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1 Supporting Information for:

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3 Worldwide impacts of humans on genetic diversity

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5 Millette K.L, Fugère V., Debyser C., Greiner A., Chain F.J.J. and Gonzalez A. 6 7 This file includes: 8 9 Supplementary Results 10 Tables S1 and S2 11 Figures S1 and S2 12 13 Supplementary Results 14 15 Database characteristics and sampling biases 16 The majority of sequences in our dataset (70.5%) belong to insect (Fig. 1b). 17 Within classes, some underlying taxonomic biases are worth noting. The dataset consists of 18 about 68% Passeriformes sequences, with a single species ( blue chaffinch, 19 teydea), endemic to the , contributing the greatest number of sequences (~2.5% in 20 6 years) of all bird species. No species dominated the fish dataset, although three speciose orders 21 (Perciformes, Cypriniformes, and Characiformes) contributed about 44% of sequences. Diptera 22 (48%) and Lepidoptera (22%) sequences dominated the insect dataset, with an agricultural pest, 23 commonly known as the seedcorn maggot (Delia platura), overwhelmingly abundant at 24 approximately 2.5% of sequences (collected over 7 years throughout the Northern Hemisphere). 25 Coleoptera sequences were relatively rare (6.8%) given the proportion of insect species that 26 belong to this order. Mammals were overrepresented by bat species (61% Chiroptera), with 27 approximately 12.6% belonging to what appears to be a yearly, long-term (1989-2010) survey of 28 Seba’s short-tailed bat (Carollia perspicillata), great fruit-eating bat (Artibeus lituratus), and 29 dark fruit-eating bat (A. obscurus) in Central and South America. 30 The human density and land use intensity values of the grid cells from which our 31 sequences originate also reveal sampling biases (Fig. 1d,e). The sequences derive from grid cells

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32 with a higher average human density (279.09 ± 7.32 SE inhabitants/km2) than the global average 33 (37.87±0.03 SE inhabitants/km2) for 5’ grid cells. Moreover, our sequences are associated with 34 locations with relatively more intensive land use than is globally representative: the average 35 proportion of a 5’ grid cell area that is under heavy anthropogenic use for all grid cells in our 36 dataset (worldwide and across all years) is 17.5% (±0.003 SE), whereas this proportion is 26.8% 37 (±0.226 SE) for cells from which our sequences originate.

