# Pure and anthropogenic components drive large-scale freshwater fish invasions

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### Invasion

We used freshwater fish biodiversity knowledge collated by and described in Milardi, et al.47. In abstract, the dataset included 3777 websites sampled 1999–2014, recorded a complete of 99 totally different fish species (35 of which had been unique and already established, even when some are restricted to areas with thermal springs), spanned > 11 levels of longitude (~ 1200 km) and 10 levels of latitude (~ 1100 km), overlaying streams at altitudes -2.7–2500 m above sea stage. Neighborhood turnover was not a related consider our research, as a result of fish communities are usually steady over these timescales and the info was collected in a restricted timeframe inside every space29,39. Moreover, time elapsed since final introductions was adequate to investigate distribution patterns after main invasions had already occurred see e.g.23,48.

Abundance of every species sampled through the monitoring was recorded with Moyle lessons (Moyle and Nichols, 1973), which had been weighted in accordance with body-size lessons with a view to get hold of a body-mass-corrected abundance, hereafter referred to easily as abundance. We then calculated an invasion diploma, i.e. the share of launched species in freshwater fish communities, primarily based on the abundance of launched and native species see e.g.9,49. A excessive invasion diploma equals to a excessive share of launched species and a low share of native species.

We additionally chosen the highest 10 invasive species as additional response variables, underneath the idea that these could be the primary parts of the invasion diploma, however would reply to totally different invasion drivers primarily based on every species’ ecology. Invasiveness rank was outlined by means of an index obtained by multiplying colonization (share of web sites colonized) and prevalence (common relative abundance within the fish neighborhood) of every launched species. The relative abundance of every of those species within the fish neighborhood was used as a response variable, being a measure akin to invasion diploma for single species.

### Invasion drivers

We examined a mixture of geographical, local weather and anthropogenic influence components as potential drivers of invasion. To keep away from temporal mismatches, we selected time intervals that overlapped as a lot as potential with our organic knowledge.

We used basin space, altitude and slope (derived from a seamless digital elevation mannequin of the entire Italian territory at 10 m decision, Tarquini, et al.50) as geographical variables.

We derived local weather knowledge from obtainable sequence of long-term nationwide monitoring (http://www.scia.isprambiente.it/). We used every day air temperature (2000–2009), measured at a complete of 2266 websites all through the nation, as a proxy for temperature regimes. We additionally used cumulated annual precipitations, variety of annual dry days (precipitation < 1 mm) and most variety of consecutive dry days (all from 2000–2009), measured at a complete of 3098 websites all through the nation, as a proxy for hydrological regimes.

We used an index the 2009 Human Footprint51, primarily based on eight variables (built-up environments, inhabitants density, electrical energy infrastructure, crop lands, pasture lands, roads, railways, and navigable waterways), as a proxy for total anthropogenic influence and propagule strain. The decrease the proxy, the smaller the anthropogenic influence. We additionally additional explored single parts of anthropogenic influence, by analyzing individually variables associated to land use in 2012 (Copernicus Land Monitoring Service—https://land.copernicus.eu/pan-european/corine-land-cover/).

We additional used an index see e.g.52, primarily based on the focus of seven totally different parameters linked to nutrient ranges (oxygen saturation, biochemical oxygen demand, chemical oxygen demand, NH4, NO3, complete P and E. coli ranges), measured at month-to-month intervals 2006–2010, at 1636 websites all through the nation, as a proxy for eutrophication ranges. Excessive proxy values correspond to low eutrophication ranges. We additional added the depth of animal farming in 2010 (numbers of animals reared, ISTAT—http://dati.istat.it/Index.aspx?DataSetCode=DCSP_CONSISTENZE).

Lastly, we used the presence of migration boundaries as a proxy for riverine habitat fragmentation. We detected migration barrier places by means of high-resolution cloud-free satellite tv for pc photos, and manually categorized them in 4 classes (small leap, excessive leap, minor dam, main dam) in accordance with their kind and measurement (as gauged from visible traits, e.g. the presence of upstream retention basins).

### Estimating invasion drivers at fish sampling factors

We derived elevation of every fish sampling level from the DEM, which we equally used to calculate the overall space of the basin above the positioning, cropped at a ten km distance from the fish sampling level. In lowland areas, the place basin determinations had been unsure attributable to low elevation gradients, we derived the identical variables from an space of 10 km radius across the sampling level. We derived the slope utilizing a ten km lengthy river community phase, centered on the fish sampling level.

We used every day temperatures, cumulated annual precipitations, variety of annual dry days, and most variety of consecutive dry days, to construct imply built-in nested Laplace approximated (INLA) annual layers for the last decade 2000–200953. We assigned to every fish sampling level the worth of the imply interpolated in a 5 km radius across the level (temperature regime proxy) or the imply over the basin above the sampling level (hydrological regime proxy).

We calculated the minimal, most, sum and imply values of the general anthropogenic influence proxy and expressed them as densities within the cropped basin above the sampling level. We used a ten km cutoff underneath the idea that it might seize essentially the most related pressures for any given sampling level, that different pressures additional upstream could be much less related as their strain could be partly dampened by environmental buffers and keep away from overlap between totally different sampling factors alongside the identical watercourse. We used an analogous calculation for the density of animal farming (variety of poultry, sheep, pigs and cattle), which had been transformed in livestock items (poultry = 0.01, cattle = 1, sheep = 0.1, pigs = 0.5) in order that they could possibly be mixed into one variable. Equally, we used the share of every land cowl class within the cropped basin, aggregated on the highest stage (i.e. Synthetic Surfaces, Agricultural areas, Forest and semi-natural areas, Wetlands, Water our bodies).

