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Rarity is a more reliable indicator of land-use impacts on soil invertebrate communities than other diversity metrics

  1. Andrew Dopheide  Is a corresponding author
  2. Andreas Makiola
  3. Kate H Orwin
  4. Robert J Holdaway
  5. Jamie R Wood
  6. Ian A Dickie
  1. Manaaki Whenua - Landcare Research, New Zealand
  2. Bio-Protection Research Centre, Lincoln University, New Zealand
  3. Manaaki Whenua – Landcare Research, New Zealand
  4. Bio-Protection Research Centre, School of Biological Sciences, University of Canterbury, New Zealand
Research Article
Cite this article as: eLife 2020;9:e52787 doi: 10.7554/eLife.52787
18 figures, 6 tables, 1 data set and 1 additional file

Figures

Figure 1 with 3 supplements
Soil invertebrate community composition differs between land-use categories.

Non-metric MDS ordinations showing differences in the composition of soil invertebrate communities detected by DNA metabarcoding in five land-use categories, for overall communities, and for individual phyla with ≥ 100 OTUs. Ordinations are based on binary Jaccard distances.

Figure 1—source data 1

Results of PERMANOVA tests for differing soil invertebrate community composition, and ANOVA tests for differing multivariate homogeneity of sample dispersions, beta diversity, and phylogenetic beta diversity, between five land-use categories.

https://cdn.elifesciences.org/articles/52787/elife-52787-fig1-data1-v1.docx
Figure 1—figure supplement 1
Multivariate homogeneity of soil invertebrate communities detected in different land-use categories.

Boxplots of multivariate sample dispersion of soil invertebrate communities detected by DNA metabarcoding in five land-use categories, for overall soil invertebrate communities, and for individual phyla with > = 100 OTUs. Letters indicate significantly differing land-use categories according to post-hoc Tukey HSD tests, for groups with significant ANOVA differences.

Figure 1—figure supplement 2
Beta diversity of soil invertebrate communities detected in different land-use categories.

Boxplots of pairwise beta diversity of soil invertebrate communities detected by DNA metabarcoding in five land-use categories, for overall soil invertebrate communities, and for individual phyla with > = 100 OTUs. Letters indicate significantly differing land-use categories according to post-hoc Tukey HSD tests, for groups with significant ANOVA differences.

Figure 1—figure supplement 3
Phylogenetic beta diversity of soil invertebrate communities detected in different land-use categories.

Boxplots of pairwise phylogenetic beta diversity (UniFrac distance) of soil invertebrate communities detected by DNA metabarcoding in five land-use categories, for overall soil invertebrate communities, and for individual phyla with > = 100 OTUs. Letters indicate significantly differing land-use categories according to post-hoc Tukey HSD tests, for groups with significant ANOVA differences.

Figure 2 with 1 supplement
Distribution of the 1000 most abundant soil invertebrate OTUs across samples and land-use categories.

The proportional abundance and distribution among samples and five land-use categories of the 1000 most proportionally abundant soil invertebrate OTUs detected by DNA metabarcoding, showing that natural forest sites have more heterogeneous assemblages of soil invertebrate OTUs than agricultural sites. Samples are ordered on the x-axis by land-use category and increasing latitude.

Figure 2—figure supplement 1
Distribution of the 1000 most abundant soil invertebrate OTUs across samples and land-use categories, with samples ordered by compositional similarity.

The proportional abundance and distribution among samples and five land-use categories of the 1000 most proportionally abundant soil invertebrate OTUs detected by DNA metabarcoding, showing that natural forest sites have more heterogeneous assemblages of soil invertebrate OTUs than agricultural sites. The data is the same as in Figure 2, but the samples are ordered on the x-axis by OTU compositional similarity.

Figure 3 with 2 supplements
Biodiversity estimates for overall soil invertebrate communities detected in different land-use categories.

