Category Archives: Paper Summaries

New Paper: Modeling Daily Stream Temperature

Our paper, “A hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags” was just published today in the journal PeerJ. We developed a statistical model of daily stream temperature for a watershed in Western Massachusetts, USA.


Observed (blue) and predicted (red) temperatures compared to air temperature (black points).

We outline the major challenges of statistical stream modeling and show how our model addresses hysteresis, autocorrelations, time lags, and avoids problems of modeling winter temperatures when the air-water relationships do not exist because of phase changes and the lower limit of water temperature. Daily stream temperature models have potential use in regulations (protection levels based on thermal classifications) and in understanding the ecology of stream organisms.

If you aren’t familiar with PeerJ you should check them out. The provide open access peer-reviewed articles for a low price. Their review process is very fast and it is the most pleasurable experience you will ever have submitting a manuscript, pre-print, or review. Check out some reviews here.


Shakespeare and Seinfeld and Salamanders, Oh My!

IMG_0064What do Shakespeare and Seinfeld have in common with Ray Bradbury and the Bible? As the title of this might might imply, they all reference amphibians. Shakespeare’s witches had their eye of newt, in Seinfeld George was desperately trying to get Frogger across the road, Bradbury’s book-burning firemen are emblazoned with a salamander, and frogs are rained down in a Biblical plague.

In our new paper in Herpetological Conservation and Biology, we review the contributions of amphibians to ecosystem services. These services that ecosystems provide for human societies include provisioning services (food, water, etc.), regulating services (flood control), cultural services (art, literature, spirituality), and supporting services (ecosystem functions and structure that support the other services). As one of the major vertebrate classes with more than 7,000 species world wide, amphibians have the potential to contribute to each of these ecosystem services directly or indirectly.

Provisioning services provided by amphibians include food (frog legs) and medical advances. Toxins from the skin of frogs have properties of analgesics more powerful than morphine without the potential addictive properties. Other skin chemicals have been shown to inhibit HIV.

Amphibians play less of a role in regulating services but may contribute to pollination in some circumstances.


Amphibian provisioning service?

In human societies, amphibians have a long history in culture. From ancient carvings and mythology, to modern video games and plush toys. As I mentioned at the beginning, amphibians have featured in literature over centuries. This was the section of the paper that was most fun. In no way could I catalog all the ways amphibians influence human culture but I point out a diverse array of influences.

The role of amphibians in ecosystem functions has received more researcher attention lately but is still poorly understood. This was part of my dissertation where I studied the effects of red-backed salamanders on ecosystem functions such as decomposition, nutrient cycling, and plant herbivory. I didn’t find strong effects of these salamanders but other researchers have found that salamander (including red-backed) and frogs can influence decomposition and nutrient cycling in terrestrial ecosystems. More research is needed to understand the conditions that mitigate these effects. In aquatic systems amphibians, especially frog larvae, influence primary production and nutrient cycling.

See our paper for more information on the role of amphibians in ecosystems or just to find some interesting cultural references to amphibians.


Hocking, D. J. and K. J. Babbitt. 2014. Amphibian Contributions to Ecosystem Services. Herpetological Conservation and Biology. 9(1):1-17. (Open Access)

Hocking, D. J. and K. J. Babbitt. 2014. The role of red-backed salamanders on ecosystem functions. PLoS ONE 9(1): e86854. DOI:10.1371/journal.pone.0086854 (Open Access)

Paper Summary: Natural Disturbance and Logging Effects on Salamanders

Paper Summary:

Hocking, D.J., K.J. Babbitt, and M. Yamasaki. 2013. Comparison of Silvicultural and Natural Disturbance Effects on Terrestrial Salamanders in Northern Hardwood Forests. Biological Conservation 167:194-202. doi:

Unfortunately, this paper is behind a paywall. Please email me if you would like a copy for educational purposes.

We were interested in how red-backed salamanders respond to various logging practices compared with natural disturbance. Specifically, we compared abundance of salamanders in the two years following a major ice-storm with clearcuts, patch cuts, group cuts, single-tree selection harvests, and undisturbed forest patches in the White Mountains of New Hampshire (Northern Appalachian Mountains). The 100-year ice storm caused ~65% percent canopy loss in the effected areas. We know that clearcutting has detrimental effects on populations of woodland salamanders but the impacts of less intense harvesting and natural disturbances is less well understood.

