UAV-LiDAR and RGB Imagery Reveal Large Intraspecific Variation in Tree-Level Morphometric Traits across Different Pine Species Evaluated in Common Gardens
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Sites and Field Measurements
2.2. Remote Sensing Data Collection
2.3. Imagery Processing
RGB and LIDAR Preprocessing, Treetop Detection, and Crown Segmentation
2.4. LIDAR- and RGB-Derived Traits
2.5. Accuracy of Automatic Tree Detection and Validation of UAV-Derived Height and Trunk Diameter
2.6. Statistical Analyses
3. Results
3.1. Accuracy of Tree Detection
3.2. Validation with In Situ Measurements
3.3. Intraspecific Variability of In Situ Traits and of LiDAR- and RGB-Derived Traits
3.3.1. Black Pine
3.3.2. Aleppo Pine
3.4. Relationships between In Situ or UAV Traits and Climate at Populations’ Origin
3.4.1. Black Pine
3.4.2. Aleppo Pine
4. Discussion
4.1. Tree Segmentation Accuracy and Field Validation
4.2. Intraspecific Differentiation in Black Pine and Associations with Climate at Origin
4.3. Intraspecific Differentiation in Aleppo Pine and Associations with Climate at Origin
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Trait Abbreviation | Trait Description | Function/Formula | Valsaín | Valdeolmos | In Situ | LiDAR-Derived | RGB-Derived |
---|---|---|---|---|---|---|---|
Traits Related to Main Trunk | |||||||
h | Total tree height calculated from canopy height model | Zonal statistic, QGIS environment | X | X | X | X | X |
half h | Half of the total tree height | X | X | X | |||
dbh | Estimated diameter at breast height | Multilinear model (for UAV-derived dbh) for black pine [35] and Aleppo pine [36] | X | X | X | X | X |
Traits related to tree biomass | |||||||
Ws | Stem biomass | Allometric equation [37] | X | X | X | X | X |
Wb2-7 | Medium branches biomass | Allometric equation [37] | X | X | X | X | X |
Wb2 + n | Thin branches + needles biomass | Allometric equation [37] | X | X | X | X | X |
Wr | Root biomass | Allometric equation [37] | X | X | X | X | X |
Traits related to crown architecture | |||||||
CBH | Height of first living branch | Cubic smooth spline followed by calculation of first and second derivative | X | X | |||
CL | Total crown length | Total tree height minus CBH | X | ||||
CL Skew | Crown height skewness | skewness function, R environment | X | ||||
h Skew | Total height skewness | skewness function, R environment | X | X | X | ||
CVCL | Coefficient of variation of crown length point dispersion around the mean | Standard deviation CL divided by mean CL | X | X | X | ||
QCD | Crown height quartile coefficient of dispersion | Q1 − Q3/Q1 + Q3 | X | X | X | ||
CA | Crown area calculated from the canopy height model | Area function, QGIS | X | X | X | X | |
h:CA | Ratio between crown height and crown area | X | X | X | X | ||
WCS | Widest crown section | CHM derived tiles with the biggest area | X | ||||
HWCS | Height of widest crown section | X | X | X | |||