The biodiversity of soil invertebrate communities detected by DNA metabarcoding declines from forested to agricultural sites according to most metrics, with the clearest declines shown by rarity metrics. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Figure 3—source data 1

Results of ANOVA tests for differing soil invertebrate biodiversity between different land-use categories, according to six biodiversity metrics.

https://cdn.elifesciences.org/articles/52787/elife-52787-fig3-data1-v1.docx
Figure 3—figure supplement 1
Biodiversity estimates for soil arthropod groups in different land-use categories.

The biodiversity of most soil arthropod groups detected by DNA metabarcoding declines from natural forest to agricultural sites, with the most consistent patterns among groups shown by rarity metrics. ‘Other insects’ consists of all insect orders other than Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. ‘Non-mites’ consist of Araneae, Opiliones, and Pseudoscorpiones. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Figure 3—figure supplement 2
Biodiversity estimates for non-arthropod soil invertebrate phyla in different land-use categories.

The biodiversity of most non-arthropod soil invertebrate phyla detected by DNA metabarcoding tends to decline from natural forest to agricultural sites, although less clearly than for arthropod groups. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Figure 4 with 2 supplements
Phylogenetic biodiversity SES estimates for overall soil invertebrate communities detected in different land-use categories.

Phylogenetic biodiversity SES estimates for soil invertebrate communities detected by DNA metabarcoding tend to decline from natural forest to agricultural sites, with the clearest decline shown by phylogenetic rarity SES. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Figure 4—source data 1

Results of ANOVA tests for differing soil invertebrate biodiversity between different land-use categories, according to three phylogenetic biodiversity SES metrics.

https://cdn.elifesciences.org/articles/52787/elife-52787-fig4-data1-v1.docx
Figure 4—figure supplement 1
Phylogenetic biodiversity SES estimates for soil arthropod groups detected in different land-use categories.

Phylogenetic endemism SES of soil arthropod groups detected by DNA metabarcoding consistently declines from natural forest to agricultural sites, but phylogenetic diversity SES and mean pairwise distance SES do not. ‘Non-mites’ consist of Araneae, Opiliones, and Pseudoscorpiones. ‘Other insects’ consists of all insect orders other than Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Figure 4—figure supplement 2
Phylogenetic biodiversity standard effect size (SES) estimates for non-arthropod soil invertebrate phyla detected in different land-use categories.

Phylogenetic endemism SES of most non-arthropod soil invertebrate phyla detected by DNA metabarcoding declines from natural forest to agricultural sites, but phylogenetic diversity SES and mean pairwise distance SES do not. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Proportions of sample variance explained by land use according to different biodiversity metrics.

The proportions of sample variation (sum of squares) explained by land use were estimated for different biodiversity metrics by non-parametric bootstrapping, based on the combinations of biodiversity metric and soil invertebrate taxonomic group for which significant land-use differences were detected by ANOVA tests. Observed mean values and 95% confidence interval limits are indicated by orange and blue vertical bars, respectively.

Location and land-use category of 75 sample sites.

Site locations were randomly selected from a nationwide 8 km grid used for regular monitoring of native species and pests, excluding any that were >1000 m altitude and ensuring they were distributed throughout New Zealand. X- and y-axes represent longitude and latitude, respectively.

Appendix 1—figure 1
Taxonomic composition of invertebrate OTUs and sequences.

Phylum and class-level taxonomic composition of terrestrial invertebrate OTUs detected in soil samples from 75 sites distributed across five land-use categories.

Appendix 1—figure 2
A phylogeny of terrestrial invertebrate COI OTU sequences detected in soil samples from 75 sites distributed across five land-use categories.
Appendix 1—figure 3
Biodiversity estimates for overall soil invertebrate communities detected in different land-use categories, with species detected in a single site excluded.

Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Appendix 1—figure 4
Biodiversity estimates for soil arthropod groups in different land-use categories, with species detected in a single site excluded.

‘Other insects’ consists of all insect orders other than Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera. ‘Non-mites’ consist of Araneae, Opiliones, and Pseudoscorpiones. Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Appendix 1—figure 5
Biodiversity estimates for non-arthropod soil invertebrate phyla in different land-use categories, with species detected in a single site excluded.

