Bird reflectance in the ultraviolet to near infrared (NIR) and mid infrared (MIR)
Data files
May 29, 2026 version files 14.54 MB
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Final.BirdData.xlsx
14.53 MB
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README.md
6.72 KB
Abstract
Animal coloration has diverse functions such as camouflage, communication, thermoregulation, protection from UV damage and more, and can be shaped by selective pressures in the environment. Some climactic selective pressures are strong enough to produce consistent patterns in many species across large-scale geographic gradients. One pattern in endothermic animals is Gloger’s rule, which predicts that populations in hot, humid areas will be darker than those in cool, dry areas. This pattern has been demonstrated in several species across latitudinal gradients and is expected to relate to the selective effects of both local thermoregulatory pressures (e.g., shortwave radiation from sunlight, air temperatures) and humidity. However, shortwave radiation from sunlight extends beyond the visible spectrum [400-700 nm] into the near-infrared; thus, it has been shown that thermal pressures often result in changes in surface reflectance characteristics beyond the visible [e.g., 700-2500 nm]. Further, heat exchange with the environment extends into the mid-infrared, including MIR heat loss through the atmospheric transmission window [7.5 - 14 um]. Here, we examine both UV-NIR absorption and MIR emittance in five species of birds that have been shown to follow, or not follow, Gloger’s rule. We show that NIR absorption varies by species and population in ways that correspond to their habitat and thermoregulatory strategies. MIR emittance, by contrast, was very stable across both species and populations but differed across populations of Northern Bobwhites. We conclude by highlighting the importance of extending coloration research into the NIR and MIR and discussing important methodological details that researchers looking to explore animal infrared reflectance should consider when designing their studies. We hope to encourage additional research teams to consider infrared radiation in their view of animals’ phenotypic diversity and possible responses to thermal challenge.
Title of dataset: Final.BirdData.xlsx
Description of the data and file structure
For this sheet: NHReflectance
The row at the top contains all individuals' ID numbers, which can be associated with the correct species using the information in the 'BirdClimateData' sheet.
This sheet contains the spectral normal-hemispherical reflectance of each specimen from 0.3 μm - 20 μm. Each column corresponds to an individual bird specimen, numbered by its catalog number from the Natural History Museum of Los Angeles County. The bird species of Melospiza melodia, Colinus virginianus, and Cyanocitta stelleri are tabulated here, in order.
For the range of 0.3 μm - 1.1 μm, raw data from the UV-Vis spectrophotometer was processed using this formula:
$$R_{nh,\lambda}=\frac{S_{nh,\lambda}-D_{nh,\lambda}}{B_{nh,\lambda}-D_{nh,\lambda}} R_{std,\lambda}$$
where $$S_{nh,λ}$$ is the spectral normal-hemispherical reflectance signal measured by the UV-Vis spectrometer, $$D_{nh,\lambda}$$ is the dark signal, $$B_{nh,λ}$$ is the baseline spectral normal-hemispherical reflectance measurement, and $$R_{std,λ}$$ is the known standard normal-hemispherical reflectance of the specular reflection standard mirror (NIST certified STAN-SSH, Ocean Optics).
For the range of 1 μm - 20 μm, raw data from the FTIR was processed using this formula:
$$R_{nh,\lambda}=\frac{S_{nh,\lambda}-D_{nh,\lambda}}{B_{nh,\lambda}-D_{nh,\lambda}}$$
where $$S_{nh,λ}$$ is the spectral normal-hemispherical reflectance signal measured by the FTIR, $$D_{nh,\lambda}$$ is the dark signal, and $$B_{nh,λ}$$ is the baseline spectral normal-hemispherical reflectance measurement.
For the overlapping regions of 1 μm - 1.1 μm between the UV-Vis spectrophotometer and the FTIR using the InGaAs detector, data was linearly interpolated betweeen the 1 μm measurement of the UV-Vis spectrophotometer to the 1.1 μm measurement of the FTIR using the InGaAs detector, indicated by the highlighted yellow rows of 702 and 1744, respectively.
For the overlapping regions of 2 μm - 2.5 μm between the InGaAs and MCT detectors for the FTIR, only data from the MCT detector was used so that the data would be continuous from 2 μm to 20 μm.
For this sheet: NNReflectance
The row at the top contains all individuals' ID numbers, which can be associated with the correct species using the information in the 'BirdClimateData' sheet.
