Development of Next Generation Techniques of fecal samples collected from nestling cactus wren

Science Center Objects

Coastal cactus wren populations have declined in southern California over the last three decades. In San Diego County, this decline has been especially noticeable in the Otay area, which in 2014 supported 14 territories on conserved lands. In the past, there were 25-53 active territories reported for this same area, with the highest estimate in 1992. There is also concern the number of active territories at other sites in MUs 3 and 4 have been reduced since 2012.

Although associated with long-term declines, neither fire nor development appear to be the primary factor responsible for the more recent and localized Otay cactus wren population decline. Multiple years of drought may have affected wren abundance by reducing arthropod food resources, which could lower fecundity and/or survival. In over half of the last 15 years there has been less than 75% of the mean 9.6 inches of rainfall in San Diego County, with five years receiving less than 5 inches. In 2014, a severe drought year, productivity was low with only 3 fledglings observed at the 14 Otay wren territories. Genetic analyses show the Otay population is isolated from nearby wren populations to the north. There is a risk that the Otay population could disappear if the decline in abundance continues; it is unlikely wrens from other areas will disperse to Otay and rescue the population demographically.

Indications are that food availability for cactus wrens may be affected by habitat quality, as characterized by the composition and abundance of native and non-native plant species, amount of bare ground, and by microsite characteristics such as soils, slope and aspect. During drought years, wrens in territories with poor quality habitat may be even more food limited. Improving habitat quality could increase food availability and enhance wren productivity and survival. Developing management strategies to increase stability of wren populations in years with low rainfall is of particular importance if droughts become more frequent, intense and prolonged in the future, as predicted by climate change models.

We are developing novel amplicon sequencing methods for dietary analyses of a species of concern, the Cactus Wren. Once assays are developed, we can deploy broader temporal and spatial monitoring efforts to assist the San Diego Association of Governments management of the cactus wren habitat.  This work will contribute to ongoing research efforts to develop genomic resources to assess habitat restoration efforts for the cactus wren


We will develop and test amplicon sequencing assays for dietary analyses of a species of concern, the coastal cactus wren (Campylorhynchus brunneicapillus sandiegensis), which have declined around the Otay area. The Otay area supports 14 territories on conserved lands.


Amy Vandergast and her team are working on identifying insects in their diet using molecular analysis of their feces.

(Public domain.)


Technician using the Illumina MiSeq

The Illumina MiSeq platform has allowed us to develop new metabarcoding approaches to determine diets from bird fecal samples.

(Credit: Deborah Iwanowicz, USGS Leetown Science Center. Public domain.)