Tortoise Population Zone Trends

Continuing my analysis of iNat tortoise and reptile data, I looked at whether the observed changes in proportion of reptile species encountered was different in urban and urbanizing zones.  I hypothesized that the continuing expansion of large cities in tortoise habitat could be contributing to their decline.

Methods

I downloaded iNat data for AZ reptile species and mapped the points in GIS. I only looked at full species instead of including named subspecies as I had in my previous analysis. Based on that previous analysis, it seemed possible that changes in subspecies identification could be accounting for some of the observed changes and I wanted to remove that potential source of bias.

I then subjectively defined polygons around the large urban zones of Phoenix and Tucson and used the Identify tool to add Phoenix and Tucson labels to all points within those areas.  Note that although the study area includes other towns in Arizona (such as Prescott and Flagstaff) I did not choose to define those areas as "urban". 

Phoenix urban zone.  220 total tortoise observations.

Tucson urban zone:  795 observations.

I also considered whether geopoint accuracy would impact the results, so I conducted the following analysis including and excluding points with no or low (greater than 1000m) accuracy.  However, because I did not see a difference I will simply present results for all data points (i.e. no geopoint accuracy exclusion).

Results: Urban Zones

The majority of tortoise observations are from urban zones, especially Tucson.

It is not possible to determine if more tortoises live around Phoenix and Tucson compared to remote areas; iNat data collection is opportunistic, so places where people live are more heavily sampled than remote areas.  This result is an important caveat to my previous results: iNat observation trends are most representative of urban zones and any observed changes do not necessarily represent changes in all areas of Arizona.

The proportion of tortoise observations has been increasing in urban zones, especially Tucson. From 2013-2025, although there is some noise early on (e.g. 2014) due to low observation counts, the general trend is apparent that Tucson increased from ~45% to ~55% of total observations, while areas outside metro zones decreased from ~40% to ~20%.

This could contradict my hypothesis (that tortoises are declining in areas of urban development), or it could be due to increased observers in urban zones.   

Reptile observations show the same overall trend of increasing observations in urban zones. The proportion of iNat reptile observations for Phoenix increased from 10% to 20%, Tucson increased from 30% to 40%, and non-urban areas decreased from 60% to 45%.

Reptile Observation Trends

I wondered whether the amount of urban versus non-urban observations could explain the changes I observed in reptile species observations.

Updated Reptile Observation Trends

The 26 species of reptiles with more than 1000 observations

There were 26 species of reptiles with more than 1000 observations in the study area.  They ranged from species with 100% urban observations (San Esteban Island Iguana, introduced) to species with 0% urban observations (Plateau Fence lizard).  The colored cells show population change from a 2018 baseline.  Look for areas of red-green or green-red, because those indicate consistent trends from 2013-2025.  Red for both indicate 2018 was a high point.  Green for both indicate 2018 was a low point.  

I then plotted % change against proportion of non-urban observations to look for trends and outliers.

First graph: The point at 100% non-urban and 50% change is Plateau Fence lizard, which is very common in Prescott and Flagstaff, maybe that area should be an urban zone.  The point above 200% change is sidewinder, maybe someone was studying them back in the day?

2nd graph.  The point at 0% nonurban and 180% change is the iguana, introduced in Tucson.

Conclusion

Urban areas do not have a consistent negative or positive impact on reptile observation trends. It would be interesting to look at observation trends of individual species in each zone, but most species do not have enough observations for a meaningful statistical analysis.

At this point I can conclude that the large and increasing share of iNat observations from urban areas definitely affects the analysis of reptile observation trends, but I have not been able to identify a consistent bias that this would introduce into my overall analysis.

Reptile Trends in Arizona

Introduction

In my previous posts, I showed that the relative proportion of iNaturalist observations was decreasing for Sonoran Desert tortoises. 

In my second post I investigated whether there were biases affecting the total number of observations, and while I found some, they did not change the results of the first post.  However, in that post I only compared total observations to large taxa that include hundreds of species, like birds, insects, and reptiles.  The question remains of the variability of other individual species besides tortoises.  Is the observed trend in tortoise observations normal or extreme?  

Looking at other individual species is problematic, because while I could assume that the actual populations of large groups of taxa would be relatively consistent over time, that assumption does not hold for individual species.  In other words, it is harder to investigate potential observer biases when looking at individual species because their populations may actually be increasing or decreasing.

Nonetheless, looking at other species can shed some light on the observed trends in tortoise observations.  I looked at other reptiles with the idea that they might have similar trends, and/or similar causes explaining their trends.  