h:HWCS | Total tree height to height of widest crown section ratio | X | X | X | |||
half h:HWCS | Half tree height to height of widest crown section ratio | X | |||||
RI | Crown height rumple index | rumple_index function, R environment | X | X | X | ||
Traits related to crown volume | |||||||
Q99p | 99th percentile of crown’s points calculated from the point cloud | X | X | X | |||
Q75p | 75th percentile of crown’s points calculated from the point cloud | X | X | X | |||
Q50p | 50th percentile of crown’s points calculated from the point cloud | X | X | X | |||
Q99d | 99th percentile of crown’s points density calculated from the point cloud | X | X | X | |||
Q75d | 75th percentile of crown’s points density calculated from the point cloud | X | X | X | |||
Q50d | 50th percentile of crown’s points density calculated from the point cloud | X | X | X | |||
Cvol025 | Crown’s volume using an alpha value of 0.25 calculated from the point cloud | alpha shape function, R environment | X | X | X | ||
CH:Cvol025 | Ratio between crown height and crown volume | X | X | X | |||
3D025:2D | Ratio between Cvol025 to crown area | X | X | X |
In Situ | LiDAR-Derived Traits | RGB-Derived Traits | ||||||
---|---|---|---|---|---|---|---|---|
Traits | Effect | Num df | F Value | p > F | F Value | p > F | F Value | p > F |
Traits related to main trunk | ||||||||
h | Subs | 4 | 8.28 | <0.0001 | 8.15 | <0.0001 | 7.13 | <0.0001 |
Subs (Pop) | 16 | 1.70 | 0.0537 | 1.57 | 0.0828 | 1.70 | 0.0534 | |
half h | Subs | 4 | / | / | 4.16 | 0.0032 | / | / |
Subs (Pop) | 16 | / | / | 2.37 | 0.0037 | / | / | |
dbh | Subs | 4 | 6.19 | <0.0001 | 4.52 | 0.0017 | 4.48 | 0.0018 |
Subs (Pop) | 16 | 1.49 | 0.1103 | 1.21 | 0.2642 | 1.31 | 0.1942 | |
Traits related to tree biomass | ||||||||
Ws | Subs | 4 | 6.30 | <0.0001 | 5.55 | 0.0003 | 4.96 | 0.0008 |
Subs (Pop) | 16 | 1.53 | 0.0969 | 1.33 | 0.1854 | 1.42 | 0.1377 | |
Wb2-7 | Subs | 4 | 6.16 | 0.0001 | 4.49 | 0.0018 | 4.21 | 0.0028 |
Subs (Pop) | 16 | 1.48 | 0.0117 | 1.18 | 0.2897 | 1.27 | 0.2213 | |
Wb2 + n | Subs | 4 | 6.16 | 0.0001 | 4.49 | 0.0018 | 4.21 | 0.0028 |
Subs (Pop) | 16 | 1.48 | 0.1159 | 1.18 | 0.2897 | 1.27 | 0.2213 | |
Wr | Subs | 4 | 6.05 | 0.0002 | 4.44 | 0.0020 | 4.07 | 0.0035 |
Subs (Pop) | 16 | 1.45 | 0.1270 | 1. | 0.3018 | 1.25 | 0.2339 | |
Traits related to crown architecture | ||||||||
CA | Subs | 4 | / | / | 2.70 | 0.0328 | 2.74 | 0.0309 |
Subs (Pop) | 16 | / | / | 0.89 | 0.5767 | 0.99 | 0.4757 | |
h:CA | Subs | 4 | / | / | 2.84 | 0.0265 | 3.20 | 0.0151 |
Subs (Pop) | 16 | / | / | 1.14 | 0.3281 | 1.45 | 0.1253 | |
CL | Subs | 4 | / | / | 9.70 | <0.0001 | / | / |
Subs (Pop) | 16 | / | / | 1.49 | 0.1120 | / | / | |
WCS | Subs | 4 | / | / | 2.94 | 0.0226 | / | / |
Subs (Pop) | 16 | / | / | 0.85 | 0.6219 | / | / | |
HWCS | Subs | 4 | / | / | 2.51 | 0.0447 | / | / |
Subs (Pop) | 16 | / | / | 2.30 | 0.0049 | / | / | |
h:HWCS | Subs | 4 | / | / | 2.19 | 0.0730 | / | / |
Subs (Pop) | 16 | / | / | 0.82 | 0.6563 | / | / | |
half h:HWCS | Subs | 4 | / | / | 2.53 | 0.0433 | / | / |