We used transects of coverboards from 80m inside each forest patch extending to 80m outside each patch into the surround, undisturbed forest. Repeated counts of salamanders under these coverboards allowed us to employ a Dail-Madsen open population model to estimate abundance in each treatment, while accounting for imperfect detection. The results were quite clear as demonstrated in this figure:

Abundance Plot by Treatment

There were slightly fewer salamanders in the ice-storm damaged sites compared with undisturbed reference sites. The single-tree selection sites were most similar to the ice-storm damage sites. The group cut, patch cut, and clearcut didn’t differ from each other and all had ~88% fewer salamanders compared with reference sites.

In addition to comparing natural and anthropogenic disturbances, we were interested in examining how salamanders respond along the edge of even-aged harvests. Wind, solar exposure, and similar factors are altered in the forest edge adjacent to harvested areas. This can result in salamander abundance being reduced in forest edges around clearcuts. Previous researchers have used nonparametric estimates of edge effects. A limitation of this methods is that effects cannot be projected well across the landscape. These methods are also unable to account for imperfect detection. We developed a method to model edge effects as a logistic function while accounting for imperfect detection. As with the treatment effects, the results are quite clear with very few salamanders in the center of the even-aged harvests, a gradual increase in abundance near the forest edge, increasingly more salamanders in the forest moving away from the edge, and eventually leveling off at carrying capacity. In this case, red-backed salamander abundance reached 95% of carrying capacity 34 m into the surrounding forest. As the model is parametric, predictions can be projected across landscapes. The equation can be used in GIS and land managers can predict the total number of salamanders that would be lost from a landscape given a variety of alternative timber harvest plans.

Hopefully other researchers find this method useful and apply it for a variety of taxa. It could also be incorporated into ArcGIS or QGIS toolboxes/plugins as a tool for land managers. You can read our paper for more details if you’re interested. In addition to methodological details there is more information on environmental factors that affect detection and abundance of salamanders in this landscape.

Edge Effects

Effects of forest management on a woodland salamander in Missouri

Effects of experimental forest management on a terrestrial, woodland salamander in Missouri by Daniel J. Hocking, Grant M. Connette, Christopher A. Conner, Brett R. Scheffers, Shannon E. Pittman, William E. Peterman, and Raymond D. Semlitsch.

This is the first post in what will hopefully becomes a series of brief summaries of my papers as they are published to further stimulate discussion. This post refers to the recent paper in Forest Ecology and Management: Please email me if you would like a copy.

Experimental Design

Red lines represent transects of coverboards. Black lines are drift fences with pitfall traps.

We were interested in how various forest management practices affect the terrestrial, woodland salamander (Plethodon albagula: Western Slimy Salamander). This was part of the larger Land-use Effects on Amphibian Populations (LEAP) project in Missouri. In 2004, we experimentally cut areas of forest surrounding amphibian breeding ponds. Around each pond there was an area that was clearcut then burned (burned to help reduce maple regeneration), a clearcut, a partial thinning cut, and an undisturbed control forest. This array of experimental treatments was replicated in four locations.

Western Slimy Salamander (Photo Credit: Bill Peterman)

Western Slimy Salamander (Photo Credit: Bill Peterman)

Woodland salamanders rely heavily on forest habitat and are sensitive to changes in temperature and moisture. They are lungless and breath through their skin. This type of respiration requires that they stay in relatively moist microhabitats, but logging alters the temperature and moisture of critical microhabitats. Although this study was originally designed to examine the effects on pond-breeding species, we took advantage of the large forestry experiment to determine if particular forest practices were better for sustaining populations of slimy salamanders. To this end, we placed coverboards in two transects in each treatment at three of these replicate forestry arrays and checked for salamanders periodically over 5 years. We have a related publication comparing carpet and wooden cover objects here.

We captured a total of 300 Western Slimy Salamanders between April 2007 and September 2011. We found significantly fewer salamanders in the burn and clear-cut treatments compared with the partial and control treatments. We also found a lower proportion of juveniles and had fewer recaptures in the burn and clearcut than in the partial and control treatments. Consistent with other studies of woodland salamanders, our results suggest that for at least the first 7 years post-harvest, clear-cutting is detrimental to woodland salamander populations. This initial reduction in abundance combined with the further reduced proportion of juveniles may have longer lasting effects even as the forest regenerates. Finally, it appears that timber harvest resulting in limited canopy thinning may be compatible with maintaining populations of Western Slimy Salamanders in Missouri.

You can read more about our findings from the LEAP project including the effects on many other species and in different regions of the country in our synthesis paper here.


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