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FairyWrenData
No full textThe aim here is to quantify the effect of the group size an individual experiences in a given year on an integrative measure of fitness in two closely related fairy-wrens (Malurus elegans and M. cyaneus). Here, we combine six separate fitness components into one aggregate fitness proxy, using the concept of reproductive value. RV describes the expected contribution by individuals of a given age- or stage-class (here group size, sex and social status) to the future long-term growth of a population. We determined six fitness components: group productivity (number of fledglings produced per group per breeding season); within-group parentage (probability of paternity/maternity within own group); extra-group paternity (number of offspring sired by male in other social group); offspring sex-ratio; juvenile and adult survival; probability of obtaining dominant status; and the probability of increasing/decreasing the group size in the next year. Reproduction was split up into a within- and extra-group parentage component, as group members can parasitize the reproductive success of the dominant breeding pair. These six fitness components were integrated using reproductive values (RVs). RVs were calculated from population matrices, which were derived from a life cycle model. The next step was then to translate our life-cycle graph into a matrix population model, in which the matrix elements consist of the six fitness components in which we are interested. We used the statistical model estimates of each fitness component derived from the field data as input to the projection matrix, which allows—using standard matrix algebra— calculating the RVs of individuals as a function of their status, sex and group size
Experimental and field survey data for amphipods and leaf litter
No full textCODE:
The analysis for this manuscript can be performed using the R code contained in the R markdown file DEF_code_Little_et_al.Rmd.
GIS FILES:
There are 11 shapefiles in this folder which are used in the R code.
EXPERIMENTAL AND FIELD DATA:
There are eight CSV files of data which are described below. Variable names and metadata are described in the README.
GF_densitytreatments_weights.csv:
This file contains weights of Gammarus fossarum amphipods used in the experiments, in milligrams. Each row represents an individual amphipod.
DV_densitytreatments_weights.csv:
This file contains weights of Dikerogammarus villosus amphipods used in the experiments, in milligrams. Each row represents an individual amphipod.
GF_weight_and_survival_data_corrected.csv:
This file contains information on the survival of G. fossarum amphipods in the density experiment, as well as the mass loss of the leaves used in the experiment. Each row represents one experimental unit (mesocosm) used in the experiment.
DV_weight_and_survival_data.csv:
This file contains information on the survival of D. villosus amphipods in the density experiment, as well as the mass loss of the leaves used in the experiment. Each row represents one experimental unit (mesocosm) used in the experiment.
Combined_Data_amphipods.csv:
This file contains the amphipod abundance information from the April 2015 field surveys (also described in Little & Altermatt 2018 Proceedings B). Each row represents one sampling point.
Combined_Data_leaves.csv:
This file contains the benthic leaf litter and amphipod abundance information from four sampling bouts: April 2015, July 2015, November 2015, and January 2016 (also described in Little & Altermatt 2018 Proceedings B and Little & Altermatt 2018 Landscape Ecology). Each row represents one sampling point at one sampling bout.
leaf_litter_trap_cumulative.csv:
This file contains the data from leaf litter traps deployed between September and December, 2015, near Lake Constance (also presented in Little & Altermatt 2018 Landscape Ecology). Traps were first deployed on September 8, 2015, for all sites. Each row represents a sampling interval at a specific site; the traps were emptied and redeployed at each site several times over the course of the autumn, so each site has several rows of data. Rows contain information about the total amount of plant material accrued in the traps between the start of sampling and the end of a given sampling interval, that is, a cumulative total during the leaf drop period.
Land_use_in_buffers.csv:
This file contains data about the area (square meters) of three types of land cover in a 1-meter buffer on either side of the stream channels in each catchment. Land cover in the buffer zones was calculated from Swisstopo GIS layers in ArcMap as described in the methods section of the manuscript
Script for extracting DNA sequences flanked by MiFish primer-match regions.
No full textFor each of the primer pair, the region with the smallest hamming distance is found in each DNA sequence. If the smallest hamming distance is larger than 3, such sequences are ignored because existence of indels or many mutations is assumed in primer-match regions. For those ignored sequences, manual extraction needs to be conducted afterwards
Error Rate Simulation Code
No full textR script used to evaluate the statistical error rates of the z-score metho
Reflectance spectra
No full textReflectance spectra of the second egg-spot and the area above the egg-spots on the anal fin of male
Patient 3 HCV alignments
No full text6 HCV sequence alignments for patient 3 - Core and NS5B regions, 3 time sample
Vegetation transects
No full textPlant species found on vegetation transects. Species that have four letter identifiers are genus species in GESP format
lippy vs non lippy body shape
No full textA tps file that contains the raw landmark coordinates and associated ID's for all 777 specimens used for body shape analysis
Local and Landscape Site information
No full textSite-level ground cover and landscape composition data. Local variables: columns 4-8, landscape variables 9-13
