Thông tin tài nguyên

Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

pmc-PMC8726463.pdf · Phiên bản 1 · 25 trang

18
Bản gốc
Trang 23 · Đoạn 59Vị trí nguồn

38. Deiner K, Renshaw MA, Li Y, Olds BP, Lodge DM, Pfrender ME. Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods in Ecology and Evolution. 2017; 8 (12):1888–98. 39. Galan M, Pons J-B, Tournayre O, Pierre E´ , Leuchtmann M, Pontier D, et al. Metabarcoding for the par- allel identification of several hundred predators and their prey: Application to bat species diet analysis. Molecular Ecology Resources. 2018 May; 18(3):474–89. https://doi.org/10.1111/1755-0998.12749 PMID: 29288544 40. Escudie´ F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, et al. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Berger B, editor. Bioinformatics. 2018 Apr 15; 34(8):1287–94. https://doi.org/10. 1093/bioinformatics/btx791 PMID: 29228191 41. Guimarães KLA, de Sousa MPA, Ribeiro FRV, Porto JIR, Rodrigues LRR. DNA barcoding of fish fauna from low order streams of Tapajo´ s River basin. Doi H, editor. PLoS ONE. 2018 Dec 21; 13(12): e0209430. https://doi.org/10.1371/journal.pone.0209430 PMID: 30576366 42. Ortega H, Hidalgo M, Giannina T, Correa E, Cortijo AM, Meza V, et al. Lista anotada de los peces de aguas continentales del Peru´ : Estado actual del conocimiento, distribucio´ n, usos y aspectos de conser- vacio´n. Ministerio del Ambiente DG de DB-M de HN UNMSM, editor. 2012. 43. Sarmiento J, Bigorne R, Carvajal-Vallejos FM, Maldonado M, Leciak E, Oberdorff T. Peces de Bolivia, Bolivian fishes [Internet]. Primera edicio´ n = First edition. La Paz: Plural Editores, 2014. ©2014; 2014.

Trang 23 · Đoạn 60Vị trí nguồn

Available from: https://search.library.wisc.edu/catalog/9910217107002121 44. Huson DH, Beier S, Flade I, Go´rska A, El-Hadidi M, Mitra S, et al. MEGAN Community Edition—Interac- tive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. Poisot T, editor. PLOS Computational Biology. 2016 Jun 21; 12(6):e1004957. https://doi.org/10.1371/journal.pcbi.1004957 PMID: 27327495 45. McKnight DT, Huerlimann R, Bower DS, Schwarzkopf L, Alford RA, Zenger KR. microDecon: A highly accurate read-subtraction tool for the post-sequencing removal of contamination in metabarcoding studies. Environmental DNA. 2019; 1(1):14–25. 46. Liu C, White M, Newell G. Selecting thresholds for the prediction of species occurrence with presence- only data. Journal of Biogeography. 2013; 40(4):778–89. 47. Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioin- formatics (Oxford, England). 2005 Oct 15; 21(20):3940–1. https://doi.org/10.1093/bioinformatics/bti623 PMID: 16096348 48. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecol- ogy Package. Ordination methods, diversity analysis and other functions for community and vegetation ecologists. California, Berkeley, USA: The Comprehensive R Archive Network; 2016. 49. McMurdie PJ, Holmes S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLOS ONE. 2013 Apr 22; 8(4):e61217. https://doi.org/10.1371/journal. pone.0061217 PMID: 23630581

Trang 23 · Đoạn 61Vị trí nguồn

50. Zhao S, Guo Y, Sheng Q, Shyr Y. Heatmap3: an improved heatmap package with more powerful and convenient features. BMC Bioinformatics. 2014; 15(Suppl 10):P16. 51. Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006 Jun 15; 22(12):1540–2. https://doi.org/10.1093/bioinformatics/btl117 PMID: 16595560 52. Burnham KP, Overton WS. Robust Estimation of Population Size When Capture Probabilities Vary Among Animals. Ecology. 1979 Oct; 60(5):927–36. 53. Linke S, Lehner B, Ouellet Dallaire C, Ariwi J, Grill G, Anand M, et al. Global hydro-environmental sub- basin and river reach characteristics at high spatial resolution. Sci Data. 2019 Dec; 6(1):283. https://doi. org/10.1038/s41597-019-0300-6 PMID: 31819059 54. QGIS Development Team. QGIS Geographic Information System [Internet]. Open Source Geospatial Foundation; 2009. Available from: http://qgis.org 55. Schneider A, Jost A, Coulon C, Silvestre M, The´ ry S, Ducharne A. Global-scale river network extraction based on high-resolution topography and constrained by lithology, climate, slope, and observed drain- age density. Geophysical Research Letters [Internet]. 2017 [cited 2020 Nov 25]; Available from: https:// hal.sorbonne-universite.fr/hal-01496152 56. R Core Team. R: A Language and Environment for Statistical Computing [Internet]. Vienna, Austria: R Foundation for Statistical Computing; 2019. Available from: https://www.R-project.org/ 57. Froese R, Pauly D. FishBase. World Wide Web electronic publication [Internet]. 2010; Available from:

Trang 23 · Đoạn 62Vị trí nguồn

www.fishbase.org PLOS ONE Fish diversity and distribution in the Tuichi basin PLOS ONE | https://doi.org/10.1371/journal.pone.0262357 January 4, 2022 23 / 25