Raw datasets and pre-assembly processing quality control The sequencing process generated a total of 88,4 M in TTR, 87,8 M in SSC, 80,2 M in TLU and 84 M in MPO paired-end raw reads. All raw datasets were initially scrutinized by the FastQC tool, trimmed with Trimmomatic, error-corrected with Rcorrector and decontaminated with Centrifuge software. The percentage of removed […] More
1. Sergio, F. et al. Top predators as conservation tools: Ecological rationale, assumptions, and efficacy. Annu. Rev. Ecol. Evol. Syst. 39, 1–19 (2008). Google Scholar 2. Estes, J. A. et al. Trophic downgrading of planet earth. Science 333, 301–306 (2011). ADS CAS PubMed Google Scholar 3. Ripple, W. J. et al. Status and ecological effects […] More
Algorithm and model performance Both XGBoost and random forests models are machine learning algorithms with better performance (higher R2 and smaller MSE value) than the linear regression model under the condition that data quality and sample size are the same. However, the models did not yield good results when the data size was small. The […] More
Calculations for hypothetical scenarios In a forest comprising three taxonomic groups, the overall fractional mortality, M, of all trees in height class i is given by $$M_i = (d_{i,1} + d_{i,2} + d_{i,3}){mathrm{/}}(n_{i,1} + n_{i,2} + n_{i,3}),$$ (1) where ni,1, ni,2, and ni,3 are the numbers of living trees in height class i and taxonomic groups […] More
If you are any type of BIPOC, your presence alone in academia will inspire BIPOC early-career researchers. Be mindful with this unexpected influence. Welcome students into your office even when you are under deadlines, as these few minutes may sway their career path. Tell them about the delight and joy you find in science, as […] More
Classifying the tree-level dataset The Sierra Nevada mountains have unique species assemblages following strong topographic gradients, with the most dominant shifts controlled by topography12,13. In the low elevations the canopy is dominated by pines, shifting to fir species in high elevations. South-facing slopes tend to be dominated by drought-tolerant species, while North-facing slopes hold species […] More
1. Lloyd-Smith, J. et al. Epidemic dynamic at the human-animal interface. Science 326, 1362–1367 (2009). CAS PubMed PubMed Central Google Scholar 2. Kilpatrick, A. M. et al. Host heterogeneity dominates West Nile virus transmission. Proc. Biol. Sci. 273, 2327–2333 (2006). PubMed Google Scholar 3. Woolhouse, M., Taylor, L. H. & Haydon, D. T. Population biology […] More
Sample collection All samples were taken from Salakphra Wildlife Sanctuary with the permission from the Department of National Parks, Wildlife and Plant Conservation (DNP), the approval number DNP 0907.4/4411. A research ethics statement was granted by the Mahidol University-Institute Animal Care and Use Committee (MU-IACUC 2016/026). Salakphra Wildlife Sanctuary (14°8′37.09″N, 99°20′33.51″E, area: ~ 860 km2) is located […] More
