between species and between survey sites. The highest proportion of individuals infected with chytrid was found at Base Camp for P.dasypus (100% of 6 individuals tested), whereas 0% of the 18 D. soralia samples collected from Base Camp tested positive for chytrid. This suggests that even at the same survey site where chytrid is present, it may not affect two species in the same way. A similar pattern can also be observed at the Cortecito study site with 33% of the 15 P.dasypus samples testing positive for chytrid but 0% of the 12 D. soralia samples testing positive. At El Danto, the proportion of infection was similar for both species. No samples were obtained for P. dasypus at Santo Tomas and only one sample was obtained for this species at Guanales. Therefore, sample size is too low to be able to compare infection rates between the species at these sites. The same is also true for Cantiles, where only one individual was encountered.