Diamonds and whiskers represent mean values ± standard errors, with individual data points represented by circles. ANOVA test statistics and trend splines are shown for cases with statistically significant biodiversity differences among land-use categories, with letters indicating differences between land-use categories detected by post-hoc Tukey HSD tests.

Appendix 1—figure 6
Patterns of environmental variables across five land-use categories.
Appendix 1—figure 7
Richness correlations between different taxonomic groups.

Numbers indicate Pearson correlation coefficients. Ellipse shape and colour represent the magnitude of correlations with p-values≤0.05.

Appendix 1—figure 8
Effective species number correlations between different taxonomic groups.

Numbers indicate Pearson correlation coefficients. Ellipse shape and colour represent the magnitude of correlations with p-values≤0.05.

Appendix 1—figure 9
Rarity correlations between different taxonomic groups.

Numbers indicate Pearson correlation coefficients. Ellipse shape and colour represent the magnitude of correlations with p-values≤0.05.

Appendix 1—figure 10
Phylogenetic diversity correlations between different taxonomic groups.

Numbers indicate Pearson correlation coefficients. Ellipse shape and colour represent the magnitude of correlations with p-values≤0.05.

Appendix 1—figure 11
Phylogenetic rarity correlations between different taxonomic groups.

Numbers indicate Pearson correlation coefficients. Ellipse shape and colour represent the magnitude of correlations with p-values≤0.05.

Appendix 1—figure 12
Mean pairwise distance correlations between different taxonomic groups.

Numbers indicate Pearson correlation coefficients. Ellipse shape and colour represent the magnitude of correlations with p-values≤0.05.