Reptile Observation Trends

I downloaded all Research Grade observations of reptiles within the tortoise study area and decided to focus on species with more than 1,000 observations over the 2013-2024 study period.  There were 26 species that fit this requirement.  

iNat page showing representative reptile species included in this analysis.  

I then conducted a similar analysis to the last blog post.  To look at the changing proportion of observations for each species over time, I divided the number of observations for each species each year by the total number of reptile and total number of non-plant observations for that year.  To compare species to one another, I normalized all species proportions to a base year, either 2013 (to look at % change since 2013) or 2018 (to look at % change since 2018).  

Changes 2013-2024

Excel can only graph 10 measures at a time (due to a limit on the number of colors?), so there are 3 graphs presented below for % change of various reptile species compared to total non-plant observations.  % change compared to other reptiles is not shown, but is summarized in the table below.

Top 10 lizards by total observations:

Plateau fence lizard had large initial increase that continued.

Western side blotched lizard had large increase in 2013 (year 11)

Common side blotched lizard has had increases, but ended very near where it began

Greater earless lizard decreased to 50% by year 5 and then held steady.

Middle 10 reptile species . Sonoran desert tortoise points are highlighted:

Mediterranean house gecko had large increase in first few years, but has decreased again since year 6 (2018)

Sonoran gopher snake has been up and down 50% at different times

All of the other species have decreased.

Bottom few reptile species. Note different Y axis:

Table of top 25 most observed reptile species in study area, listed from most to least observed:

Average change when normalized to total observations in less than 4%, but standard deviation is 50%.

Largest increase was Plateau Fence Lizard 240% change as a % of total observations, and 333% change as a percent of reptiles. Other species with large increases were red-eared slider and western side-blotched lizard.

Largest decrease was Gila Monster, only observed 38% as much in 2024 compared to 2013 total observations, or 52% as much compared to total reptile observations.  Other species with large decreases were Gopher snakes, western banded gecko, and Sonoran desert tortoise.  

The large variability in % change means that the standard deviation is also quite large.  Therefore, few if any of these changes would be statistically significant.   For example, even the large decrease in proportion of gila monster observations is not more than 2 standard deviations from the mean.

It is interesting to note that these results are largely consistent when species are compared against reptiles or all non-plant taxa.  Therefore this analysis does not help explain the apparent decrease of total reptiles compared to all non-plant taxa since 2013 that I noted in my previous blog post.

Changes 2018-2024

To show all species on one graph, I used Tableau to visualize the % change each species.  In this case I am comparing each species to total reptile species, but again I present comparison data for both total reptile and total non-plant observation in the table below.

Summary table:

Average change when normalized to total observations in less than 10%, and less than 1% when compared to just reptiles. but standard deviation is still more than 30%.

Largest increase was western side-blotched lizard with more than 200% change compared to either total non-plant or total reptile observations.   Other species with large increases were long-nosed snake with more than 150% change.

Largest decrease was still Gila Monster, which continued to decline since 2018.  It was only observed 50% as much in 2024 compared to 2018 when compared to total non-plant or total reptile observations.  Other species with large decreases were northern black-tailed rattlesnakes, sonoran desert tortoises, meditgerranean house geckos, and clark's spiny lizard.

Identifications to species versus subspecies can be a source of bias

The large increase in western side blotched lizard, a subspecies of common side blotched  lizard that did not show a large increase, could be due to Identifications favoring the subspecies.  Same could be true for Sonoran Gopher snake, a subspecies of gopher snake that showed a decrease.  The increase/decrease between the subspecies and species could be due to a cultural shift as identifiers increasingly favor the use of the subspecies.   Note that Northern black-tailed rattlesnake is also a subspecies (of Western black tailed rattlesnake), but almost all of the observations in AZ are consistently identified to the subspecies, so the large decrease in observations of this subspecies is probably not due to identifier bias.

Conclusions

While tortoise was not statistically different from all other reptiles, its decline is among the largest, grouped with other species of conservation concern.

For changes across reptiles, there are several possible hypotheses for the observed changes.  Some species are probably actually increasing or decreasing.  Species increasing in places people live would be observed more often.  But:  even if that is generally true, it is not consistently true.  Otherwise most common species would consistently increase and least common would consistently decrease.

I rejected my hypothesis that common reptiles are observed more and less common are now observed less frequently.  However, there does seem to be more variability in less observed species.  This is why I set the lower limit for this analysis at 1,000 total observations.  Even 1,000 isn’t very many, just 100-200 observations/year.  These small sample sizes could explain some of the variability.

