Co-occurrence and abundance of pollinators and pests in horticultural systems in Africa using an integrated Earth observation-based approach

Figures & data

Figure 1. Map of the study area comprising Gatanga, Kandara and Maragua sub-Counties in Murang’a County, Kenya, with overlaid sampled avocado farms, elevation and other surface features.

Figure 2. Flow diagram of the approach adopted for the species distribution modelling, co-occurrence analysis, and species abundance modelling of avocado pollinators, flower visitors and pests. ASCII = American Standard Code for Information Interchange; MaxEnt = maximum entropy.

Table 1. Summary of the vegetation indices used in the mapping of cropping patterns and non-croplands, as adopted from Aduvukha et al. (2021).

No.	Index	Formula	Reference
1	Atmospherically resistant vegetation index-2 (ARVI2)	$-0.18+1.17\ast \left(\frac{\mathit{NIR}-\mathit{Red}}{\mathit{NIR}+\mathit{Red}}\right)$	(Kaufman and Tanre 1992)
2	Enhanced vegetation index (EVI)	$2.5\ast \frac{\mathit{NIR}-\mathit{Red}}{\mathit{NIR}+6\ast \mathit{Red}-7.5\ast \mathit{Blue}+1}$	(Ahamed et al. 2011)
3	Green normalized difference vegetation index (GNDVI)	$\frac{\mathit{NIR}-\mathit{Green}}{\mathit{NIR}+\mathit{Green}}$	(Gitelson, Kaufman, and Merzlyak 1996)
4	Modified soil adjusted vegetation index (MSAVI)	$\frac{\left(\mathit{NIR}-\mathit{Red}\right)\left(1+\mathit{L}\right)}{\mathit{NIR}+\mathit{Red}+\mathit{L}}$	(Qi et al. 1994)
5	Normalized difference vegetation index (NDVI)	$\frac{\mathit{NIR}-\mathit{Red}}{\mathit{NIR}+\mathit{Red}}$	(Tucker et al. 1979)
6	Normalized difference water index (NDWI)	$\frac{\mathit{NIR}-\mathit{SWIR}3}{\mathit{NIR}+\mathit{SWIR}3}$	(Gao 1996)
7	Soil adjusted vegetation index (SAVI)	$\left(\frac{\mathit{NIR}-\mathit{Red}}{\mathit{NIR}+\mathit{Red}+0.5}\right)\ast \left(1+0.5\right)$	(Huete 1988)
8	Two-band enhanced vegetation index (EVI2)	$2.5\ast \frac{\mathit{NIR}-\mathit{Red}}{\mathit{NIR}+2.4\ast \mathit{Red}+1}$	(Jiang et al. 2007)

Note: NIR= near-infrared band; L= 2*s*(NIR-Red) *(NIR-s* Red)/(NIR+Red), where s is the slope of the soil line from a plot of red versus near-infrared brightness values.

Table 2. Vegetation phenological variables that were used in mapping of cropping patterns and non-croplands, as adopted from Araya (2017) and Aduvukha et al. (2021).

No.	Phenological variable	Definition of the NDVI curve and physiological description
1	Onset_value	The NDVI value at the start of the growth (seedling growth stage)
2	Onset_time	The time when the growth onset is achieved
3	Max_value	The maximum NDVI value in the season
4	Max_time	The time when the Max_value is attained (anthesis growth stage)
5	Offset_value	The NDVI value at the end of the season
6	Offset_time	The time when growth offset is attained (senescence growth stage)
7	LengthGS	The length of the growing season
8	BeforeMaxT	The length of time between onset and Max_value
9	AfterMaxT	The length of time between Max_value and offset
10	GreenUpSlope	The rate of increase in NDVI value between onset and offset
11	BrownDownSlope	The rate of decrease in NDVI value between Max_value and offset
12	TINDVI	The area under the NDVI curve between onset and offset
13	TINDVIBeforeMax	The area under the NDVI curve between onset and Max_value
14	TINDVIAfterMax	The area under the NDVI curve between Max_value and offset
15	TINDVIAsymmetry	The difference between TINDVIBeforeMax and TINDVIAfterMax

Table 3. The remote sensing datasets combination scenarios and number of variables for the classification of cropping patterns and non-croplands, as highlighted in Aduvukha et al. (2021).