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Table S1. Coefficients (and standard error) of fixed effects from all models fitted in the stepwise model selection procedure described in the main text. ‘Step’ represents the model selection step, starting with a full model including all possible two-way interactions (step 1), which is then simplified until all remaining terms are statistically-significant (i.e., with a parameter confidence interval that does not overlap zero) or contribute to significant two-way interactions. Parameters from final models (step 3 or 4 depending on class and scale) are shown in Figure 3 of the main text. yr. = year. lat. = latitude; long. = longitude; LU = land use intensity; HD = human density. Colons denote two-way interactions. scale class step yr lat long LU HD yr:lat yr:long yr:LU yr:HD lat:long lat:LU lat:HD long:LU long:HD LU:HD 0.08 mammals 1 0.05 -0.28 -0.03 0.01 -0.08 0.06 0.02 -0.11 -0.02 0.02 -0.08 0.17 -0.02 0.03 0.02 (0.04) (0.05) (0.06) (0.06) (0.06) (0.04) (0.04) (0.05) (0.05) (0.04) (0.04) (0.04) (0.05) (0.05) (0.03) 0.08 mammals 2 0.07 -0.26 0 0 -0.04 -0.12 0.11 (0.04) (0.05) (0.05) (0.04) (0.05) (0.03) (0.03) 0.08 mammals 3 0.07 -0.26 0 -0.04 -0.12 0.11 (0.04) (0.05) (0.04) (0.05) (0.03) (0.03) 0.08 1 0.12 -0.05 0.01 -0.14 0.13 0 0.04 0.08 -0.08 0 (0.05) -0.06 0 0.02 0 (0.05) -0.04 (0.05) (0.05) (0.06) (0.06) (0.06) (0.05) (0.04) (0.05) (0.05) (0.06) (0.06) (0.05) (0.04) 0.08 birds 2 0.14 -0.05 -0.01 -0.16 0.11 (0.05) (0.05) (0.05) (0.06) (0.06) 0.08 birds 3 0.17 -0.09 (0.04) (0.04) 0.08 fishes 1 0.06 -0.17 -0.02 0.01 0.09 0.05 0.01 -0.01 -0.06 0.07 0.05 -0.05 0.05 0.07 -0.01 (0.04) (0.05) (0.05) (0.05) (0.05) (0.04) (0.04) (0.04) (0.04) (0.04) (0.05) (0.05) (0.05) (0.05) (0.04) 0.08 fishes 2 0.08 -0.18 -0.03 0.01 0.08 (0.03) (0.05) (0.05) (0.04) (0.05) 0.08 fishes 3 0.08 -0.17 (0.03) (0.04) 0.08 insects 1 -0.02 -0.06 0.01 -0.05 -0.01 -0.05 0.01 -0.03 -0.01 -0.05 0.08 -0.04 0.04 -0.03 0 (0.02) (0.03) (0.03) (0.03) (0.03) (0.02) (0.02) (0.02) (0.02) (0.02) (0.03) (0.04) (0.02) (0.02) (0.02) 0.08 insects 2 -0.02 -0.07 0 -0.04 -0.03 -0.05 -0.05 0.05 0.03 (0.02) (0.03) (0.02) (0.02) (0.03) (0.02) (0.02) (0.02) (0.02) 0.08 insects 3 -0.02 -0.07 0.01 -0.04 -0.02 -0.05 -0.04 (0.02) (0.03) (0.02) (0.02) (0.03) (0.02) (0.02) 0.08 insects 4 -0.03 -0.06 0 -0.05 -0.05 (0.02) (0.03) (0.02) (0.02) (0.02) 1 mammals 1 0.05 -0.25 -0.01 -0.06 0.01 0.03 0.07 -0.04 -0.03 -0.01 0.02 0.08 0.02 -0.05 0.02 (0.05) (0.06) (0.07) (0.08) (0.07) (0.04) (0.05) (0.07) (0.07) (0.05) (0.06) (0.06) (0.07) (0.07) (0.06) 1 mammals 2 0.04 -0.24 -0.03 -0.04 0.02 (0.04) (0.05) (0.06) (0.06) (0.07) 1 mammals 3 -0.23 (0.05) 1 birds 1 0.08 -0.07 0 0.08 -0.05 0.02 -0.01 0.05 -0.05 -0.01 -0.09 0.01 -0.06 0.05 -0.14 (0.05) (0.05) (0.06) (0.06) (0.07) (0.04) (0.04) (0.05) (0.05) (0.05) (0.06) (0.07) (0.05) (0.05) (0.05) 1 birds 2 0.09 -0.08 0 0.02 -0.02 -0.12

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(0.04) (0.05) (0.05) (0.05) (0.06) (0.04)