Tables

Key resources table
Reagent type
(species) or resource
DesignationSource or referenceIdentifiersAdditional
information
Sequence-based reagentmICOIintFDOI:10.1186/1742-9994-10-34GGWACWGGWTGAACWGTWTAYCCYCC
Sequence-based reagentHCO2198PMID:7881515TAAACTTCAGGGTGACCAAAAAATCA
Commercial assay or kitNucleoSpin Tissue kitMacherey-Nagel740741.4
Software, algorithmcutadapthttps://github.com/marcelm/cutadaptv 1.11
Software, algorithmUSEARCHhttps://www.drive5.com/usearch/v 9.0.2132_i86linux32
Software, algorithmVSEARCHhttps://github.com/torognes/vsearchv 2.4.0
Software, algorithmRhttps://www.r-project.org/v 3.52
Software, algorithmphylo.endemismhttps://davidnipperess.blogspot.com/2012/07/phyloendemism-r-function-for.html
Appendix 1—table 1
Results of ANOVA tests for significant derived land-use rank (DLUR) trends for overall soil invertebrate communities and each biodiversity metric.
MetricTermDfSum Sq.Mean Sq.F stat.R2P
RichnessDLUR133428.0733428.078.180.110.006
Residuals67273678.564084.750.89
Effective SpeciesDLUR11163.401163.404.660.070.034
Residuals6716728.67249.680.93
RarityDLUR125771.7425771.7431.940.32<0.001
Residuals6754061.04806.880.68
Phylogenetic DiversityDLUR11234.541234.5411.170.140.001
Residuals677404.70110.520.86
Phylogenetic RarityDLUR1311.22311.2231.710.32<0.001
Residuals67657.649.820.68
Mean Pairwise DistanceDLUR10.000.000.990.010.324
Residuals670.110.000.99
Phylogenetic Diversity SESDLUR125.6325.635.620.080.021
Residuals67305.464.560.92
Phylogenetic Rarity SESDLUR1549.79549.7948.950.42<0.001
Residuals67752.5611.230.58
Mean Pairwise Distance SESDLUR111.1611.163.280.050.075
Residuals67228.003.400.95
Appendix 1—table 2
Results of mixed-model ANOVA tests for derived land-use rank (DLUR), land-use category (LCAT), and taxonomic group differences and interactions for each biodiversity metric.
MetricTermDfSum sq.Mean sq.F stat.P
RichnessDLUR1277.45277.457.740.007
LCAT3205.3568.451.910.137
Group1615737.52983.6027.43<0.001
DLUR:Group161014.9163.431.770.031
LCAT:Group482425.3750.531.410.037
Effective SpeciesDLUR166.4566.459.280.003
LCAT336.9312.311.720.173
Group163000.93187.5626.19<0.001
DLUR:Group16155.719.731.360.155
LCAT:Group48293.706.120.850.749
RarityDLUR1222.86222.8624.71<0.001
LCAT317.235.740.640.594
Group163082.62192.6621.36<0.001
DLUR:Group16421.7926.362.92<0.001
LCAT:Group48318.826.640.740.908
Phylogenetic DiversityDLUR112.9712.9712.830.001
LCAT34.731.581.560.208
Group16520.0332.5032.14<0.001
DLUR:Group1662.753.923.88<0.001
LCAT:Group4888.351.841.82<0.001
Phylogenetic RarityDLUR14.144.1431.77<0.001
LCAT30.280.090.720.543
Group1638.742.4218.56<0.001
DLUR:Group1610.120.634.85<0.001
LCAT:Group486.940.141.110.288
Mean Pairwise DistanceDLUR10.210.212.870.096
LCAT30.210.070.950.421
Group1619.111.1916.40<0.001
DLUR:Group162.930.182.510.001
LCAT:Group484.200.091.200.169
Appendix 1—table 3
Results of ANOVA tests for effects of spatial attributes (latitude and altitude) and land-use category on overall invertebrate community biodiversity metrics.
MetricTermDfSum Sq.Mean Sq.F stat.R2P
RichnessLatitude179.4979.490.020.0000.882
Altitude172529.2872529.2820.190.236<0.001
Land use411761.722940.430.820.0380.518
Residuals62222736.153592.520.725
Effective SpeciesLatitude1283.47283.471.190.0160.280
Altitude12241.172241.179.410.1250.003
Land use4597.76149.440.630.0330.645
Residuals6214769.66238.220.825
RarityLatitude1465.12465.120.600.0060.443
Altitude117387.7417387.7422.330.218<0.001
Land use413699.463424.874.400.1720.003
Residuals6248280.46778.720.605
Phylogenetic DiversityLatitude10.750.750.010.0000.933
Altitude11740.881740.8816.780.202<0.001
Land use4464.28116.071.120.0540.356
Residuals626433.33103.760.745
Phylogenetic RarityLatitude12.962.960.300.0030.586
Altitude1164.59164.5916.680.170<0.001
Land use4189.5747.394.800.1960.002
Residuals62611.749.870.631
Mean Pairwise DistanceLatitude10.000.000.390.0060.536
Altitude10.000.000.680.0100.411
Land use40.010.001.410.0820.241
Residuals620.100.000.902
Appendix 1—table 4
Results of ANOVA tests for effects of the first three components of a PCA on environmental covariates, plus land-use category, on overall invertebrate community biodiversity metrics.

A PCA was carried out on spatial (latitude and altitude) and soil chemistry variables (pH, C, N, C:N ratio, Olsen P, Total P, Ca, Mg, K, Na, cation exchange capacity, base saturation), of which the first three components explained 70.25% of variation.