Variable combination	Number of variables
Sentinel-2 bands only	40
Sentinel-2 bands and Sentinel-1	48
Sentinel-2 bands and vegetation indices	48
Sentinel-2 bands and vegetation phenology	55
Sentinel-2 bands, vegetation indices and Sentinel-1	56
Sentinel-2, vegetation indices and vegetation phenology	63
Sentinel-2, vegetation phenology and Sentinel-1	63
Sentinel-2, vegetation indices, vegetation phenology and Sentinel-1	71

Table 4. Normalized difference vegetation index (NDVI) of dry and wet seasons description and range, as described in Adan et al. (2021).

	NDVI range
NDVI intensity description	Dry season	Wet season
High	0.537–0.853	0.559–0.865
Medium	0.318–0.537	0.345–0.559
Low	<0.318	<0.345

Table 5. Predictor variables used in spatial distribution and abundance analysis of avocado pollinators, flower visitors, and pests.

Variable	Unit	Resolution	Year	Source
Average temperature	°C	1 km	1970–2000	(Fick and Hijmans 2017)
Precipitation	mm	1 km	1970–2000	(Fick and Hijmans 2017)
Solar radiation	kJ m^−2 day^−1	1 km	1970–2000	(Fick and Hijmans 2017)
Wind speed	m s^−1	1 km	1970–2000	(Fick and Hijmans 2017)
Relative humidity (morning)	%	10-arc minutes	1961 - 1990	(Kriticos et al. 2012)
Relative humidity (afternoon)	%	10-arc minutes	1961-1990	(Kriticos et al. 2012)
Elevation	m	1 km		(Fick and Hijmans 2017)
Slope	%rise	1 km	n/a	Derived from elevation
Hillshade	n/a	1 km	n/a	Derived from elevation
Aspect	degrees	1 km	n/a	Derived from elevation
Cropping pattern	n/a	10 m	2018	Aduvukha et al. (2021)

n/a=not applicable.

Table 6. Variables selected after performing multicollinearity analysis using the variance inflation factor (VIF) of a minimum of 10 for avocado pollinators, flower visitors, and pests.

	Variable	VIF <10
Avocado pollinators/Flower visitors	aspect	1.11
	cropping pattern	1.01
	hillshade	1.18
	precipitation	7.53
	morning relative humidity	5.52
	slope	1.34
	wind speed	3.43
Avocado pest	aspect	1.10
	cropping pattern	1.12
	hillshade	1.16
	precipitation	4.07
	afternoon relative humidity	2.72
	slope	1.24
	solar radiation	8.69
	wind speed	4.14

Figure 3. Map of cropping pattern and non-croplands in Kandara, Maragua and Gatanga sub-Counties, Murang’a County, Kenya (Aduvukha et al. 2021).

Figure 4. Mean area under the curve (AUC) to two decimal places for predicting spatial distribution probability of (a) Apis mellifera, (b) Hymenoptera excluding A. mellifera, (c) Syrphidae (d) Calliphoridae (e) Bactrocera dorsalis, and (f) Thaumatotibia leucotreta.

Table 7. Contribution (%) of predictor variables to Apis mellifera, Hymenoptera excluding A. mellifera, Syrphidae, and Calliphoridae spatial distribution probability from maximum entropy (MaxEnt) models using the jackknife test.

Variable	Apis mellifera	Hymenoptera excluding A. mellifera	Syrphidae	Calliphoridae
Cropping pattern	26.60	39.40	57.80	9.50
Aspect	1.60	25.00	0.30	1.80
Hillshade	0.20	6.10	0.00	0.10
Precipitation	28.60	7.20	33.70	45.50
Morning relative humidity	4.40	0.10	0.10	0.30
Slope	0.50	1.40	0.00	1.10
Average temperature	0.00	2.00	0.00	0.00
Wind speed	38.10	18.70	8.00	41.70

Table 8. Contribution (%) of predictor variables to Bactrocera dorsalis and Thaumatotibia leucotreta spatial distribution probability from maximum entropy (MaxEnt) models using the jackknife test.