1 birds 3 0.1 0.03 -0.01 -0.13 (0.04) (0.05) (0.06) (0.04) 1 fishes 1 0.08 -0.19 0 0.05 0.02 0.02 0.01 0.06 -0.11 0.06 -0.06 0.04 -0.06 0.11 -0.01 (0.04) (0.06) (0.06) (0.05) (0.06) (0.04) (0.04) (0.04) (0.04) (0.04) (0.06) (0.05) (0.06) (0.05) (0.05) 1 fishes 2 0.09 -0.18 0 0.07 0.02 -0.08 0.07 (0.03) (0.05) (0.05) (0.05) (0.05) (0.03) (0.04) 1 fishes 3 0.09 -0.17 -0.01 0.06 -0.08 0.07 (0.03) (0.05) (0.05) (0.04) (0.03) (0.04) 1 insects 1 -0.03 -0.19 -0.01 0.01 -0.04 -0.05 -0.01 -0.02 -0.02 -0.01 -0.06 0.03 0.02 -0.01 -0.05 (0.02) (0.03) (0.03) (0.03) (0.03) (0.02) (0.02) (0.02) (0.02) (0.03) (0.04) (0.04) (0.03) (0.03) (0.03) 1 insects 2 -0.03 -0.17 -0.01 0.03 -0.05 -0.03 (0.02) (0.03) (0.02) (0.03) (0.03) (0.02) 1 insects 3 -0.03 -0.17 -0.01 0.03 -0.04 (0.02) (0.03) (0.02) (0.03) (0.03) 1 insects 4 -0.17 (0.02) 2 mammals 1 0.01 -0.24 0.01 0.04 -0.04 0.05 0.08 -0.08 0 -0.05 -0.05 0.17 0 (0.07) -0.06 -0.03 (0.04) (0.06) (0.07) (0.07) (0.07) (0.04) (0.05) (0.07) (0.06) (0.06) (0.06) (0.06) (0.07) (0.06) 2 mammals 2 -0.01 -0.22 -0.01 0 -0.03 0.1 (0.04) (0.06) (0.06) (0.06) (0.07) (0.04) 2 mammals 3 -0.22 -0.03 0.1 (0.06) (0.05) (0.04) 2 birds 1 0.06 -0.1 0 -0.01 0.03 0.02 0.02 0.05 -0.08 0.01 -0.06 -0.04 -0.07 0.01 -0.09 (0.04) (0.06) (0.06) (0.07) (0.07) (0.04) (0.04) (0.05) (0.05) (0.06) (0.07) (0.07) (0.05) (0.06) (0.05) 2 birds 2 0.07 -0.1 -0.02 -0.08 0.04 (0.04) (0.05) (0.05) (0.06) (0.06) 2 birds 3 0.07 -0.09 (0.04) (0.05) 2 fishes 1 0.09 -0.2 -0.01 0.07 0.01 0 -0.01 0.09 -0.11 0.05 -0.12 0.07 -0.12 0.1 (0.05) 0 (0.03) (0.06) (0.06) (0.06) (0.07) (0.04) (0.04) (0.04) (0.04) (0.05) (0.07) (0.05) (0.07) (0.05) 2 fishes 2 0.09 -0.17 0.02 0.08 0 0.09 -0.12 0.03 (0.03) (0.05) (0.06) (0.06) (0.06) (0.04) (0.04) (0.04) 2 fishes 3 0.09 -0.18 0.08 0.01 0.09 -0.12 (0.03) (0.05) (0.06) (0.06) (0.04) (0.04) 2 insects 1 -0.04 -0.2 -0.02 0.03 -0.01 -0.05 -0.02 0 -0.05 -0.01 -0.13 0.04 -0.02 0 (0.03) -0.08 (0.02) (0.04) (0.03) (0.03) (0.04) (0.02) (0.02) (0.02) (0.02) (0.03) (0.04) (0.04) (0.03) (0.03) 2 insects 2 -0.04 -0.19 0 0.03 -0.02 -0.04 -0.05 -0.08 -0.08 (0.02) (0.03) (0.02) (0.03) (0.03) (0.02) (0.02) (0.03) (0.03) 2 insects 3 -0.04 -0.19 0.03 -0.02 -0.04 -0.05 -0.08 -0.08 (0.02) (0.03) (0.03) (0.03) (0.02) (0.02) (0.03) (0.03) 4 mammals 1 -0.02 -0.23 0.03 0.14 -0.12 0.08 0.09 0.01 -0.01 -0.07 -0.06 0.14 0.09 -0.12 -0.1 (0.05) (0.07) (0.08) (0.09) (0.1) (0.04) (0.05) (0.07) (0.07) (0.07) (0.07) (0.08) (0.08) (0.09) (0.06) 4 mammals 2 -0.05 -0.23 0.01 0.06 -0.02 (0.04) (0.06) (0.07) (0.07) (0.09) 4 mammals 3 -0.25 (0.06) 4 birds 1 0 -0.09 -0.02 0.04 0.01 0.03 0.05 0.08 -0.14 0.02 -0.04 -0.05 -0.12 0.01 -0.09 (0.04) (0.06) (0.06) (0.08) (0.08) (0.04) (0.04) (0.05) (0.05) (0.06) (0.08) (0.08) (0.06) (0.06) (0.05) 4 birds 2 0.02 -0.08 -0.04 -0.01 0.02 -0.09 -0.14 (0.04) (0.06) (0.05) (0.06) (0.07) (0.03) (0.05)

