Monday, June 13, 2016

The Slyest Seed Predator: Interactions Between Red Fox and Whitebark Pine in the Greater Yellowstone Ecosystem

High on the Beartooth Plateau, YERC researchers studying the rare mountain fox population there observed never-before-seen behavior that may help to explain the population's persistence in such an extreme environment: the adaptable foxes were raiding red squirrel middens for their whitebark pine seeds.  But whitebark pines in the Greater Yellowstone Ecosystem face threats on multiple fronts; so what does that mean for these native foxes? As part of our efforts to collaborate with other groups working on important issues affecting the GYE, we provided the following cover story for the Whitebark Pine Ecosystem Foundation's newsletter, Nutcracker Notes

The Slyest Seed Predator: Interactions Between Red Fox and Whitebark Pine in the Greater Yellowstone Ecosystem
By Patrick Cross, Yellowstone Ecological Research Center
Originally appeared in Nutcracker Notes, Summer 2015

"Aha, there's a fox scat for you, Joel!" I proclaimed, pointing ahead with my ski pole across the otherwise unblemished snow. 

It was a crisp January day, with alpine sunshine sparkling off ice crystals suspended in the mountain air, high on the Beartooth Plateau near Top of the World, Wyoming.  Field technician Joel Forrest and I were there to conduct snow tracking surveys, collecting habitat use data that could explain why the red foxes that live there seem different from those at lower elevations.  With kit-rearing dens up to 9,400' (2,820 m) and year-round occupation of elevations as high as 11,000' (3,300 m), this is the highest known fox population in North America.  It is also distinguished by unique physical and genetic characteristics: visitors to nearby Yellowstone National Park have long noticed the lighter blond coat colors and gray underfur of its foxes living at high elevations compared to the rich red found at lower elevations, and recent genetic studies have revealed significant differences between foxes across an elevational gradient within the ecosystem3.  Suspecting that behavioral differences could be contributing to these observations, we wanted to compare genetic and habitat use patterns high in the Beartooths to those lower down in Yellowstone4, hoping to identify the mechanisms driving this diversity.

But as we skied closer, I noticed that there was something odd about this scat.  It was not composed of the fine gray hair and tiny bones one would expect from a predator of small rodents; instead it prickled with rigid, angular, broken bits of brown shells.  If it wasn't for its small size and its being found in the wrong season, it could have been mistaken for a late-summer grizzly bear scat.  This fox scat was packed with crunched whitebark pine nuts.

Later, over beers at the Miners Saloon in Cooke City, Montana, we reported our discovery to Jesse Logan, an expert on the area's whitebark ecology as well as its trout fishing and powder skiing. 

"I think you are on to something here," Jesse said, encouraging us to continue documenting this apparently novel behavior, which was easy to do since the whitebark pine nuts would have a major effect on fox activity throughout the rest of the winter. 

In the following months, we found pine nuts in nearly half of the 30 scats collected across the territories of multiple foxes, often in large quantities accounting for most or all of the scat's content.  And on several occassions, our snow tracking surveys even led us deep into the forests, far from the edge territory that foxes generally prefer, to the raided red squirrel middens that had yielded the nutritious food.  The snow around these sites, which were usually at the base of a grand old spruce or whitebark, would be packed down from so many fox tracks and have cone bracts, bark, needles, and other debris from the excavated midden strewn all over its surface.  There would also be short trails leading away from the midden to smaller packed down rest sites where the fox would carry a whole cone, pull off its waxy, purple bracts, pluck out the seeds, and drop the empty husk before returning to the midden for another.  Surely this was a more effective way to obtain calories than by diving through the deep snow after a small, scurrying vole.  And foxes were not the only carnivores enjoying pine nuts that winter: we also observed several American marten scats that were obviously loaded with pine nuts.

The following winter, we did not find any pine nuts in the fox scats collected, but this was expected since we had not heard as many raucous Clark's nutcrackers that summer, nor did we see the overloaded tree tops like we had the summer before.  Whitebark pine often exhibit the cyclical reproduction strategy known as 'mast seeding' in which cone production is high in some years and low in others so as to discourage seed predators from settling in.  Although there is substantial variation in these cycles from whitebark stand to stand given their site-specific environmental conditions, researchers from the Interagency Grizzly Bear Study Team conducting cone count transects throughout the ecosystem rated the first year of this study (2012-2013) a "generally good cone production year" for the ecosystem, while the following year was rated a "generally poor cone production year."  That second winter, the foxes consumed more snowshoe hare, which seems like a formidable advisary for a predator that, at about 9 lbs (4 kg), is no bigger than the average house cat  ̶  they may look bigger, but it is all fluff.  Nevertheless, we recovered snowshoe hare remains from over 70% of fox scats that winter, compared to less than 25% the winter before.  Also that winter's field tech, Jake Kay, and I both recorded numerous kill sites while snow tracking, yet neither of us found any excavated squirrel middens. 

Almost everyone who has seen these foxes, or even just their tracks, in such an extreme environment has wondered, 'what do they eat up here all winter?' and clearly the answer is whatever they can find.  Surviving in the subalpine requires a fair deal of adaptability, which is something that the red fox, the most widely distributed terrestrial carnivore in the world, excels at.