This sheet contains the spectral normal-normal reflectance of each specimen from 0.3 μm - 20 μm. Each column corresponds to an individual bird specimen, numbered by its catalog number from the Natural History Museum of Los Angeles County. The bird species of Melospiza melodia, Colinus virginianus, Cyanocitta stelleri, Bubo virginianus, and Corvus Corax are tabulated here, in order.
For the range of 0.3 μm - 0.7 μm, raw data from the reflectance probe was processed using this formula:
$$R_{nn,\lambda}=\frac{S_{nn,\lambda}-D_{nn,\lambda}}{B_{nn,\lambda}-D_{nn,\lambda}}$$
where $$S_{nn,λ}$$ is the spectral normal-normal reflectance signal measured by the reflectance probe, $$D_{nn,\lambda}$$ is the dark signal, and $$B_{nn,λ}$$ is the baseline spectral normal-normal reflectance measurement.
For the range 0.7 μm - 1 μm, there is no raw data that can be processed so a linear interpolation between the 0.7 μm measurement of the probe and the 1 μm measurement of the FTIR using the InGaAs detector was performed.
The data from 1 μm - 20 μm uses the normal-hemispherical data collected by the FTIR. For the overlapping regions of 2 μm - 2.5 μm between the InGaAs and MCT detectors for the FTIR, only data from the MCT detector was used so that the data would be continuous from 2 μm to 20 μm.
For the sheets: NHAbsorptanceCoefficients and NNAbsorptance Coefficients
These sheets contain the absorptance coefficients of each specimen, processed using the reflectance data. The titles "NH" and "NN" refer to which type of reflectance data was being used. Each column corresponds to an individual bird specimen, numbered by its catalog number from the Natural History Museum of Los Angeles County. Each row represents the range for which the absorptance coefficient is calculated: Total (meaning 0.3 μm - 20 μm), 300 nm - 700 nm, and 400 nm - 700 nm.
The formula used to calculate spectral absorptance, $$\alpha_\lambda$$ is:
$$\alpha_{\lambda} = 1 - \rho_{\lambda}$$
where $$\rho_\lambda$$ is spectral reflectance, and it is assumed the bird is completely opaque.
Then to calculate the absorptance coefficient, the following formula is used:
$$\alpha_{s} = \frac{\int_0{\infty}\alpha_{\lambda}G_{sol,\lambda}d\lambda}{\int_0{\infty}G_{sol,\lambda}d\lambda}$$
where $$G_{sol,\lambda}$$ is the spectral solar irradiation provided by the ASTM G-173 Spectra. This integral is truncated to the appropriate spectral ranges, as specified by the row.
For the sheet: EmittanceCoefficients
This sheet contains the emittance coefficients of each specimen, processed using the reflectance data. Each column corresponds to an individual bird specimen, numbered by its catalog number from the Natural History Museum of Los Angeles County. Each row shows the total emittance coefficient calculated using the total (meaning 0.3 μm - 20 μm) spectrum, as te birds are assumed to have a surface temperature of 313K.
From Kirchhoff's Law, we relate absorptance and emittance with:
$$\alpha_\lambda = \epsilon_\lambda$$
assuming that the bird is a diffuse emitter, assuming a optically rough surface so the emittance is independent of direction and that the feathers are dielectric.
The formula is used to calculate emittance:
$$\epsilon_{nh} = \frac{\int_0{\infty}\epsilon_{\lambda}I_{b,\lambda}(T_s)d\lambda}{\int_0{\infty}I_{b,\lambda}(T_s)d\lambda}$$
where $$I_{b.\lambda}$$ is the spectral blackbody emittance value at wavelength, $$\lambda$$, and bird surface temperature, $$T_s$$, assumed to be 313K. The integral is truncated to be between 0.3 μm - 20 μm.
For this sheet: BirdClimateData
This sheet contains the climate data associated with each specimen. The first four columns are the catalogged information regarding each individual bird specimen, listing its catalog number, trinomen, geograhic location, and gender from the Natural History Museum of Los Angeles County. The next seven columns refer to the most recent climate data obtained from the NOAA National Centers for Environmental Information’s (NCEI) Annual Climate Maps tool. The closest NOAA station that had both temperature and precipitation to the specimen's geographic location (Column 3) was used.