MetricTermDfSum Sq.Mean Sq.F stat.R2P
RichnessPC1112142.5712142.573.250.0400.076
PC2126135.3626135.367.000.0850.010
PC31414.99414.990.110.0010.740
Land use440528.7010132.182.710.1320.038
Residuals61227885.013735.820.742
Effective SpeciesPC11497.15497.152.020.0280.161
PC21618.84618.842.510.0350.118
PC3111.1911.190.050.0010.832
Land use41725.81431.451.750.0960.151
Residuals6115039.07246.540.841
RarityPC1111905.8811905.8815.250.149<0.001
PC217487.417487.419.590.0940.003
PC31233.36233.360.300.0030.587
Land use412569.113142.284.020.1570.006
Residuals6147637.01780.930.597
Phylogenetic DiversityPC11503.99503.994.790.0580.032
PC21812.16812.167.720.0940.007
PC3110.9810.980.100.0010.748
Land use4897.84224.462.130.1040.087
Residuals616414.27105.150.742
Phylogenetic RarityPC11147.45147.4515.350.152<0.001
PC2198.3898.3810.240.1020.002
PC3110.3410.341.080.0110.304
Land use4126.5431.633.290.1310.017
Residuals61586.159.610.605
Mean Pairwise DistancePC110.0020.0021.4320.0210.236
PC210.0010.0010.4780.0070.492
PC310.0020.0020.9960.0150.322
Land use40.0060.0010.8630.0510.491
Residuals610.1050.0020.906
Appendix 1—table 5
Results of ANOVA tests for significant derived land-use rank (DLUR) trends for each taxonomic group and biodiversity metric.
MetricGroupTermDfSum Sq.Mean Sq.F stat.R2P
RichnessCollembolaDLUR128.93528.9352.6490.0390.108
Residuals65710.11010.9250.961
ColeopteraDLUR1335.849335.8499.9610.1310.002
Residuals662225.21033.7150.869
DipteraDLUR1615.926615.92618.0120.214<0.001
Residuals662256.83934.1950.786
HymenopteraDLUR1293.041293.04119.0240.229<0.001
Residuals64985.82315.4030.771
LepidopteraDLUR1476.785476.78519.3280.227<0.001
Residuals661628.08324.6680.773
HemipteraDLUR126.78826.7882.9200.0440.092
Residuals64587.1669.1740.956
other insectsDLUR174.53174.5318.9680.1230.004
Residuals64531.9098.3110.877
non-mitesDLUR145.41245.4122.9240.0430.092
Residuals651009.45415.5300.957
mitesDLUR10.2810.2810.0080.0000.930
Residuals662359.71935.7531.000
MalacostracaDLUR10.0440.0440.0460.0010.831
Residuals3432.7060.9620.999
myriapodsDLUR11.5181.5180.5550.0170.462
Residuals3287.4532.7330.983
AnnelidaDLUR167.63767.6374.4560.0650.039
Residuals64971.39315.1780.935
MolluscaDLUR10.2400.2400.0140.0000.906
Residuals641082.24516.9101.000
NematodaDLUR1110.491110.4910.5590.0080.457
Residuals6713243.798197.6690.992
PlatyhelminthesDLUR10.1750.1750.1950.0040.661
Residuals4943.9820.8980.996
RotiferaDLUR1201.555201.5550.6350.0100.428
Residuals6620954.136317.4870.990
TardigradaDLUR10.1770.1770.4690.0150.499
Residuals3011.3230.3770.985
Effective SpeciesCollembolaDLUR10.5300.5300.2730.0040.603
Residuals65126.2001.9420.996
ColeopteraDLUR113.59513.5953.8660.0550.053
Residuals66232.0673.5160.945
DipteraDLUR144.60244.60210.9670.1420.002
Residuals66268.4114.0670.858
HymenopteraDLUR121.82621.8264.6140.0670.036
Residuals64302.7684.7310.933
LepidopteraDLUR162.71962.71912.3840.1580.001
Residuals66334.2575.0640.842
HemipteraDLUR10.6660.6660.2810.0040.598
Residuals64151.7752.3710.996
other insectsDLUR11.1861.1860.8490.0130.360
Residuals6489.4621.3980.987
non-mitesDLUR16.5396.5391.9970.0300.162
Residuals65212.8053.2740.970
