DOI: 10.5061/dryad.tmpg4f55k
title: Habitat selection and refuge-use by a color polymorphic salamander reveal behavioral niche differences

description: Color polymorphic species provide an excellent opportunity to investigate
 the ecology and evolution of intraspecific niche differences. The
 red-backed salamander, Plethodon cinereus, is a fully terrestrial lungless
 salamander with two common color forms, striped and unstriped. Previous
 research suggests the morphs may be differentially adapted to surface and
 subsurface microhabitats, with the unstriped morph being more fossorial.
 This hypothesis predicts that the unstriped morph should be more sensitive
 to the risks of surface activity (e.g., thermal stress, dehydration,
 predation), and therefore be more selective than striped morphs when
 choosing soil surface microhabitats. To test this hypothesis, we
 experimentally manipulated leaf litter mass in small forest patches
 (~0.45m2). Leaf litter addition reduced soil temperatures, buffered
 against changes in air temperature, and likely provided physical
 protection from predators. Over three years, we found that unstriped
 adults responded positively to leaf litter addition, but striped adults
 did not. In addition, unstriped morphs spent significantly more time in
 protective refuges (opaque, moistened tubes) than striped morphs in
 laboratory assays. Taken together, the field and laboratory results
 support the hypothesis that the unstriped morph is more sensitive to the
 risks of surface activity, and therefore is more likely to be fossorial.
 This difference in microhabitat use, combined with spatiotemporal
 variation in leaf litter accumulation on the forest floor, may play an
 important role in the maintenance of the polymorphism.
description: Habitat selection by striped and unstriped red-backed salamanders
 was studied in a field experiment where leaf litter abundance on the
 forest floor was manipulated. Refuge-use by striped and
 unstriped red-backed salamanders was studied in a laboratory
 assay.
description: # Habitat selection and refuge-use by a color polymorphic salamander
 reveal behavioral niche differences
 [https://doi.org/10.5061/dryad.tmpg4f55k](https://doi.org/10.5061/dryad.tmpg4f55k) There are three data files, and four R Markdown files submitted as part of this manuscript. ## Description of the data and file structure The **"2018-2021 adults-BSM.csv"** file has data from the leaf litter experiment in the field. A few abbreviated headers are clarified here: "ACO" = artificial over object, LL = leaf litter treatment, "Sal" = salamander", "pres" = present. This file contains both count and presence/absence data (0/1) for the salamanders. In addition, blank cells represent cases where the data were not collected/available for some reason (described in manuscript). These should be treated as blanks/missing data, not as zeros. The **"Adult individuals 2018-2021.csv"** file is arranged differently, with every adult salamander from the field experiment occurring in its own row. Headings are self explanatory except for LL_tx, which is "Leaf litter treatment". Again, blank cells represent cases where the data were not collected/available for some reason (described in manuscript). These should be treated as blanks/missing data, not as zeros. The **"REFUGE experiment sp 22.csv"** file has data from the behavioral and feeding assays. *Columns A-G show data from the behavioral assay. The headers are as follows:* Individual = the individual salamander ID Morph = color morph, where U = unstriped and S= striped SUM COMPLETELY OUT = the number of observations where salamander was completely out of refuge SUM PARTIALLY OUT = the number of observations where salamander was partially out of refuge, i.e., head out of refuge, but tail in refuge SUM IN = The number of observations where salamander was completely in refuge SUMOUT2 = SUM COMPLETELY OUT + SUM PARTIALLY OUT TOTAL OBS = total number of observations across all three behavioral categories, which adds to 34. *Columns I-K show the results of the feeding assay, which was separate from the behavioral assay. Headers are as follows:* totfly = total umber of flies consumed. totflyprop = the proportion of flies eaten (out of 20 flies offered) logittrans = the logit transformation of totflyprop *Columns N-T show the feeding assay data re-arranged so that the foraging success of 18 salamanders with highest refuge-use could be compared to the foraging success of 18 salamanders with the lowest refuge use. The headers are as follows:* Individual = the individual salamander ID Morph_R = color morph, where U = unstriped and S= striped SUM IN_R = The number of observations where salamander was completely in refuge Refuge use = the 18 salamanders (independent of color morph) with the highest SUM IN_R values are assigned the categorical variable "High", and the 18 salamanders (independent of color morph) with the lowest SUM IN_R values are assigned the categorical variable "Low". totfly_R = total umber of flies consumed. totflyprop_R = the proportion of flies eaten (out of 20 flies offered) logittrans_R = the logit transformation of totflyprop *Columns V-AA show data used to investigate the repeatability of refuge-use behavior across trials. Headers are as follows:* Individual = the individual salamander ID Morph = color morph, where U = unstriped and S= striped T1_In = number of observations of the salamander completely "in" the refuge during Trial 1 T1_Out2 = number of observations of the salamander "out" + "partially out" of refuge during Trial 1 T234_In = number of observations of the salamander completely "in" the refuge, summed over Trials 2, 3, and 4 T234_Out2 = number of observations of the salamander "out" + "partially out" of refuge, summed over Trials 2, 3, and 4 ## Code/Software There are 4 R Markdown files. "Markdown-morph frequencies" shows code/analyses for the chi square and glmm investigating leaflitter, temperature, and moisture effects on presence of striped and unstriped morphs (data file "2018-2021 adults-BSM.csv") "Markdown-soil-temp-moist" shows code/analyses for the effect of the leaf litter manipulation on soil temperature and moisture (data file "2018-2021 adults-BSM.csv") "Markdown-comp-selected habitats-niche diffs & svl" has code/analyses for the comparison of microhabitats that were selected by striped and unstriped morphs. It also has comparison of body size (snout-to-vent-length) of striped vs unstriped adults (data file "Adult individuals 2018-2021.csv") "Markdown-refuge-experiment" had code/analyses for the behavioral assay in lab comparing refuge-use and foraging success of striped vs unstriped morphs (data file "REFUGE experiment sp 22.csv")