Stable isotope analysis reveals shifts in diet of a breeding montane bird
Data files
Jan 03, 2024 version files 353.21 KB
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Deckel_Data.xlsx
305.06 KB
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README.md
3.87 KB
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swth.community.xlsx
18.06 KB
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swth.community2.xlsx
17.16 KB
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swth.whole.xlsx
9.06 KB
Abstract
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 (>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.
README: 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 (https://www.youtube.com/watch?v=\\\\_-Vjqg5pe3M).
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.