mitesDLUR11.0641.0640.2560.0040.615
Residuals66274.7164.1620.996
MalacostracaDLUR10.0070.0070.0360.0010.852
Residuals346.7540.1990.999
myriapodsDLUR10.6370.6370.6100.0190.441
Residuals3233.4141.0440.981
AnnelidaDLUR115.53015.5309.8020.1330.003
Residuals64101.4001.5840.867
MolluscaDLUR14.3294.3291.0210.0160.316
Residuals64271.4454.2410.984
NematodaDLUR116.68216.6820.5710.0080.452
Residuals671955.70129.1900.992
PlatyhelminthesDLUR10.0940.0940.3400.0070.563
Residuals4913.6220.2780.993
RotiferaDLUR1131.612131.6122.6150.0380.111
Residuals663321.55050.3270.962
TardigradaDLUR10.1740.1740.6300.0210.434
Residuals308.2910.2760.979
RarityCollembolaDLUR12.8912.8911.3310.0200.253
Residuals65141.1732.1720.980
ColeopteraDLUR1263.306263.30625.7860.281<0.001
Residuals66673.93010.2110.719
DipteraDLUR1422.250422.25051.6910.439<0.001
Residuals66539.1398.1690.561
HymenopteraDLUR1102.088102.08819.3990.233<0.001
Residuals64336.8095.2630.767
LepidopteraDLUR1256.685256.68536.2000.354<0.001
Residuals66467.9837.0910.646
HemipteraDLUR116.81616.8167.0480.0990.010
Residuals64152.6952.3860.901
other insectsDLUR141.82841.82814.9030.189<0.001
Residuals64179.6312.8070.811
non-mitesDLUR165.61465.61413.7570.175<0.001
Residuals65310.0204.7700.825
mitesDLUR137.89537.8955.6750.0790.020
Residuals66440.6986.6770.921
MalacostracaDLUR10.1260.1260.2410.0070.627
Residuals3417.7450.5220.993
myriapodsDLUR14.4264.4263.5110.0990.070
Residuals3240.3471.2610.901
AnnelidaDLUR147.96647.96617.0570.210<0.001
Residuals64179.9722.8120.790
MolluscaDLUR115.08115.0812.9920.0450.088
Residuals64322.5355.0400.955
NematodaDLUR1197.691197.6916.0080.0820.017
Residuals672204.66432.9050.918
PlatyhelminthesDLUR10.3330.3330.8540.0170.360
Residuals4919.1120.3900.983
RotiferaDLUR1157.017157.0172.0330.0300.159
Residuals665097.29277.2320.970
TardigradaDLUR10.3040.3041.1970.0380.283
Residuals307.6130.2540.962
Phylogenetic DiversityCollembolaDLUR10.7110.7111.5050.0230.224
Residuals6530.7180.4730.977
ColeopteraDLUR121.95221.9529.6880.1280.003
Residuals66149.5442.2660.872
DipteraDLUR140.10640.10619.3840.227<0.001
Residuals66136.5572.0690.773
HymenopteraDLUR121.84821.84812.7310.1660.001
Residuals64109.8301.7160.834
LepidopteraDLUR142.88042.88020.4420.236<0.001
Residuals66138.4462.0980.764
HemipteraDLUR15.7735.7733.8830.0570.053
Residuals6495.1471.4870.943
other insectsDLUR118.45618.45613.6310.176<0.001
Residuals6486.6521.3540.824
non-mitesDLUR113.61213.6127.0640.0980.010
Residuals65125.2591.9270.902
mitesDLUR17.9757.9752.9260.0420.092
Residuals66179.9242.7260.958
MalacostracaDLUR10.4680.4680.7550.0220.391
Residuals3421.0690.6200.978
myriapodsDLUR10.0020.0020.0050.0000.944
Residuals3215.6130.4881.000
AnnelidaDLUR110.57110.57113.5780.175<0.001
Residuals6449.8250.7790.825
MolluscaDLUR11.0721.0720.3790.0060.540
Residuals64181.1562.8310.994
NematodaDLUR10.0020.0020.0000.0000.985
Residuals67305.6604.5621.000
PlatyhelminthesDLUR11.3141.3142.0570.0400.158
Residuals4931.3050.6390.960
RotiferaDLUR15.4445.4442.6650.0390.107
Residuals66134.8092.0430.961
TardigradaDLUR10.1740.1741.5940.0500.217
Residuals303.2790.1090.950
