Understanding Anura responses to rainforest fragmentation and oil palm agriculture

Project Description

PhD Candidate: Juan Manuel Aguilar León

Supervisors: Michael Bruford, Benoît Goossens and Pablo Orozco-terWengel

Institution: Cardiff University

Research questions:

The main aim of this project is to characterize the effects of palm oil agriculture (and other land conversion processes) and consequent forest fragmentation, on anuran (here frog) diversity at different spatial scales in eastern Sabah.


To assess these effects, we will use a combination of species diversity and distribution analysis with a measure of evolutionary diversity using molecular methods and, at a smaller spatial scale, analyse the demographic processes occurring in and around palm oil dominated fragmented landscapes using a combination of population genetic methods and ecological surveys.

Frog communities will be surveyed across eastern Sabah to provide diversity comparisons between primary, fragmented and continuous forest focusing on five sites each at the Tabin Wildlife Reserve, Deramakot Forest Reserve, Kabili Sepilok Forest Reserve. Danum Valley and larger Lower Kinabatangan Wildlife Sanctuary (LKWS) forest fragments. Five transects will be surveyed at each site and key vegetation characteristics, species abundance, richness and endemism will be estimated for forest restricted, plantation advantage and limited plantation penetration.

Intensive surveys will be carried out within and among forest and oil palm sites within the LKWS. In addition, estimates of migration and gene-flow will be carried out for the most abundant species across the Sanctuary to compare and contrast estimates of genetic diversity within species. Analyses will be carried out on three frog species (terrestrial specialist, plantation specialist and generalist).

Transect methods are routinely used to determine intraspecific and interspecific changes in amphibian populations within sites and across changing environmental features. Transects will be established across the LKWS, and will be monitored and sampled on a regular basis during the field work. Transects will include three major habitat types: (1) Secondary forest fragments, (2) oil palm plantations and (3) edge habitat between forest and plantation. Transects will be characterized using 13 habitat parameters of potential relevance for anuran populations (number of trees, mean and variance of tree diameter, number of logs, mean log diameter, canopy cover, variance in canopy cover, understory vegetation density (grid sampling), gradient, leaf litter cover and weight, green vegetation cover, number and width of streams, total length of all superficial water bodies and for oil palm plantations habitat, the age of palms will be recorded). Each transect should be sampled a minimum of twice during the raining season and during the dry season. Each transect will be sampled for frogs during the period of maximum frog activity.

The visual encounter survey method (VES) of standardized transects will be used to measure frog species richness and abundance within eleven habitat blocks of the LKWS. DNA sampling of frogs will be done by buccal swabs DNA will extracted using a QIAgen DNeasy tissue kit (QIAgen) following the manufacturer’s protocol, with a few additional steps. Mitochondrial DNA barcoding will be carried out for all species using a fragment of the cytochrome oxidase subunit I (COI) and a the 16S ribosomal RNA genes to estimate phylodiversity among sites and regions, enabling and independent assessment of the evolutionary processes underlying frog assemblage structure in the region. Next generation sequence (NGS) will be used to develop microsatellite markers to estimate genetic structure and diversity for each site, and in combination with statistical modelling to distinguish between historical, niche and neutral community processes.

To assess the effects of habitat type on the abundance (number of individuals), species richness (number of species) and diversity of anurans I will use a mix of several ecological techniques including Generalized Linear Mixed Model (GLMM). Patterns of frog community structure and composition will be explore using non-metric multidimensional scaling (NMDS) ordination and to test significant differences in the overall community structure between fragments and oil palm plantations I will use Analysis of Variance Using Distance Models (ADONIS) and correlation analysis. Genetic analysis such as genetic structure, gene flow, genetic diversity, demographic changes, phylogenetics and phylodiversity will also be be performed.

Expected outcomes:

Tropical rain forest are becoming increasingly fragmented due to anthropogenic landscape changes, fragmentation have been an increasing threat for biodiversity in this ecosystem. Changes in natural habitats due to fragmentations affect individuals of different species in a variety of ways especially for the decrease of habitat availability, changes in spatial configuration and habitat quality of fragments. Therefore empirical data on the ecological plasticity and sensitivity of a wide range of species are essential for effective conservation planning and formulation of management plans. The focus of recent studies addressing the consequences of habitat fragmentation on tropical biota has been mainly directed towards large mammals such as orangutans and elephants (Goossens et al 2005; Estes et al 2012). To date very little is known about how amphibians cope with habitat fragmentations and understand the consequences of fragmentation is vital for conservation of frog communities.

This project will produce a combination of ecological data, species diversity, phylogenetic, phylogeographic and population genetic data, allowing us to expand our knowledge on frog conservation communities and to formulate adequate conservations plans related to fragmented habitat due to oil palm agriculture. As some amphibians are well known as an excellent biodiversity indicators, we will be able to get an overview of the current biodiversity level in the area.