Carrion fly-derived DNA metabarcoding is an effective tool for mammal surveys: Evidence from a known tropical mammal community.

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and camera trapping. We collected 1,084 flies in 29 sampling days, conducted metabarcoding with mammal-specific (16S) and vertebrate-specific (12S) primers, and sequenced amplicons on Illumina MiSeq. For taxonomic assignment, we compared blast with the new program protax, and we found that protax improved species identifications. We detected 20 mammal, four bird, and one lizard species from carrion fly metabarcoding, all but one of which are known from BCI. Fly metabarcoding detected more mammal species than concurrent transect counts (29 sampling days, 13 species) and concurrent camera trapping (84 sampling days, 17 species), and detected 67% of the number of mammal species documented by 8 years of transect counts and camera trapping combined, although fly metabarcoding missed several abundant species. This study demonstrates that carrion fly metabarcoding is a powerful tool for mammal biodiversity surveys and has the potential to detect a broader range of species than more commonly used methods.

Differential effects of unusual climatic stress on capuchin (Cebus capucinus) and howler monkey (Alouatta palliata) populations on Barro Colorado Island, Panama.

Though the harmful effects anthropogenic disturbances pose to wild primates are well appreciated, comparatively little is known about the effects of natural disturbances. From December 2010 to January 2011, different mortality patterns were observed for two primate species, capuchins and howler monkeys, on Barro Colorado Island (BCI), Panama. Unusually high rainfall in 2010 was associated with census and cadaver data indicating the rapid loss of >70% of the capuchin population in late 2010 to early 2011. In contrast, over this same period, no decline was documented for howler monkeys and cadaver data for howlers was unexceptional. The high mortality experienced by the capuchin population was unexpected and its extent was not fully appreciated until the event was largely over. Explanations proposed for it included effects of hypothermia, disease or a shortage of some essential nutrient(s). Of these, the dietary explanation seems most probable. BCI capuchins depend most heavily on arthropod foods in December, when few higher quality ripe fruits are available. The unprecedented high rainfall in December 2010 is hypothesized to have largely eliminated the arthropod peak expected on BCI each December. A lack of protein-rich arthropods, when coupled with the climatic and nutritional stress capuchins generally experience at this time of year, appears to have precipitated the rapid die-off of most of the island's capuchin population. As howler monkeys obtain dietary protein primarily from leaves, a shortage of edible arthropods would not affect howler numbers. Comparison of our 2010 data with similar data on earlier primate/mammalian mortality events reported for BCI and for Corcovado, Costa Rica indicates that our understanding of the effects of natural disturbances on wild primate populations is not profound. We suggest that more research be devoted to this increasingly timely topic, so important to conservation policy.