Sonoran Desert Tortoise - Follow Up

In my previous post "Sonoran Desert Tortoise Population Status", I argued that a decline in the ratio of tortoise observations to total iNaturalist observations indicated a possible decline in the actual population of tortoises.  

However, that conclusion rests on the assumption that opportunistic "citizen science" observers have not changed their preferences in photographing other animals.  This could happen if people became less interested in tortoises, or if they became more interested in other taxa.  

Part 1: Trends in Other Taxa

I analyzed various other well-represented taxa in the iNat data to look for possible trends in observer preferences.  Specifically, I looked at all Research Grade (RG) iNat observations of amphibians, reptiles, insects, birds, and plants in the study area: 

Data table with total RG amphibian, reptile, insect, bird, and plant observations in the study area each year.

These are large taxa made up of many species and I expected that the ratio of observations would remain relatively consistent. 

Count of observations by taxa 2013-2024

Observations of all taxa have increased over the last 10 years, but some appear to have increased more than others. I divided the count of each taxa's observations by total observations to investigate proportional changes in the ratio of various taxa:

Ratio of various taxa to total observations 2013-2024

The ratio of various taxa has changed over time.  Specifically, the ratio of plant observations to total observations doubled in 2017.  I don't think this could be due to an actual increase in the number of plants in AZ.  

Instead, I think this must be an indication of a changed bias toward plants, perhaps due to specific iNat users who focus on plants, or a general trend toward more plant-focused observers on iNat.  Plants, because they don't run away, are arguably the easiest organisms to photograph; it could be that as iNat has grown there are now more casual users biased toward photographing easier to observe organisms.  

Regardless of why iNat users are observing proportionally more plants, this appears to be a source of bias that should be corrected in my analysis.    

To correct for the large increase in plant observations, I compared various taxa to total non-plant observations: 

Ratio of various taxa to total non-plant ("total2") observations 2013-2024

This shows a fairly consistent observation ratios for the major animal taxa over the last 10 years.  While there is some year to year variability, there are no long term trends, except reptiles.  Reptiles in general are photographed 71% as often in 2024 compared to 2013. Most of this drop occurred from 2015-2017, with no major changes since then.  It is not clear why reptiles as a group declined in representation.  There are other reptile species of conservation concern besides tortoises and it is possible that reptiles actually are declining, or there could be other sources of observer bias in the data, similar to the trend in plant observations above.

Except for reptiles, all taxa ratios stayed within approximately +/- 15%:

Table: percent change in ratios of various taxa since 2013 and 2017.

Part 2: Another Look at the Tortoise Trend

The analysis in Part 1 led to a refinement in the total observation count used to create ratios, and helped set a baseline for expected change in ratios over the last 10 years.  I used this information to reassess the observed decline in ratio of tortoise observations.  

Tortoise observations were compared to various taxa and to total non-plant observations:

Percent change in the ratio of tortoises to various taxa and to total non-plant ("total2") observations 2013-2024

The ratio of tortoise observations has decreased since 2013 for all 4 animal taxa investigated, and for total non-plant observations.  The decline is remarkably consistent for amphibians, birds, and total non-plant observations ("total2"), and fairly consistent for insects.  The ratio of tortoise to reptile observations tends to fluctuate over time, while maintaining the same overall negative trend.

While most animal taxa ratios show less than 15% change from baseline (Part 1), tortoises are observed 66-84% (mean 72%) in 2024 compared to 2017, and 35-57% (mean 43%) in 2024 compared to 2013:

Table: percent change of tortoise observations to various taxa and to total non-plant observations.

Conclusions

Tortoises show large declines compared to various representative animal taxa and compared to all non-plant observations.  This is the same result I found in my original blog post when I compared tortoises to all observations.  

The result was not affected by removing a potential source of user bias, showing that the original result is robust to some observational biases.  Of course, there will always be more sources of bias that could be analyzed and corrected for.  However, the fact that correcting for one source of bias didn't change the result makes me somewhat more confident that this result is directionally correct.

Conversely, the fact that I did find a large source of observer bias makes me wonder whether there are other large biases in iNat observation trends.  Without analyzing all sources of bias (why did reptiles change in 2017?) these results must remain clouded by potential uncertainties.  

The result was also not affected by which taxa I compared tortoises with, showing that the original result is robust to choice of comparison.  Tortoises appear to be declining, whether they are compared to all observations, all animals, amphibians, reptiles, insects, or birds.  While it is possible that one or more of these taxa are affected by observational bias, the fact that they all point in the same direction makes me more confident that this result is directionally correct and reflects an actual downward population trend.