Variable	Bactrocera dorsalis	Thaumatotibia leucotreta
Cropping pattern	47.00	44.30
Aspect	1.50	0.70
Hillshade	0.00	1.10
Precipitation	1.90	3.80
Afternoon relative humidity	1.50	0.30
Slope	1.10	28.50
Solar radiation	1.60	0.40
Average temperature	42.90	19.80
Wind speed	2.60	1.00

Figure 5. Spatial distribution probability of avocado pollinators (a) Apis mellifera, (b) hymenoptera excluding Apis mellifera, and (c) Syrphidae; avocado flower visitors (d) Calliphoridae and avocado pests (e) Bactrocera dorsalis (f) Thaumatotibia leucotreta predicted using the maximum entropy (MaxEnt) model. The dark blue color indicates a low spatial distribution probability, while the red color represents a high spatial distribution probability. The resolution of the maps is 10 m in relation to spatial resolution of the cropping pattern variable.

Figure 6. Spatial distribution probability of co-occurrence of (a) avocado pollinators and flower visitors (b) avocado pests and (c) avocado pollinators, flower visitors and pests. The light green color indicates a low probability of co-occurrence spatial distribution, while the yellow and the red colors represent a medium and a high probability of co-occurrence, respectively. The resolution of the maps is 10 m in relation to spatial resolution of the cropping pattern variable.

Table 9. The abundance (n) and relative abundance (%) of avocado pollinators, flower visitors, and pests.

Avocado pollinators, flower visitors and pests	Abundance (n)	Relative abundance (%)
Apis mellifera	503	80.48
Syrphidae	58	9.28
Calliphoridae	64	10.24
Total	625	–
Bactrocera dorsalis	25,433	96.62
Thaumatotibia leucotreta	889	3.38
Total	26,322	–

Table 10. Summary of the relationship between the environmental variables and the abundance of avocado pollinators, flower visitors, and pests depicting the regression coefficient estimates and p-value (p ≤ 0.05).

Avocado pollinators, flower visitors and pests	Environmental variables	Estimate	p-value
Apis mellifera	(Intercept)	8.53	0.69
	aspect	−0.00	0.34
	hillshade	−0.01	0.24
	slope	0.03	0.19
	precipitation	0.01	0.60
	average temperature	−0.23	0.61
	morning relative humidity	−0.14	0.58
	wind speed	3.74	0.17
Syrphidae	(Intercept)	−32.40	0.33
	aspect	0.00	0.27
	hillshade	−0.00	0.71
	slope	0.02	0.49
	precipitation	0.02	0.92
	average temperature	0.48	0.49
	morning relative humidity	0.22	0.56
	wind speed	4.46	0.13
Calliphoridae	(Intercept)	5.31	0.80
	aspect	0.00	0.75
	hillshade	0.01	0.18
	slope	−0.24	0.40
	precipitation	−0.01	0.76
	average temperature	−0.32	0.53
	morning relative humidity	−0.13	0.59
	wind speed	3.66	0.31
Bactrocera dorsalis	(Intercept)	73.56	0.025*
	aspect	−0.00	0.00*
	precipitation	−0.38	<0.001*
	hillshade	0.04	4.15e-08*
	slope	0.04	0.12
	afternoon relative humidity	0.08	0.48
	average temperature	1.16	0.19
	wind speed	−1.99	0.20
	solar radiation	−0.00	0.22
Thaumatotibia leucotreta	(Intercept)	127	0.00**
	aspect	5.47e-04	0.62
	precipitation	−8.11e-02	0.43
	hillshade	−5.97e-04	0.95
	slope	−5.07e-02	0.13
	afternoon relative humidity	3.48e-02	0.83
	average temperature	1.29e+00	0.24
	wind speed	1.74e+00	0.34
	solar radiation	−7.68e-03	0.03*

*Significant variables (p ≤ 0.05).

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Data availability statement

All datasets presented in this study are included in the article and can be made available by the authors upon request.