Subs (Pop) | 16 | / | / | 1.21 | 0.2694 | / | / | |
h Skew | Subs | 4 | / | / | 5.73 | 0.0003 | / | / |
Subs (Pop) | 16 | / | / | 1.89 | 0.0257 | / | / | |
CL Skew | Subs | 4 | / | / | 2.66 | 0.0349 | / | / |
Subs (Pop) | 16 | / | / | 1.74 | 0.0457 | / | / | |
QCD | Subs | 4 | / | / | 5.79 | 0.0002 | / | / |
Subs (Pop) | 16 | / | / | 1.20 | 0.2787 | / | / | |
RI | Subs | 4 | / | / | 14.88 | <0.0001 | / | / |
Subs (Pop) | 16 | / | / | 1.29 | 0.2118 | / | / | |
Traits related to crown volume | ||||||||
Q99p | Subs | 4 | / | / | 3.83 | 0.0055 | / | / |
Subs (Pop) | 16 | / | / | 1.21 | 0.2670 | / | / | |
Q99d | Subs | 4 | / | / | 2.86 | 0.0257 | / | / |
Subs (Pop) | 16 | / | / | 2.61 | 0.0013 | / | / | |
Q75d | Subs | 4 | / | / | 2.92 | 0.0234 | / | / |
Subs (Pop) | 16 | / | / | 2.58 | 0.0015 | / | / | |
Q50d | Subs | 4 | / | / | 2.92 | 0.0234 | / | / |
Subs (Pop) | 16 | / | / | 2.52 | 0.0019 | / | / | |
CVCL | Subs | 4 | / | / | 8.88 | <0.0001 | / | / |
Subs (Pop) | 16 | / | / | 1.18 | 0.2926 | / | / | |
Cvol025 | Subs | 4 | / | / | 4.98 | 0.0009 | / | / |
Subs (Pop) | 16 | / | / | 0.96 | 0.4994 | / | / | |
H:Cvol025 | Subs | 4 | / | / | 2.88 | 0.0250 | / | / |
Subs (Pop) | 16 | / | / | 1.11 | 0.3556 | / | / | |
3D025:2D | Subs | 4 | / | / | 7.82 | <0.0001 | / | / |
Subs (Pop) | 16 | / | / | 0.95 | 0.5152 | / | / |
Pinus Nigra | Pinus Halepensis | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
In Situ Traits | In Situ Traits | ||||||||||
Step | Variable | Partial R2 | F Value | p > F | Average Squared Canonical Correlation | Step | Variable | Partial R2 | F Value | p > F | Average Squared Canonical Correlation |
1 | dbh | 0.73 | 11.46 | 0.001 | 0.24 | 1 | Wb2-7 | 0.31 | 5.20 | 0.002 | 0.08 |
2 | h | 0.85 | 22.26 | <0.001 | 0.51 | ||||||
3 | Ws | 0.56 | 4.64 | 0.025 | 0.68 | ||||||
UAV–LiDAR-derived traits | UAV–LiDAR-derived traits | ||||||||||
1 | CVCL | 0.87 | 28.83 | <0.001 | 0.29 | 1 | Q75d | 0.29 | 4.76 | 0.003 | 0.07 |
2 | Cvol025 | 0.77 | 13.27 | <0.001 | 0.54 | 2 | CVCL | 0.31 | 5.24 | 0.002 | 0.15 |
3 | h | 0.70 | 8.61 | 0.003 | 0.60 | ||||||
UAV–RGB-derived traits | UAV–RGB-derived traits | ||||||||||
1 | h | 0.71 | 10.54 | 0.001 | 0.24 | 1 | Wb2-7 | 0.22 | 3.29 | 0.019 | 0.06 |
2 | h:CA | 0.69 | 8.89 | 0.002 | 0.46 | 2 | dbh | 0.14 | 1.91 | 0.126 | 0.09 |
3 | h | 0.19 | 2.54 | 0.053 | 0.13 |
In Situ | LiDAR-Derived Traits | RGB-Derived Traits | ||||||
---|---|---|---|---|---|---|---|---|
Trait | Effect | Num df | F Value | p > F | F Value | p > F | F Value | p > F |
Traits related to main trunk | ||||||||
h | Ecotype | 4 | 2.96 | 0.0196 | 4.22 | 0.0023 | 5.54 | 0.0002 |
Pop (Ecotype) | 47 | 2.41 | <0.0001 | 2.71 | <0.0001 | 2.65 | <0.0001 | |
half h | Ecotype | 4 | / | / | 4.22 | 0.0023 | / | / |
Pop (Ecotype) | 47 | / | / | 2.71 | <0.0001 | / | / | |
dbh | Ecotype | 4 | 6.28 | <0.0001 | 2.79 | 0.0261 | 2.49 | 0.0426 |
Pop (Ecotype) | 47 | 1.54 | 0.0152 | 1.81 | 0.0012 | 1.60 | 0.0088 | |
