Major Goals of the Philippine PIRE Project

What are the major goals of the project?

This study will measure centennial scale changes in the evolutionary potential of at least 20 species of marine fishes in the Philippines using advanced genomic analyses of fishes collected over a century ago and contemporary collections at the same locations. The genomic impacts will be compared to larger scale biodiversity changes using 1970’s collections of Philippine marine fishes that will be replicated to directly measure species and community scale changes. Together, these investigations will give an unprecedented insight into anthropogenic impacts on marine biodiversity and evolution.

Our overarching question is whether and to what extent genetic and species level changes have taken place over the past century of intense fisheries exploitation and habitat degradation in the Philippines. We will focus on three primary questions: To what extent has genetic diversity been lost from marine species in the Philippines, and are some species more susceptible than others to loss of genetic diversity? Have overfishing and habitat loss reduced gene flow between marine populations? To what extent do genetic diversity and species diversity reveal similar changes over a century of human impacts?

We have preliminary data from Restriction-site Associated DNA (RAD) analysis that clearly demonstrate Albatross specimens can be used to investigate population level genetic changes in fishes of the Philippines over the past century. Based on these data, we estimate that 75% of Albatross fish can be genotyped. As a whole, given the historical age of the Albatross collections, we believe our pilot sequencing results demonstrate a very reasonable sequencing success rate that can be further optimized during additional protocol development as part of this study.

We will analyze single-locality populations of at least 20 species, comparing over a century of genetic changes. The most suitable Albatross specimens include over 79,000 fishes in 23,877 lots from the Philippines (NMNH online database), with 81 lots containing more than 80 specimens. Of these, 48 lots have species that we are confident can be currently collected from local fish markets and in the field. We propose to directly compare genetic differences between Albatross era populations and present day populations using a combination of RAD capture and Illumina sequencing to accurately and precisely detect fishing-induced declines in genetic diversity.

The first use of the genetic data will be to test whether species have experienced fundamental genetic changes over the past century. Changes in the genetic makeup of populations are expected, given the intense level of exploitation of fisheries worldwide and in the Philippines in particular. In addition, there has been substantial loss in habitat quantity and quality, even for those species not fished intensively.  Stronger genetic drift and loss of genetic diversity may be caused by a reduction in effective population size (Ne), either through fishing or through habitat loss. We will test for this explicitly by estimating Ne in the Albatross specimens and in the modern samples using single-sample methods. Linkage disequilibrium among physically unlinked loci is higher in smaller populations, providing a powerful tool for estimating Ne. Recent declines in Ne leave characteristic signatures of a genetic bottleneck, though the large population sizes of marine fishes can limit these effects. To complement our analyses of heterozygosity, allelic richness, and Ne through time, we will also test specifically for bottleneck signatures in our modern samples. We will apply the same analyses to the Albatross samples to test whether these bottleneck signatures are new, and not indicative of events before the 1900s.

The second use of the genetic data will be to examine consequences of the expected decreases in population size and genetic diversity on connectivity over time between different locations in the Philippines. Over exploitation and habitat degradation are expected to reduce population sizes, which in turn decrease larval output, increase population fragmentation and genetic drift, and consequently produce stronger genetic structure between populations. Assessing the decrease in connectivity in both a spatial and temporal context in this study will provide insight into the evolutionary consequences of these factors.

The third use of the genetic data will be to observe what species diversity changes have occurred after four decades of habitat degradation and exploitation on coral reefs of the Philippines and how this compares to changes in genetic diversity from the Albatross material. In the Philippines, the consequences of both a peak in species diversity and a peak in threat to this diversity can be directly measured because of Smithsonian natural history collections completed in 1978 and 1979 in the central Visayan region, which are particularly suited to measuring biodiversity changes over time. PI Carpenter and Collaborator Alcala participated in these collections and are intimately familiar with their protocols and methodologies.

Our Plan for Educational Activities will integrate research activities with field, laboratory, and classroom education. The research and education activities and goals are highly interdependent because of the need to complete research in the Philippines by students and early career professionals. This need stems from international agreements (i.e. Convention on Biological Diversity) that call into question transfer of raw genetic material between countries and represents permitting challenges in many countries. The optimal model to ensure no questions in this regard is for all the DNA extractions to be done within the country where the samples originate. It relies on the long-term residence of U.S. students and post-docs in the Philippines to complete initial genetic laboratory work alongside Filipino collaborators. This will fulfill one of the project’s primary education goals: to provide an international research opportunity for U.S. students that promotes long-term research and education collaboration by working alongside Filipino students and scientists. The summer semester of each year will be dedicated to field and educational activities in the Philippines. Early career professionals, graduate students, and undergraduates will spend one or more semesters per year in the Philippines completing all the field and initial laboratory work required. This will be coupled with the teaching of advanced genomic courses by post-docs and senior scientists in a classroom experience offered to both U.S. and Filipino students, and coordinated with the laboratory and field work of the research objectives.

In order to frame both the genetic and species level changes that we will directly measure over time with respect to changes in the overall marine biodiversity of the Philippines, we also propose to collaborate with current, on-going efforts in the Philippines to conduct a National Philippine Red List for marine species, based on assessment of the population and conservation status of all marine fishes present in Philippine waters. Essentially, data on genetic and species level changes from the proposed research will provide critical data to assess marine species population changes over time based on established International Union for the Conservation of Nature (IUCN) Red List assessment methodology (IUCN 2001). Completion of a Philippine National Red List, based in part on data produced from this proposal, will essentially serve as a Philippine equivalent of the US Endangered Species Act and as such, will transform conservation and fisheries management in the Philippines.