DOI: 10.5061/dryad.4f4qrfjjf
title: Adaptive and non-adaptive convergent evolution in feather reflectance of Channel Islands songbirds

description: Convergent evolution is widely regarded as a signature of adaptation. But
 testing the adaptive consequences of convergent phenotypes is challenging,
 making it difficult to exclude non-adaptive explanations for convergence.
 Here, we combined feather reflectance spectra and phenotypic trajectory
 analyses with visual and thermoregulatory modeling to test the adaptive
 significance of dark plumage in songbirds of the California Channel
 Islands. By evolving dark dorsal plumage, island birds are generally less
 conspicuous to visual-hunting raptors in the island environment than
 mainland birds. Dark dorsal plumage also reduces the energetic demands
 associated with maintaining homeothermy in the cool island climate. We
 also found an unexpected pattern of convergence, wherein the most
 divergent island populations evolved greater reflectance of near-infrared
 radiation. However, our heat flux models indicate that elevated
 near-infrared reflectance is not adaptive. Analysis of feather
 microstructure suggests that island-mainland differences are related to
 coloration of feather barbs and barbules rather than their structure. Our
 results indicate that adaptive and non-adaptive mechanisms interact to
 drive plumage evolution in this system. This study sheds light on the
 mechanisms driving the association between dark color and wet, cold
 environments across the tree of life, especially in island birds.
description: # Adaptive and non-adaptive convergent evolution in feather reflectance of
 Channel Islands songbirds
 [https://doi.org/10.5061/dryad.qrfj6q5nk](https://doi.org/10.5061/dryad.qrfj6q5nk) This dataset contains museum specimen information, raw dorsal and ventral feather reflectance values, heat flux simulation outputs, and visual modeling outputs. ## Description of the data and file structure *bird_database_linked_dryad.csv*: * **arctos_id** = specimen ID in arctos database * **genus** = abbrevation of genus + species name * **arctos_name** = scientific name in arctos database * **mvz_name** = name of specimen in MVZ database * **mvz_specimen_id** = specimen ID in MVZ database * **common_name** = common name of species * **original_file_id_name** = abbreviated genus + species name * **file_id_name** = abbreviated genus + species name * **spp** = abbreviated genus + species name * **file_file_numbers** = unique numbers associated with files from each specimen * **file_ID** = ID given to file set from each specimen * **id** = ID given to each specimen * **MY_ID** = ID given to each specimen in author's notes * **measurement_ID** = ID given to set of measurements taken from each sample * **side** = surface of the bird measured (dorsal or ventral) * **locale** = location of specimen collection (island or mainland) * **sex** = biological sex of specimen (male or female) * **county** = county that specimen was collected in * **date** = date of specimen collection * **year** = year specimen was collected * **month** = month specimen was collected * **molt_time** = was specimen collected during potential time of molt (based on phenology information in Billerman et al. 2022)? * **breeding** = was specimen collected during breeding season (1 = yes; 0 = no)? * **lat** = latitude specimen was collected at * **long** = longitude specimen was collected at. Cells that contain "n/a" are from specimens lacking that specific information. *contrast_results.csv*: this file contains the output from coldist analyses in Pavo. * **species** = common name of species * **population** = location of specimen collection (island or mainland) * **estimate** = noise-weighted Euclidean distance between bird and environment * **lower** = lower 95% confidence interval of estimate * **upper** = upper 95% confidence interval of estimate * **surface** = dorsal or ventral surface of bird * **vision** = visual model used (violet- or uv-sensitive) * **contrast** = type of visual contrast modeled (achromatic or chromatic). *hourly_thermoregulatory_costs.csv*: this file contains the Endoscape heat flux simulation outputs. * **type** = endoscape model type (bird in this case) * **species** = common name of species * **feather_phenotype** = mainland or island feather phenotype * **mass_phenotype** = mainland or island body mass phenotype * **activity_pattern** = diel activity pattern of organism (diurnal in this case) * **site** = location where heat flux simulations were modeled (island or mainland) * **wind** = environmental wind speed (m/s) * **posture** = posture of organism relative to sun (degrees) * **fiber_density** = the density of insulation fibers (fibers cm^-2) * **shade** = percentage of time organism spends in shade * **feather_depths** = depth of plumage (m) * **orientation** = orientation of organism relative to sun (degrees) * **shape** = shape of organism, which describes changes in organism characteristic dimension (m) * **mass** = body mass of organism (g) * **surface_area** = surface area of organism (m) * **doy** = day of year * **hour** = hour of day * **Srad** = solar radiation (W*m^-2) * **Rabs** = radiation absorbed from sun, sky, and ground (W*m^-2) * **Remi** = radiation emitted by organism (W*m^-2) * **Tes** = standard operative temperature (C) * **Tref** = ambient air temperature (C) * **soil_ref** = is organism above or below soil? * **Te_dorsal** = operative temperature of dorsal surface (C) * **Hi_d** = organsim effective conductance (W^-1C^-1) * **Ri_d** = organism radiative conductance (W^-1C^-1) * **Ks** = skin conductance of animal (W^-1C^-1) * **Kf_d** = feather conductance (W^-1C^-1) * **Ksfi_d** = conductance of skin and feathers in series (W^-1C^-1) * **Ke_d** = effective conductance of animal (W^-1C^-1) * **Ke_theoretical** = theoretical conductance of organism (W^-1C^-1) * **Tb** = body temperature (Celsius) * **Qgen** = net sensible heat flux from organism (W) * **Cooling_costs_avg** = average energetic cooling costs (J) * **Cooling_costs_sum** = sum of energetic cooling costs (J) * **Heating_costs_avg** = average energetic heating costs (J) * **Heating_costs_sum** = sum of energetic heating costs (J). *raw_reflectance_dorsal_averaged.csv* and *raw_reflectance_ventral_averaged.csv*: these files contain raw reflectance values from 350 to 2500 nm for each bird specimen (each cell is the proportion of light reflected off of the organism at a particular wavelength). Reflectance values have been averaged across 5 feather patches on either the dorsal or ventral surfaces. This file also includes individual ID (**Individual**), genus name (**Species**), and population (mainland or island; **Locality**). *sites_Endoscape.csv*: this file contains hourly minimum and maximum temperatures for Santa Cruz Island and the California mainland used in the heat flux simulations. * **site_id** = island or mainland location * **site** = island or mainland location * **latitude** = latitude of location * **longitude** = longitude of location * **elevation** = elevation (m) of location * **tminx** = minimum temperature at hour of day x * **tmaxx** = maximum temperature at hour of day x. *bird_properties.csv*: this file contains biophysical characteristics of island and mainland bird populations used in the heat flux simulations. * **species** = scientific name * **spp_concat** = genus and specific epithet merged * **code** = four letter code of common name * **abbrev** = abbreviation of scientific name * **common_name** = common name of organism * **feather_phenotype** = mainland or feather phenotype * **mass_phenotype** = mainland or feather body mass phenotype * **type** = type of endoscape model to be used (bird in this case) * **activity_pattern** = general diel activity of organism (all diurnal in this case) * **mass** = body mass (g) * **density_of_fibers** = the density of insulation fibers (fibers cm^-2) * **shortwave_absorptance_dorsal** = the shortwave absorptance of the dorsal surface of animal (expressed as proportion of total) * **shortwave_absorptance_ventral** = the shortwave absorptance of the ventral surface of animal (expressed as proportion of total) * **longwave_absorptance** = absorptance of the animal to longwave radiation (expressed as proportion of total) * **insulation_conductivity** = thermal conductivity of insulation (W m^-1 K^-1) * **insulation_length_dorsal** = the length of the dorsal insulation from the tip of the feather to the base near the skin (m) * **insulation_length_ventral** = the length of the ventral insulation from the tip of the feather to the base near the skin (m) * **insulation_depth_dorsal** = the depth of the dorsal insulation from the outer surface of the insulation to the skin (m) * **insulation_depth_ventral** = the depth of the ventral insulation from the outer surface of the insulation to the skin (m) * **length** = length of animal, not including tail feathers (m) * **width** = width of the animal (m) * **height** = height of the animal (m) * **emissivity** = emissivity of the animal * **physiology_known** = runs an extra set of simulations that incorporates empirical relationships related to water loss, metabolism, and body = temperature (0 = unknown; 1 = known); recommended to set to 0 * **version** = used for downstream data organization if simulations were run with known physiology; recommended to set to 'no_physiology' * **water threshold** = a user defined value for cooling costs that can determine when an organism seeks shade and ceases activity * **physiology_known_master** = redundant with physiology_known * **body_temperature_min** = normothermic body temperature of the animal (C) * **body_temperature_max** = the maximum body temperature of the animal (C) * **lower_critical_temperature** = the lower critical temperature of the animal, default set to 25C * **upper_critical_temperature** = the upper critical temperature of the animal, default set to 35C. ## Code/Software visual_modeling.txt: this file contains the R code used to run the visual models in the package pavo. RRPP_code.txt: this file contains the R code used to run the multivariate trajectory analyses in the package RRPP.