Cumulative Effects of Coastal Watershed Land Use on Chironomidae (Insecta: Diptera) Communities of Neotropical Estuaries in Costa Ric

Chironomidae assemblages are likely to provide a useful measure of biotic integrity in Neotropical estuaries of Costa Rica, which lack an intensive estuarine bioassessment tool to support environmental monitoring. However, little is known about chironomid communities in these estuaries and the cumulative effects of watershed land use on chironomid communities have not been studied. The purpose of this dissertation was to (1) quantify land cover change of six watersheds on the Caribbean coast of Costa Rica between 2001 and 2014, (2) describe all steps of the Chironomidae surface-floating pupal exuviae method in detail, including sample collection, laboratory processing, slide mounting, and genus identification, (3) investigate Chironomidae species diversity of nine estuaries across a land use gradient on the Caribbean coast of Costa Rica, (4) compare the relative effectiveness of five different DNA extraction protocols and direct PCR in isolation of DNA from chironomid pupal exuviae, and (5) assess the efficiency of using standard DNA barcoding for species identification of chironomid pupal exuviae. I found that watershed-scale land use analyses showed agricultural expansion and deforestation in watersheds on the northeastern coast and secondary forest regrowth on the southeastern coast of Costa Rica. I identified 228 morphospecies and 70 genera from 17,071 Chironomidae surface-floating pupal exuviae collected from nine Neotropical estuaries and that a Chironomidae Index of Biotic Integrity successfully discriminated estuaries with differing degrees of stress across a land use gradient. I extracted genomic DNA from 61.2% of 570 sampled pupal exuviae. The NucleoSpin RTM Tissue XS Kit, DNeasyRTMRTM Blood and Tissue kit, and QuickExtract(TM) DNA Extraction Solution provided the best results in isolating DNA from single pupal exuviae. A total of 36.3% of 190 sampled pupal exuviae resulted in high-quality sequences for Costa Rica, but none matched known species. This knowledge is important if these aquatic communities are to be used more effectively in future biological monitoring, conservation, and integrated water resource management of Neotropical estuaries.