## 3 Results
### Structural Alteration Index Results Across Forest Classes  
The structure and composition varied across the sampled sites, with the most altered sites in the plains landscape (i.e., those with high _SAI_ levels--CL8 and CL7) characterized by a low cover of _Aspidosperma quebracho-blanco_ and _Neltuma flexuosa_ (Figure S3.1). These sites also exhibited a simplified vertical structure, low litter dry weight, lower seedling density of woody species, and cover and basal area of _Celtis el'ennerb'iana_, high percentages of bare soil and high cover of _N. flexuosa_ in the low woody layer, and of _Geoffreea decoricans_ in all layers. In contrast, the most preserved sites (i.e., those with low _SAI_ levels) on plains landscape (mature forests of CL 2) and partially also those of the foothills (mature forests of CL 1) exhibited opposite values for these structural variables. Sites with intermediate structural alteration (i.e., those with medium _SAI_ levels), mainly referable to low closed forest (CL 5) and shrublands (CL 6), were characterized by high cover of _A. quebracho-blanco_ in the low woody layer, _Larrea divaricata_ in the lower and middle woody layers, and _Parkinsonia praecox_ in all layers as well. These sites also showed high horizontal heterogeneity and tree density (S2, Figures S2.1 and S2.2). Furthermore, the most altered sites in the foothills, such as grasslands with trees (CL8) and savannas (CL7) (i.e., with high _SAI_ levels), showed low \begin{table}
\begin{tabular}{c c c c c c} \hline  & \multicolumn{2}{c}{**BI\({}_{2}\)**} & \multicolumn{2}{c}{**MCARI\({}_{\rm Sent}\)**} & \multicolumn{2}{c}{**NDWI\({}_{\rm Gao}\)**} \\ \hline
**Predictors** & **Estimates** & **CI** & **Estimates** & **CI** & **Estimates** & **CI** \\ \hline Interc. & 1925.15 *** & 1899.50–1990.80 & 151.35 *** & 142.83–159.87 & 0.19 *** & 0.16–0.21 \\ CL 2 & \(-\)24.74 & \(-\)163.98–141.51 & 0.49 & \(-\)17.58–18.85 & 0.15 *** & 0.09–0.21 \\ CL 3 & 29.02 & \(-\)67.06–125.65 & 1.88 & \(-\)10.66–14.42 & \(-\)0.00 & \(-\)0.04–0.04 \\ CL 4 & 203.88 *** & 95.04–312.72 & 22.71 ** & 8.60–36.83 & 0.04 & \(-\)0.00–0.09 \\ CL 5 & 243.49 *** & 157.91–329.07 & 15.57 ** & 4.47–26.67 & 0.03 & \(-\)0.01–0.07 \\ CL6 & 335.22 *** & 246.93–40.81 & 19.02 *** & 7.91–30.12 & \(-\)0.06 *** & \(-\)0.10–0.02 \\ CL 7 & 1516.11 *** & 1419.49–1612.74 & 38.47 *** & 25.94–51.01 & \(-\)0.05 *** & \(-\)0.09—0.01 \\ CL8 & 1510.42 *** & 1401.56–1619.28 & 23.59 *** & 9.46–37.71 & \(-\)0.10 *** & \(-\)0.14—0.05 \\ \multicolumn{2}{c}{**Random Effects**} \\ \(\sigma^{2}\) & & 33,259.42 & 1316.25 & 0.00 & \\ \(\tau_{00}\) & & 93,595.66 \({}_{\rm ID\_transectMonth}\) & & 156.27 & \\ ICC & & & 1D\_transectMonth & & 0.02 \({}_{\rm ID\_transectMonth}\) \\ N & & 0.74 & 0.54 & 0.91 \\ \multicolumn{2}{c}{N} & 49 \({}_{\rm ID\_transectMonth}\) & 49 \({}_{\rm ID\_transectMonth}\) & & 49 \({}_{\rm ID\_transectMonth}\) \\ \hline Observ & & 33,157 & 33073 & 33120 \\ Marg R\({}^{2}\)/Cond & & 0.706/0.923 & 0.047/0.564 & 0.126/0.923 \\ R\({}^{2}\) & & & & \\ \hline \end{tabular}  
* \(p\) \(<\) 0.05 *** \(p\) \(<\) 0.01 *** \(p\) \(<\) 0.001.  
\end{table} 
Table 4: Linear mixed models (LMMs) of spectral indices by forest conservation classes. The fixed component of the model provides estimates, confidence intervals (CIs), and \(p\)-values for both the intercept and slope. The random effects are presented as explained variance (\(\sigma\)2), variance of the random intercept (\(\tau\)00), and intra-class correlation coefficient (ICC). The goodness-of-fit is quantified using marginal and conditional R\({}^{2}\) values, which respectively capture the impact of fixed and fixed + random components in the model. Forest types and conservation levels (CL number) refer to mature forests on foothills (CL 1), mature forests on plains (CL 2), closed forests on foothills (CL 3), closed forests on plains (CL 4), low closed forests on plains (CL 5), shrublands (CL 6), savannas (CL 7), and grasslands with trees (CL 8). cover of _A. quebracho-blanco_ and _N.