1. The calculation of the density estimates

The density estimates were calculated as follows:

The authors developed field surveys in 24 sites and used available estimations for both periods (2010 and 2018) based on a 27 camera-trap stations array for 30 days (2010 survey) and 60 days (2018 survey). The surveys covered a total area of ca.81 km2, with a mean distance of 1.5 km. Sites were selected according to their importance as priority regions for jaguar conservation [3,4] and previous knowledge of the working groups.

The authors identified jaguar individuals by data obtained by camera trap surveys and used recapture models to estimate densities. Capture-recapture models were estimated after building capture histories for each site with 30-days sampling periods; we then estimated abundance values under seven models that differ in the source of variation in capture probability (i.e., individual heterogeneity, behavior, time, and combinations). The best model was selected using a discriminant function developed by [5] and canonical estimators developed by [6]. Camera locations were used to develop a Minimum Convex Polygon (MCP) between stations, to which we added a buffer based on the Mean Maximum Distance Moved (MMDM) and estimated the density as the abundance over the MCP and buffer area. Density estimates were obtained for different representative habitat types for jaguar landscapes in Mexico. In 2005, the Commission for Protected Natural Areas (CONANP), SEMARNAT, and the National Autonomous University of Mexico held the 1st Symposium on the Mexican Jaguar in the 21st Century [3]. More than 25 experts on the jaguar in Mexico participated in this event, and among the topics discussed were the priority areas for jaguar conservation in Mexico. This exercise of prioritization of areas was based on the following criteria: i) presence of jaguar populations, recent studies or expert knowledge; ii) presence of suitable habitat within the current distribution area of the species, based on recent records of jaguars and expert knowledge; and iii) presence of isolated records of jaguars. Based on these criteria, the prioritization generated three groups: Priority I, those regions that still maintain jaguar populations; Priority II, regions that have considerable extensions of suitable habitat for the jaguar, but the presence of the species has not been systematically evaluated; and Priority III regions where there are isolated records of jaguars, supported by systematic studies or anecdotal observations, but which no longer have considerable areas of natural vegetation that would allow for the persistence of a jaguar population. Experts agreed upon these regions [7], taken up in various Mexican government documents [8], and supported by recent publications [4,9–11].

Potential distribution models were implemented using jaguar records and landscape information for both periods of time (2008 and 2018). The authors built a time-calibrated species distribution model using available information for both times to properly identify the available habitat coverage in each of the previously identified jaguar conservation regions. Details on each of the models are provided in the Methods section. The authors estimated habitat suitability for jaguars for both periods using the time-calibrated species distribution models, discriminating between primary and secondary vegetation.

Based on the density estimation, the authors calculated 95% confidence intervals for each site estimation and for each region to have the most conservative estimates based on the lower intervals for each region. The authors then had mean, maximum, and minimum density estimates on each region based on multiple estimations. Using the most conservative estimate for available primary vegetation habitat and the lower limit (lower interval) of the most conservative estimate for secondary vegetation habitats, the authors extrapolated the number of individuals to the total available habitat within suitable environmental conditions calibrated for each time-period for the region. Finally, with total estimations per region, the authors estimated Mexico’s most conservative number of individuals, calibrated by time-period and vegetation types (optimal and suboptimal habitats).

2. The use of CAPTURE model for estimating densities

The use of the MMDM, based on closed population capture-recapture approaches, estimates were positively correlated with the density estimates, while the use of the Mh, MMDM and SECR models produced very similar results [12]. The authors used the mean maximum distance moved (MMDM) to estimate buffer width under a capture-recapture framework. Although they acknowledge that SECR is a more recent approach, the authors consider that classic capture-recapture models are still a valid approach, as reflected in the literature [13,14]. The authors acknowledge the limitations in interpreting their results because the density estimates are different across habitats, regions, and periods and, that local and regional scale population monitoring programs are still necessary to better understand the estimation in remote regions. However, the authors understand that CAPTURE is now not considered the most reliable approach, this was the best model, considering the data limitations, when they did their analysis.

3. The absence of jaguar contacts in areas where jaguar is known to be present

It was unexpected that there were no records in Calakmul in the 2018 sampling period as this study site is known to have good number of jaguars [15,16]. The authors report that camera trap malfunction was discarded as the camera traps recorded other mammals in the area. The authors suggest a logging prospection study undergoing in the area as a possible cause for the absence, as jaguars leave the sampling and other sites when unusual human activities occur [17–19].

Supporting information