Phylogenetic RarityCollembolaDLUR10.1650.1654.0700.0590.048
Residuals652.6400.0410.941
ColeopteraDLUR18.1518.15126.0350.283<0.001
Residuals6620.6630.3130.717
DipteraDLUR110.22110.22140.0130.377<0.001
Residuals6616.8590.2550.623
HymenopteraDLUR13.5363.53619.3190.232<0.001
Residuals6411.7130.1830.768
LepidopteraDLUR16.9316.93136.8770.358<0.001
Residuals6612.4050.1880.642
HemipteraDLUR10.4670.4674.0950.0600.047
Residuals647.3060.1140.940
other insectsDLUR12.7522.75215.7550.198<0.001
Residuals6411.1800.1750.802
non-mitesDLUR14.0734.07316.1590.199<0.001
Residuals6516.3840.2520.801
mitesDLUR12.3032.30311.0520.1430.001
Residuals6613.7520.2080.857
MalacostracaDLUR10.0210.0210.3140.0090.579
Residuals342.2360.0660.991
myriapodsDLUR10.2000.2004.7080.1280.038
Residuals321.3590.0420.872
AnnelidaDLUR12.0242.02425.9660.289<0.001
Residuals644.9890.0780.711
MolluscaDLUR11.4181.4183.5700.0530.063
Residuals6425.4240.3970.947
NematodaDLUR11.5741.5744.9430.0690.030
Residuals6721.3280.3180.931
PlatyhelminthesDLUR10.0000.0000.0020.0000.966
Residuals492.8730.0591.000
RotiferaDLUR10.7010.7013.0200.0440.087
Residuals6615.3210.2320.956
TardigradaDLUR10.0950.0953.5430.1060.070
Residuals300.8010.0270.894
Mean Pairwise DistanceCollembolaDLUR10.0280.0281.1930.0180.279
Residuals651.5020.0230.982
ColeopteraDLUR10.0020.0020.0970.0010.757
Residuals661.3380.0200.999
DipteraDLUR10.0050.0050.1270.0020.722
Residuals662.3750.0360.998
HymenopteraDLUR10.4210.4217.0010.0990.010
Residuals643.8500.0600.901
LepidopteraDLUR10.0020.0020.0640.0010.801
Residuals662.3250.0350.999
HemipteraDLUR10.1130.1131.2110.0190.275
Residuals645.9680.0930.981
other insectsDLUR10.0390.0390.6310.0100.430
Residuals643.9860.0620.990
non-mitesDLUR10.2110.2112.8250.0420.098
Residuals654.8470.0750.958
MitesDLUR10.4670.46713.8850.174<0.001
Residuals662.2220.0340.826
MalacostracaDLUR10.6890.6891.9570.0540.171
Residuals3411.9680.3520.946
myriapodsDLUR10.1370.1370.5980.0180.445
Residuals327.3180.2290.982
AnnelidaDLUR10.4360.4367.8050.1090.007
Residuals643.5740.0560.891
MolluscaDLUR10.2280.2282.5770.0390.113
Residuals645.6510.0880.961
NematodaDLUR10.0010.0010.1680.0030.683
Residuals670.5510.0080.997
PlatyhelminthesDLUR10.5400.5401.5280.0300.222
Residuals4917.3130.3530.970
RotiferaDLUR10.0070.00714.1780.177<0.001
Residuals660.0330.0010.823
TardigradaDLUR10.1340.1341.3770.0440.250
Residuals302.9100.0970.956

Data availability

Sequence data, metadata, processed data, bioinformatic processing and analysis code used to generate the results in the manuscript (with one exception, detailed below) are deposited in the Manaaki Whenua-Landcare Research DataStore, accessible at: https://doi.org/10.7931/w3j3-5v40. Our sample sites include many Māori and/or privately-owned locations. We have have removed site location details from our metadata out of respect for concerns of Māori and other landowners. The removal of site location details precludes recreation of the map of sample site locations (Figure 6) and analyses of latitude effects, but otherwise has no impact on our results.

The following data sets were generated

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