Jones et al. "Megafire" paper is bad science

A recent paper by Gavin Jones et al. "Megafires: an emerging threat to old-forest
species" claims to describe negative effects of the 2014 King fire on California spotted owl occupancy and space use. There have been several previous papers by other authors documenting how severe fire has little or no effect on spotted owl occupancy, and that they forage in high severity patches preferentially. Jones et al. (2016) claim their data describe for the first time, a strong negative impact of severe fire on spotted owls. The paper has fatal flaws in their analyses that render their results and discussion categorically incorrect.

• Only 1 year of post-fire data.
• Very small sample sizes. Authors of "Megafires: an emerging threat to old-forest
  species" don't provide 2014 occupied site sample size, but 2014 occupancy rate was 0.57, so one can compute approximate 2014 pre-fire occupied site sample sizes of 17 burned and 9 unburned sites. Only 14 burned sites were in the big high-severity patch, so they are making a claim of large extinction effects from 8 severely burned, previously occupied sites, versus 9 unburned sites.
• Excluding the temporal trend from the occupancy analysis is the most onerous fatal flaw. Jones et al. neglected to include the temporal trend effect in colonization and extinction rates that were described in Tempel & Gutierrez 2013 using the same data up to 2010 as were used by Jones et al. (2016). The population is in freefall, yet the authors compared their 1 year of post fire data against all previous years without accounting for the temporal trend in colonization and extinction. Jones et al. did a separate analysis of trend in occupancy, but that was not included in the dynamic occupancy modelling. Including a pre-fire trend in the analysis would swamp the effect the authors attributed to fire. Furthermore, the hockeystick ‘segmented’ trend in Fig 3e and WebTable 4 is ad hoc and unjustified. The temporal trend graphs Jones et al. should have presented and included in their dynamic occupancy analysis were the linear or quadratic trend (most likely the quadratic trend based on WebTable4)
  

Figure 1 from Tempel & Gutierrez 2013 showing annual rates of occupancy, colonization, and extinction probabilities. Temporal trends existed in both colonization and extinction probabilities, but Jones et al. (2016) neglected to include these trends in their analysis of fire effects in 2015.

Annual spotted owl site occupancy data from El Dorado density study area with linear trend.

Annual spotted owl site occupancy data from El Dorado density study area with a quadratic trend.

• Compositional analysis of foraging habitat as done by the Jones et al. 2016 Megafire paper is inappropriate for central place foragers like spotted owls. By omitting the distance to center effect and analyzing simplistic ratios rather than resource selection functions, radiotelemetry results and discussion are invalid.
• Inaccurate scholarship was evident in the text as well. e.g.,
  • p. 300 “In the western US, major reforms in forest fire management have been proposed to restore low-and moderate-severity fire regimes through forest tree thinning (North et al. 2015).” This citation neglects the literature supporting a natural mixed-severity fire regime in the Sierra Nevada.
  • pg. 304 "The observation that lower-severity fire is benign, and perhaps even moderately beneficial, to spotted owls is consistent with previous studies (Roberts et al. 2011; Lee et al. 2012)." Both those studies found no effect on occupancy from mixed-severity fire, as is common in the Sierra Nevada with a mix of low, moderate, and high severity burn.
  • p. 305, “because owls were not individually marked in the Rim Fire study, some detections at “occupied” sites may have involved individuals from neighboring territories or non-territorial “floaters” (Lee and Bond 2015), both of which may have contributed to inflated estimates of territory occupancy.” This exact same situation exists in the data analysed by Jones et al., data were collected as described in Tempel & Gutierrez 2013, “We included both nocturnal and diurnal surveys in our occupancy analyses.”  During nocturnal surveys leg bands are usually not resighted, therefore detections at occupied sites would have been similarly inflated by individuals from neighboring territories or non-territorial floaters.

This Jones et al. study area is the lone example of severe fire having a strong negative effect on spotted owls.
The study was funded by the US Forest Service, and California Department of Forestry and Fire Protection, groups with a financial interest in promoting thinning logging of our forests in the name of protecting them from severe fire.