So it was not surprising when, at the completion of its metamorphosis from raw field data to spreadsheets to statistical analyses, we found significant variance in the food items consumed between the two winters of this study.  But we were surprised when we likewise analyzed the habitats used between the two winters and again found statistically significant variance.  During the first winter when whitebark seeds were available, there was a significant spike in the usage of mature spruce-fir cover types, while the following winter saw a more even distribution of habitat useage as the spike in mature spruce-fir leveled off and more mid-successional forest stages were used.  To understand why, we turn to red squirrel ecology. 

Because of interannual variance in whitebark cone production due to mast seeding, pure whitebark stands are generally considered poor squirrel habitat since they lack the diversity of food types needed to sustain squirrels during low cone production years.  And where there are no squirrels, there are no squirrel middens.  Spruce-fir cover types, on the other hand, often have a significant whitebark component in addition to more consistent but less nutritious food sources.  This makes them better squirrel habitat and the most likely places where whitebark seeds would be available to foxes, thus explaining the significant spike in spruce-fir habitat use corresponding with the significant spike in whitebark pine nut consumption. 

Ever since we found that first nutty scat high on the Beartooth Plateau, we were excited since it was, to the best of our knowledge, the first time foxes were recorded using whitebark pine nuts, adding them to the long list of animals that directly benefit from whitebark pine.  But the combined results of these statistical analyses are far more profound since they suggest that, beyond simply using this novel food source, the foxes were actually changing their habitat use behavior in response to its availability.  Perhaps this is a clue pointing to why these high elevation foxes are distinct; perhaps they have evolved in this landscape where whitebark pine play such an important role; perhaps the foxes themselves, like the Clark's nutcrackers, red squirrels, and grizzly bears, play an interactive role in this particular system.  In reality, these findings do more to raise new questions than they do to answer our original questions, which may just be the result of good science, but we can be confident that whitebark pine nuts are an important resource facilitating the persistence of this fox population in such an extreme environment.

This past spring, I met up with Jesse again at the Miners, and this time he had questions for me: how cold did it get up there last winter? what is the snowpack like right now? did you see any blood red brood trees infested with mountain pine beetles?  When he later returned from a day of bark chipping on the Beartooth Plateau in the very area where the fox-excavated squirrel middens were located, his report was grim: wriggling beetle larvae were thriving in those high forests unaccustomed to the epidemic pest.  Should the Beartooth Plateau experience the dire whitebark declines that have happened in other parts of the Greater Yellowstone Ecosystem, the adaptability of its remarkable population of red foxes will be put to the test.


May 20th was Endangered Species Day, an opportunity to reflect on the beauty and value of
wildlife, and acknowledge the role the Endangered Species Act (ESA) plays in protecting our
most threatened species from extinction. A key requirement of the ESA is that decisions about
protecting wildlife must be based on the best available science. But for the science to be
credible, it has to come from the independent scientific community, and not be tied to political

Unfortunately there have been an alarming number of instances when this is not the case. For
example, in 2014 the Department of the Interior declared gray wolves recovered nationwide
because the Fish & Wildlife Service (FWS) claimed the wolves occupied most of the remaining
suitable habitat in the U.S. when in fact, some two dozen states in the historic range of gray
wolves were, and are still, vacant. Those states were declared unsuitable for wolves by the
FWS on grounds that human tolerance for wolves was so low there and that wolves would be
poached by citizens or killed by government agents seeking to protect livestock interests. And
not so coincidentally in 2014, we witnessed a wolf pack colonizing California’s suitable habitat
to become the first wolves there since 1924. If FWS policy had been implemented, California
might not have seen this re-colonization.

In fact none of the available science supported the FWS claim, and what evidence there was
showed that tolerance for wolves was even higher outside their current range. Furthermore,
the purpose of the ESA is to prevent extinction by abating threats that push a species to that
point. So the FWS is not authorized to circumvent a threat by redefining suitable habitat; it is
required to combat threats and recover listed species, as the ESA states, “across all or a
significant portion of range.” (ESA 16 USC § 1531)

Initially these and other objections fell on some deaf ears as the FWS pointed to a non-peer-
reviewed genetic analysis suggesting the northeastern U.S. was not gray wolf habitat because a
new species had lived there. To its credit, the FWS set up a peer review of that analysis, but
then some within the agency attempted to remove scientists who had been critical of the
agency. The uproar that followed led to a much-improved independent scientific review
process led by the National Center for Ecological Analysis and Synthesis, which then
unanimously decided that the FWS’s earlier decisions were not well supported by the available

If we look at the history of decisions about carnivores under the ESA, we see similar disregard
for the best available science. Since 2005 the FWS has lost nearly a dozen federal court cases
trying to remove protections for wolves, grizzly bears, and wolverines. In each case, the courts
sided with plaintiff’s claims that the Department of the Interior misinterpreted the ESA or did
not follow the ESA mandate to base its decisions, “…solely on the best scientific and
commercial data available.”