Traits related to tree biomass | ||||||||
Ws | Ecotype | 4 | 8.52 | <0.0001 | 5.09 | 0.0005 | 5.11 | 0.0005 |
Pop (Ecotype) | 47 | 1.46 | 0.0285 | 1.87 | 0.0007 | 1.73 | 0.0026 | |
Wb2-7 | Ecotype | 4 | 8.76 | <0.0001 | 5.32 | 0.0003 | 4.93 | 0.0007 |
Pop (Ecotype) | 47 | 1.38 | 0.0539 | 1.67 | 0.0048 | 1.68 | 0.0045 | |
Wb2 + n | Ecotype | 4 | 8.52 | <0.0001 | 5.06 | 0.0005 | 5.06 | 0.0005 |
Pop (Ecotype) | 47 | 1.44 | 0.0334 | 1.79 | 0.0015 | 1.69 | 0.0038 | |
Wr | Ecotype | 4 | 8.10 | <0.0001 | 3.72 | 0.0055 | 3.00 | 0.0182 |
Pop (Ecotype) | 47 | 1.44 | 0.0334 | 1.75 | 0.0021 | 1.47 | 0.0265 | |
Traits related to crown architecture | ||||||||
HWC | Ecotype | 4 | / | / | 3.68 | 0.0058 | / | / |
Pop (Ecotype) | 47 | / | / | 1.85 | 0.0009 | / | / | |
h Skew | Ecotype | 4 | / | / | 1.98 | 0.0967 | / | / |
Pop (Ecotype) | 47 | / | / | 1.59 | 0.0101 | / | / | |
CVCL | Ecotype | 4 | / | / | 4.30 | 0.0020 | / | / |
Pop (Ecotype) | 47 | / | / | 1.27 | 0.1126 | / | / | |
QCD | Ecotype | 4 | / | / | 1.81 | 0.1251 | / | / |
Pop (Ecotype) | 47 | / | / | 1.50 | 0.0206 | / | / | |
Traits related to crown volume | ||||||||
Q99d | Ecotype | 4 | / | / | 7.38 | <0.0001 | / | / |
Pop (Ecotype) | 47 | / | / | 1.33 | 0.0762 | / | / | |
Q75d | Ecotype | 4 | / | / | 7.27 | <0.0001 | / | / |
Pop (Ecotype) | 47 | / | / | 1.33 | 0.0757 | / | / | |
Q50d | Ecotype | 4 | / | / | 5.54 | 0.0002 | / | / |
Pop (Ecotype) | 47 | / | / | 1.31 | 0.0903 | / | / | |
3D025:2D | Ecotype | 4 | / | / | 1.92 | 0.1068 | / | / |
Pop (Ecotype) | 47 | / | / | 2.35 | <0.0001 | / | / |
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Lombardi, E.; Rodríguez-Puerta, F.; Santini, F.; Chambel, M.R.; Climent, J.; Resco de Dios, V.; Voltas, J. UAV-LiDAR and RGB Imagery Reveal Large Intraspecific Variation in Tree-Level Morphometric Traits across Different Pine Species Evaluated in Common Gardens. Remote Sens. 2022, 14, 5904. https://doi.org/10.3390/rs14225904
Lombardi E, Rodríguez-Puerta F, Santini F, Chambel MR, Climent J, Resco de Dios V, Voltas J. UAV-LiDAR and RGB Imagery Reveal Large Intraspecific Variation in Tree-Level Morphometric Traits across Different Pine Species Evaluated in Common Gardens. Remote Sensing. 2022; 14(22):5904. https://doi.org/10.3390/rs14225904
Chicago/Turabian StyleLombardi, Erica, Francisco Rodríguez-Puerta, Filippo Santini, Maria Regina Chambel, José Climent, Víctor Resco de Dios, and Jordi Voltas. 2022. "UAV-LiDAR and RGB Imagery Reveal Large Intraspecific Variation in Tree-Level Morphometric Traits across Different Pine Species Evaluated in Common Gardens" Remote Sensing 14, no. 22: 5904. https://doi.org/10.3390/rs14225904
APA StyleLombardi, E., Rodríguez-Puerta, F., Santini, F., Chambel, M. R., Climent, J., Resco de Dios, V., & Voltas, J. (2022). UAV-LiDAR and RGB Imagery Reveal Large Intraspecific Variation in Tree-Level Morphometric Traits across Different Pine Species Evaluated in Common Gardens. Remote Sensing, 14(22), 5904. https://doi.org/10.3390/rs14225904