We calculated the eutrophication proxy as a imply of INLA-interpolated annual layers and projected these over the river community. We then used the imply (and relative SD) of the proxy utilizing a ten km lengthy river community phase, centered on the fish sampling level.

For habitat fragmentation we used three variables: the variety of reachable boundaries alongside the river community, the imply distance of reachable boundaries, and a habitat fragmentation index. This index used reachable boundaries solely, and was constructed as:

$$frac{1}{{frac{pi }{2}}}tan left( {frac{1}{barrier ,distance} occasions barrier ,class } proper)$$

(1)

To differ non-linearly between 0 (least fragmented) and 1 (most fragmented). We selected a ten km cutoff for these variables, because it was in step with different measures and the typical distance most freshwater fish species are anticipated to maneuver up or downstream54, recognizing that some species have each shorter and longer migration spans.

### Knowledge evaluation

After a preliminary evaluation we retained the next variables for a full evaluation and grouped them in 4 giant invasion drivers teams: Geography (slope, altitude), Local weather (imply values of temperature and precipitation, in addition to imply most variety of dry days (drought)), Human components (imply densities of human footprint and livestock items, imply eutrophication index and habitat fragmentation index) and Land use (percentages of broad land cowl lessons). We used imply densities, slightly than absolute values, making an attempt to scale back any area-dependent results.

We developed Booster Regression Tree (BRT) fashions for each invasion diploma and the highest 10 invasive taxa. BRT fashions are amongst a household of methods used to advance single-classification or regression timber by combining the outcomes of sequentially match regression timber to scale back predictive error and enhance total efficiency55,56,57. BRT fashions have been proven to have superior efficiency over linear modeling methods particularly with knowledge which are typically extremely skewed, equivalent to environmental knowledge55,58, and are thought-about an environment friendly technique to explain non-linear relationships between variables and mechanically incorporate interactions between variables. We decreased explanatory variables in every closing BRT mannequin by utilizing a mixture of variable significance (VI) scores, analysis of interactions, and partial dependency responses (see under) following the strategy outlined by Elith, et al.55 to attenuate overfitting. All variables with VI < 7 had been deleted and the remaining variables had been used to develop the ultimate BRT mannequin. Calculations of VI values are primarily based on the variety of occasions a variable is chosen for splitting, weighted by the squared enchancment to the fashions because of every cut up, averaged over all timber. After a primary run, we used the BRT evaluation residuals to check for spatial autocorrelation (SAC) by means of the Moran’s I check and, the place SAC was discovered, we constructed a SAC autocovariate that was fed into the mannequin to account for SAC. Ultimate mannequin alternative relied on greatest mannequin match, and residuals had been examined to verify that spatial autocorrelation was decreased. The relative significance of every variable is scaled in order that the sum provides to 100, with greater numbers indicating stronger affect on the modeled response. When two variables that we interpreted as explaining the identical kind of variation throughout the identical stressor kind, and displaying the identical kind of response sample, occurred within the prime 10 most necessary variables, we stored just one variable within the closing mannequin, except dropping one of many variables decreased the CV R2 (cross-validation R2) past an affordable stage, primarily based on knowledgeable judgement. We used CV R2 (cross validation) values as an alternative of R2 to match efficiency amongst BRT fashions as a result of CV R2 values are extra conservative and fewer more likely to be inflated by potential overfitting. We calculated CV R2 values by holding 25% (bag fraction) of the websites out for every regression tree cut up, then used the withheld websites to check the share of deviance defined by the cut up55. We used partial dependency plots to visualise the course of particular person drivers results on the response variable, after accounting for the typical results of all different explanatory variables in every closing mannequin55,56. A partial dependency plot is a scatter plot of a person driver vs biotic metric and the modeled response kind for that metric, the place the response curves point out the final form, course, and potential breakpoints (i.e., impact ranges) for every driver. We ran Moran’s I check and constructed a SAC autocovariate utilizing a Voroni tessellation with the capabilities of the spdep bundle59, together with testing for unfavourable SAC. We ran BRT fashions utilizing the gbm bundle60,61 and particular code from Elith, et al.55. As a result of Elith et al.’s code optimizes the variety of timber run in every mannequin, the variety of timber can differ for every mannequin; nonetheless, all fashions had no less than 1000 timber.

We investigated the collinearity of variables by means of the variance inflation issue (VIF) inside every variable group, and we excluded collinear variables (VIF > 8) from variation partitioning and RDA analyses. We carried out variation partitioning by means of a partial regression to seek out the relative contributions of every group of invasion drivers (i.e., Geography, Local weather, Human components and Land use) in explaining invasion diploma. The overall variation was thus partitioned into totally different parts: the variance defined by a single group of explanatory variables, the variance collectively defined by variables of two or three teams and unexplained variance (Legendre & Legendre, 2012). The importance of distinctive fractions was examined utilizing permutation-based ANOVA with 999 permutations62. Geography (slope), Local weather (imply temperature, imply precipitation, imply drought), Human components (human footprint, animal farming, eutrophication, river fragmentation) and Land use (all land use subclasses) had been in the end retained. We used the varpart operate of the “vegan” R bundle62 to partition the variance, and the “eulerr” R bundle63 to signify the outputs by means of area-proportional Euler-Venn diagrams.

We additionally used Redundancy Evaluation (RDA) to analyze the variation of the highest 10 invasive species defined by invasion drivers64, utilizing adjusted R2 values to report the variance defined. We used the RDA operate of the “vegan” R bundle62 to run this evaluation and check the importance of axes utilizing permutation-based ANOVA with 499 permutations.

All analyses had been carried out in R31.

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