So now we are looking for a constructive, cooperative, and lasting solution because science and
courts were created by humankind to seek the truth. On Endangered Species Day, Robert
Crabtree, Adrian Treves, Camilla Fox and Dave Parsons, in collaboration with the Union of
Concerned Scientists, submitted a petition to Interior Secretary Jewell and Commerce Secretary
Pritzker with the signatures of nearly 1,000 US scientists and scholars.

Our request was simple: respect the law and put the independent scientific community back in
charge of determining the best available science.

Thursday, June 9, 2016

Estimating Plant Production Using Satellites

Yellowstone Ecological Research Center geospatial scientist recently published a peer-reviewed manuscript in the journal of Carbon Balance and Management titled "Evaluation of modeled net primary production using MODIS and landsat satellite data fusion".  YERC staff developed a novel technique to combine information from different satellite sensors to improve our estimates of ecosystem productivity.

We expanded on an existing ecosystem model called the Carnegie-Ames-Stanford-Approach (CASA) ecosystem model developed by co-author and affiliate scientist, Christopher Potter.  Using high resolution LandSat data to classify ecosystems and medium resolution MODIS data to acquire vegetation information we were able to improve net primary productivity estimates in certain landscapes.

So, what is Net Primary Productivity?

NPP is the total accumulation of carbon by plants minus the amount of carbon lost by plants. Plants capture solar energy and convert it into nutrients which then drives most biotic processes on Earth. Therefore, understanding climate change's effect on NPP are an issue of central relevance to humanity, in part due to possible limitations on the extent to which NPP in managed ecosystems can provide adequate food and fiber for growing populations.

Measurement of NPP presents many challenges in any ecosystem, and particularly in heterogeneous environments such as wetland, cultivated, ex-urban, and mountainous landscapes. Traditionally, NPP has been calculated by harvesting and measuring dry biomass or from eddy flux towers estimates. Measuring dry biomass is labor- and time-intensive and logistically impossible to perform at scales other than the small plot. Eddy flux towers measure the amount of CO2 being exchanged with the atmosphere across a landscape. This technique can cover a larger area than using small plot biomass measurements. However, eddy flux tower measurements are affected by wind direction and atmospheric conditions, and logistical limitations have led to under-representation of tower sites in remote, disturbed, or degraded ecosystems.

In this manuscript we describe how we have developed a new approach to improve the spatial resolution and potentially the accuracy of the CASA NPP model by using an image fusion technique, whereby high resolution, Landsat-derived land cover is fused with MODIS MOD13A1 Enhanced Vegetation Index (EVI) data. The proportion of each land cover type within each pixel area was used to influence the ecosystem model result. This technique produced CASA model predictions of monthly NPP at 0.004 degree (approx. 500-meter) resolution for North America from 2000-2010 that were compared to tower flux estimates of NPP for evaluation.

Processing steps for the modified CASA algorithm. 1) Identify 500-m MODIS pixels containing >90% cover of the same NLCD land cover class. 2) Using pure-pixels identified in step 1 as points, interpolate (IDW) mixed pixel EVI values as if the interpolated cell were pure for each cover class. 3) Run CASA for all cover types using the corresponding pure-pixel interpolated EVI raster developed in step two. 4) Multiply the CASA outputs by the fractional % cover raster. 5) Sum the outputs from step 4.

We evaluated seventeen Ameriflux towers spread across the Continental United States (CONUS) were combined to evaluate monthly NPP estimates from the modified CASA model. Using a NPP:GPP ratio of 40% in the tower flux measurements, 1030 monthly data values plotted against the CASA model outputs resulted in an overall R2 of 0.72. Averaging NPP for a three cell by three cell buffer around the flux tower location resulted in a slight decrease in correlation between modeled NPP and flux tower measurements (R2 = 0.71). Removing flux tower sites that have been recently disturbed or managed the overall R2 increases to 0.82. The revised CASA monthly NPP estimates were found to be 25% lower overall than the tower-based NPP measurements, for reasons explained below. 

On a seasonal basis, the modified CASA model most closely matched the tower flux NPP during summer (R2 = 0.58) and autumn (R2 = 0.72), and most poorly in the winter (R2 = 0.22). Correlations were also relatively low in the spring, showing a R2 = 0.48. Tower sites in the Northeast and northern Midwest showed the highest levels of correlation (Table 2), with the Sylvania Wilderness flux tower in northern Michigan returning a R2 = 0.93 and the Morgan Monroe State Forest flux tower in Indiana a correlation of R2 = 0.93. Southern and western CONUS tower sites matched most poorly with CASA model estimates, with the Donaldson flux tower in Florida showing the lowest correlation of R2 = 0.01 and the ARM-SGP main tower in Oklahoma returning an R2 = 0.08. When grouped by land cover types, the combination of deciduous broadleaf forests monthly NPP measurements matched most closely with CASA model estimates, resulting a correlation of R2 = 0.88, followed by croplands (R2 = 0.73), grasslands (R2 = 0.65), and evergreen needleleaf forests (R2 = 0.57).

To learn more, read our manuscript here.