DOI: 10.5061/dryad.1zcrjdg06
title: Stable isotope analysis reveals shifts in diet of a breeding montane bird

description: Insectivorous breeding birds require access to high quality prey to
 produce a successful nest. A lack of suitable prey (e.g., low nutritional
 quality or low invertebrate availability) that fulfill energetic demands
 can negatively affect nestling growth and survival. In high elevation
 ecosystems (&gt;900 m), cooler and wetter climates can have negative
 influences on invertebrate availability which in turn can affect bird
 diets. Yet we lack studies of how diet composition changes over elevation
 gradients. Here, we assessed the diet of Swainson’s Thrush (Catharus
 ustulaus) within the White Mountains, New Hampshire using stable isotope
 analysis and DNA metabarcoding. We found that the proportion of
 detritivore arthropods in thrush diets increased with elevation, while the
 proportion of predatory arthropods and overall niche-width declined.
 Further, we show that high-elevation thrushes had diets that were
 different in composition, but similar in diversity to thrushes at
 low-elevation sites. Lepidoptera, araneae, and coleoptera were important
 diet items across all elevations, but increases in woodlice and ghost
 spiders contributed to familial-level differences in diet composition at
 high-elevation sites. This research suggests montane breeding birds may be
 consuming low quality prey (i.e., millipedes) at high elevation sites, due
 to either availability or preference. With considerations due to climate
 change, environmental contamination, and residual impacts on the diet and
 nutrient availability for breeding montane birds, understanding diet
 composition changes along environmental gradients can provide information
 on nutrient availability for species that breed in harsh climatic
 conditions. Future work on invertebrate availability and nutritional
 composition, daily energy expenditure, and dietary niche would help
 contribute to important context to conserving montane birds within these
 sensitive, high elevation systems.
description: # Description of the data and file structure This data describes how we
 used stable isotope mixing models (MixSIAR) to determine the proportion of
 dietary prey items within the diet of a montane breeding bird, the
 Swainson's Thrush along an elevation gradient. We collected prey
 items (invertebrates) and took blood samples of consumers across an
 elevational gradient to understand if dietary items changed with
 elevation. All helpful code is attached in the section below. Raw data
 used in code/analysis is all under "Deckel_Data" excel file,
 except for 3 .cvs files that were used in SIMPER dietary analysis
 (swth_community, swth_community2, and swth.whole). DNA metabarcoding data
 is labeled "SWTH_diversity" in the "Deckel_Data" excel
 file. \##Detailed data context description In the "Deckel_Data"
 excel file, below is a brief explanation for content and units used:
 -Weight (milligrams [mg]) -Bin symbolizes 1 of 4 elevational bins that
 invertebrates or samples were put into, depending on what elevation they
 were collected at. BEF = 200 meters; LOW = 500-700 meters; MED = 701 - 999
 meters; HIGH = 1000-1,200 meters. When there is a "19" or
 "21" next to the value, this indicates the year (19 = 2019, 21 =
 2021) -When Bin is given a numerical value (1-4) this corresponds with the
 above. 1= BEF, 2=LOW, 3=MED, 4=HIGH. -Time denotes the time of season
 samples were collected. NOTE: we didnt use time in the analysis because
 sample sizes were too small. 1 = late May/early June; 2 = mid June; 3 =
 late June/early July; 4 = mid July -c_method indicates the collection
 method used to collect that invertebrate order. LL = leaf litter samples,
 and SN = sweep net samples -d13cm is the delta 13 carbon mean for that
 group. -d13csd is the delta 13 carbone standard deviation for that group.
 -d15nm is the delta 15 nitrogen mean for that group -d15sd is the delta 15
 nitrogen standard deviation for that group -CN is the carbon to nitrogen
 ratio for that group -d13C is the delta 13 carbon for that group -d15N is
 the delta 15 nitrogen for that group -elev = elevation (in meters) -Group
 indicates what source group that invertebrate was pooled into. Det =
 detritivores, Herb = herbivores, and Pred = predators. Same for the
 "source" column. -Lowercase n indicates the sample size of that
 group. -Community: this column represents the year those samples were
 collected. -Classification: this corresponds with the "bin"
 above, and is a numerical value (1=BEF, 2=LOW, 3=MED, 4=HIGH) -iso1: this
 is the first isotopic value used for the SIBER niche analysis, and
 represents delta Carbon 13 -iso2: this is the second isotopic value used
 for this analysis, and represents delta Nitrogen 15 -individual: this is
 specifically included in the "SWTH_diet_by_individual2" and
 represents the individual Swainson's Thrush and everything that was
 picked up during the DNA metabarcoding analysis. -reads: indicates the
 number of reads picked up in the DNA metabarcoding analysis for that
 invertebrate in that individual's diet -count: number of individual
 invertebrates counted at that elevation. -NA: not applicable, or, values
 were not collected (for unknown reasons) for that individual. ##
 Sharing/Access Information Link to a publicly available video on how to
 interpret, write, or understand code from Brian Hayden can be found on
 YouTube (). ##
 Code/Software Code is attached as an rMarkdown file to this submission.
 Each section is labeled to help the reader understand the step by step
 process that was using for the analyses. The first ~800 lines of code are
 from the MixSIAR models and package. Line 815 - 1,000 are what was used to
 run SIBER isotopic niche width models, and finally, lines 1,004 to 1,048
 describe how we evaluated the diet diversity portion with the DNA
 metabarcoding analysis using SIMPER.