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4 birds 3 0.03 -0.04 -0.01 0.04 -0.09 -0.14 (0.04) (0.05) (0.06) (0.07) (0.03) (0.05) 4 fishes 1 0.08 -0.2 0.01 0.08 -0.06 -0.03 -0.07 0.1 -0.03 0.07 -0.05 0.03 -0.1 0.12 -0.01 (0.03) (0.07) (0.07) (0.08) (0.08) (0.04) (0.04) (0.04) (0.04) (0.05) (0.08) (0.06) (0.08) (0.05) (0.06) 4 fishes 2 0.1 -0.2 0.02 0.09 -0.06 0.06 0.05 (0.03) (0.06) (0.06) (0.07) (0.06) (0.03) (0.04) 4 fishes 3 0.11 -0.18 (0.03) (0.05) 4 insects 1 -0.03 -0.15 -0.02 0.01 0.03 -0.05 -0.03 0 -0.03 -0.02 -0.08 0.02 0.02 -0.01 -0.09 (0.02) (0.04) (0.03) (0.04) (0.05) (0.02) (0.01) (0.02) (0.02) (0.03) (0.05) (0.04) (0.03) (0.03) (0.03) 4 insects 2 -0.02 -0.13 -0.01 0.05 0 -0.03 -0.07 (0.02) (0.03) (0.03) (0.03) (0.04) (0.01) (0.03) 4 insects 3 -0.02 -0.13 0.05 0 -0.03 -0.07 (0.02) (0.03) (0.03) (0.04) (0.01) (0.03)

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Table S2. Parameter estimates (and standard error) for fixed effects in time series models. All models included a fixed effect of year, random intercepts for ‘grid cell’ and ‘species’, and a population-specific random slope and intercept for the effect of ‘year’. For each class, four models were fitted: one with only year as a fixed effect (model 1; i.e. what is reported in the main text), and one each for three additional fixed effects (latitude, land use intensity or human density) and their two-way interaction with year.

latitude land use land human human class model year latitude:year (absolute) intensity use:year density density:year Aves 1 0.27 (0.27) Aves 2 0.32 (0.28) 0.06 (0.23) -0.37 (0.26) Aves 3 0.21 (0.26) -0.12 (0.24) 0.25 (0.26) Aves 4 0.26 (0.25) -0.02 (0.23) -0.27 (0.26) Actinopterygii 1 -0.07 (0.09) Actinopterygii 2 -0.08 (0.09) -0.03 (0.13) -0.05 (0.09) Actinopterygii 3 -0.06 (0.09) 0.24 (0.14) 0.00 (0.1) Actinopterygii 4 -0.08 (0.09) 0.05 (0.11) -0.07 (0.08) Insecta 1 -0.06 (0.04) Insecta 2 -0.04 (0.04) 0.38 (0.05) -0.10 (0.04) Insecta 3 -0.10 (0.04) -0.04 (0.09) 0.02 (0.04) Insecta 4 -0.11 (0.04) 0.14 (0.09) -0.01 (0.04) Mammalia 1 0.01 (0.04) Mammalia 2 0.00 (0.04) -0.25 (0.1) 0.03 (0.04) Mammalia 3 0.01 (0.04) -0.12 (0.19) -0.04 (0.05) Mammalia 4 -0.01 (0.05) 0.22 (0.25) -0.07 (0.05)

7 a rS = 0.83 species 1 5 20 100 500

2 5 10 20 50 200 500 2,000 b sequences number of species of number 1 10 100 1,000

1985 1995 2005 2015 c year 1,000 number of populations of number 1 10 100

1985 1995 2005 2015

year

Figure S1. Relationships among the (spatial or temporal) distribution of sequences, populations, and species in our dataset. (a) Relationship between the number of species and the number of sequences available in all 5’ grid cells with at least 2 sequences, along with the Spearman correlation coefficient (rS) of the relationship. Note that axes are logged. (b, c) Number of species (b) and populations (c) available in the dataset for each year and animal class (birds, bony fishes, insects, and mammals).

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● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● fixed effect of year of effect fixed 1.0 0.0 0.5 1.0 −

3456345634563456

minimum number of years in time series b population trend population trend population 0.4 0.0 0.4 − 1.0 0.0 1.0 2.0 − 3.0 3.5 4.0 4.5 5.0 5.5 6.0 3.0 3.5 4.0 4.5 5.0 5.5 6.0

number of years number of years population trend population trend population 1.0 0.0 0.5 1.0 − 0.2 0.0 0.2 0.4 − 4 6 8 10 12 4 6 8 10 12 14 number of years number of years

Figure S2. Effect of time series duration on temporal trends in genetic diversity. (a) Results of random slopes models when using increasingly more stringent criteria for time series inclusion. Symbols indicate parameter estimates (with 95% confidence intervals) for the fixed effect of time/year estimated by models, when the minimum duration of time series is set at 3, 4, 5 or 6 years. The analysis described in the main text used 3 years as the minimum number of samples. (b) Relationship between time series duration and population trends estimated by models presented in Fig. 5 of the main text. Thick black lines illustrate the fit of linear regression models; none of these models had a slope significantly different from 0 at a = 0.05.