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Scaling between macro- to microscale climatic data reveals strong phylogenetic inertia in niche evolution in plethodontid salamanders


Farallo, Vincent; Muñoz, Martha; Uyeda, Josef; Miles, Donald (2020), Scaling between macro- to microscale climatic data reveals strong phylogenetic inertia in niche evolution in plethodontid salamanders, Dryad, Dataset,


Macroclimatic niches are indirect and potentially inadequate predictors of the realized environmental conditions that many species experience. Consequently, analyses of niche evolution based on macroclimatic data alone may incompletely represent the evolutionary dynamics of species niches. Yet, understanding how an organisms’ climatic (Grinnellian) niche responds to changing macroclimatic conditions is of vital importance for predicting their potential response to global change. In this study, we integrate microclimatic and macroclimatic data across 26 species of plethodontid salamanders to portray the relationship between microclimatic niche evolution in response to changing macroclimate. We demonstrate stronger phylogenetic signal in microclimatic niche variables than at the macroclimatic scale. Even so, we find that the microclimatic niche tracks climatic changes at the macroscale, but with a phylogenetic lag at million-year timescales. We hypothesize that behavioral tracking of the microclimatic niche over space and phenology generates the lag: salamanders preferentially select microclimates similar to their ancestral conditions rather than adapting with changes in physiology. We demonstrate that macroclimatic variables are weak predictors of niche evolution and that incorporating spatial scale into analyses of niche evolution is critical for predicting responses to climate change.


Two data files are included:

1) Includes mean and standard error values for 5 microclimatic conditions collected from 26 species of Plethodontid salamanders, including leaf litter depth, soil moisture, soil temperature, air temperature at 1 meter, and relatvie humidity at 1 meter (and one for logit transformed values of relative humidity).  This data set also include mean and standard error values of temperature and precipitation macroclimatic data extracted from Wordclim Ver. 2.0 (March-July) for both the sampling locations of our study and museum records used by Kozak and Wiens 2010.  


2) Includes direct measurements of 5 microclimatic conditions collected during random habitat surveys including leaf litter depth, soil moisture, soil temperature, air temperature at 1 meter, and relatvie humidity at 1 meter.  These habitat surveys were conducted in conjunction with time constraint surveys for salamander presence.  Each row contains the habitat measures for a single point (e.g., each row is for one single random habitat point and each survey had ~10 points) and identifying information about the survey along with the number of each of 26 species of salamanders found during that entire survey (I will mention it multiple times to be clear, the species counts in each row are for the individuals surveys (group of ~10 rows) and not indivudal habitat points (1 row). This is explained in more detail in the useage notes and in comments on the excel file itself. 


All excel files include additional comments to help explain any aspects of the data set that may be confusing. 

Usage Notes

For data set one, the data can easily be easily used to calculate half-life, lambda, and cont maps using trhe mean values and standard errors (when possible) using the functions and packages presented in the manuscript.  

For data set two, additional processoing is required.  Each row contains data that pertains to both a specific random habitat point and the entire survey as a while (~10 random points per habitat survey).  Data in each row that pertains to the entirety of a survey includes the site identifier, the date and time of the survey, latitude and longitude in WGS84 for the survey, and the results of the time contraint survey for the ENTIRE survey.  The data thsi is for only one specific points incluides the 5 indvidual habitat measurements.

I have included this as a comment in the excel file as well.  

The number of salamanders captured (Columns L through AK) are NOT for an individual point, but rather the particular survey as a whole (each survey includes ~10 random points).

For example for the Survey conducted at site HHM1 on 5/31/2014 at 10:19 PM there was 1 Plethodon cinereus encountered, but this is listed for each of the 10 random habitat points.

As another example for the survey at site MLH4 on 7/11/2014 at 8:39 PM there were 7 Eurycea wilderae and 1 Psuedotriton ruber encountered, and again this is listed for each random point during this survey (denoted by the site id, date, and time).

You can see in all cases, the number encountered is listed for each random point in the data set.  This was accounted for in our analyses as we were using the number encountered per survey or at a given site and not for each individual habitat  point. This was the easiest way to structure the data for all of our analyses.  Please contact me if you have further questions or want additional clarification.


National Science Foundation, Award: EF124848

Explorers Club

American Philosophical Society

Sigma Xi

Society for the Study of Evolution

Ohio University