Characterization of a western North American carnivore community using PCR-RFLP of cytochrome b obtained from fecal samples

We developed a simple and reliable method to identify carnivore scats to species using PCR and RFLP of a portion of the mtDNA cytochrome b gene, which works for seven of the most common carnivores in western North America. We identified a short (196 bp) polymorphic region of cytochrome b which would be easily amplifiable even from degraded DNA, developed a primer set, and isolated a set of three restriction enzymes (HpaII, DdeI, HpyCH4V) that would identify the seven target species. In order to test whether this protocol would effectively identify scats obtained in the field we collected 243 carnivore scats from 12 sites in the San Francisco Bay area. Eighty five percent (206) of our samples successfully amplified and were subsequently identified to species using our RFLP protocol. We selected 108 of these samples to sequence; our species identifications based on sequencing were identical to those obtained using our PCR-RFLP method. Our PCR-RFLP method is a simple and efficient means to identify carnivore scats to species, eliminating the need for sequencing, which is costly and requires more laboratory equipment. The technique can also be modified depending on the species present at a particular site. It allows for rapid and noninvasive assessment of multiple carnivore taxa and is particularly useful for surveying populations across many sites

Data from: From canopy to seed: loss of snow drives directional changes in forest composition

Climate change is altering the conditions for tree recruitment, growth, and survival, and impacting forest community composition. Across southeast Alaska, USA, and British Columbia, Canada, Callitropsis nootkatensis (Alaska yellow-cedar) is experiencing extensive climate change-induced canopy mortality due to fine root death during soil freezing events following warmer winters and the loss of insulating snowpack. Here, we examine the effects of ongoing, climate-driven canopy mortality on regeneration and identify potential shifts in stand trajectories due to loss of a single canopy species. We sampled canopy and regenerating communities across the extent of C. nootkatensis decline in southeast Alaska to identify the drivers of C. nootkatensis canopy mortality and regeneration as well as post-decline regenerating community composition. Across the plot network, C. nootkatensis exhibited significantly higher mortality than co-occurring conifers across all size classes and locations. Regenerating community composition was highly variable but closely related to the severity of C. nootkatensis mortality. Callitropsis nootkatensis canopy mortality on the plot network was correlated with winter temperatures and precipitation as well as soil drainage, with C. nootkatensis regeneration abundances and regenerating community composition best explained by available seed source. In areas of high C. nootkatensis mortality, C. nootkatensis regeneration was low and was replaced by Tsuga. Our study suggests that climate-induced forest mortality is driving alternate successional pathways in forests where C. nootkatensis was once a major component. These pathways are likely to lead to long-term shifts in forest community composition and stand dynamics. Our analysis fills a critical knowledge gap on forest ecosystem response and rearrangement following the climate-driven decline of a single species, providing new insight into stand dynamics in a changing climate. As tree species across the globe are increasingly stressed by climate change-induced alteration of suitable habitat, identifying the autecological factors contributing to successful regeneration, or lack thereof, will provide key insight into forest resilience and persistence on the landscape