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Title: Amazonian and Atlantic forest connections over time: bird lineages with disjunct distribution as models to test these connections

Author: Tainá Rocha

Repository of niche and molecular analysis for disjoint Amazon and Atlantic forest birds

Status: In progress

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Steps for niche analysis :

1. Compiled occurrence records for species. Here we'll use 2 workflows for this step:

   • Rocc (https://github.com/saramortara/rocc)
   • spocc (https://github.com/ropensci/spocc)

2. Clean occurence (R base funtions)

   • Remove wrong records
   • Remove too old records
   • Remove duplicates
   • Specialist check

3. Climatic variables. We'll use two dataset of climatic variables.

   • Paleoclim: http://www.paleoclim.org/ (The most complete and recent data with better resolution)
   • Chelsa: https://chelsa-climate.org/

4. Exploratory data analysis

   • Extract environmental values of points
   • Build a principal component analysis (PCA)
   • Select the most important variables for species

5. Niche analysis

   • Niche similarity using humbolds package (https://github.com/jasonleebrown/humboldt)

6. Ecological Niche models using two different approaches and two different workflows

   • modler package: using different algorithms to map niches suitability (https://github.com/Model-R , https://github.com/Model-R/modleR).
   • ntbox package: using using ellipsoids to model niches suitability (https://github.com/luismurao/ntbox/)

7. nicheEvol

   • I need to study more this package (https://github.com/hannahlowens/nichevol)

Steps for molecular analysis.

1. Compiled sequences from genebank.... ??? Other sources ??

   • Lipaugus vociferans
   • Schiffornis tudina
   • Xiphorhynchus guttatus
   • Xiphorhynchus guttatoides

2. Phylogenetic tree...

   • ML and Baeysian Trees (?)
   • Molecular date (?)
   • Biogeobears ?

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Light gray boxs for datasources

Gray box for filtered data

Blue boxs for R packages and softwares to process the data

Yellow boxes for analysis