Input Data

Input Data

PhyloGeoPlot combines phylogenetic, geographic, and optionally environmental and trait information.

The principal input types are:

• a phylogenetic tree;
• geographic occurrence data;
• an optional offset file;
• optional quantitative trait metadata;
• an optional environmental raster.

Phylogenetic tree

Phylogenetic trees are supplied in Newick (.nwk) format.

Example:

((taxon_A:0.12,taxon_B:0.10):0.05,taxon_C:0.18);

The identifiers used in the tree should correspond to the identifiers used in the occurrence data.

A Newick tree may be generated externally or constructed from aligned sequence data using the PhyloGeoPlot preprocessing tools.

See Preprocessing.

Geographic occurrence data

Geographic records are supplied as CSV data.

The file must provide sufficient information to associate occurrence records with taxa or tree nodes and geographic coordinates.

Typical fields include:

node
latitude
longitude

Additional fields may contain specimen identifiers, taxonomic information, traits, or other metadata.

GBIF exports can be reformatted using the preprocessing tools described on the Preprocessing page.

Trait metadata

Quantitative metadata can be associated with occurrences and represented through color encoding.

Examples include:

• caffeine concentration;
• morphological measurements;
• environmental values;
• ecological measurements;
• physiological traits.

Trait values may be merged with occurrence data before visualization.

Offset file

An offset file can be used to adjust the position of tree elements or labels in the linked visualization.

This is particularly useful when long taxon names or dense tree structures would otherwise overlap.

Example files are provided in:

examples/sample_data/use_case_1/
examples/sample_data/use_case_2/

Raster data

Environmental rasters are supplied as GeoTIFF files.

Potential raster variables include:

• elevation;
• temperature;
• precipitation;
• vegetation indices;
• climatic variables;
• environmental suitability;
• other continuous spatial variables.

Raster processing is handled through Rasterio.

The raster is optional. PhyloGeoPlot can produce linked tree-map visualizations without an environmental raster.

Coordinate reference systems

Geographic occurrence coordinates and raster data must refer to compatible geographic locations.

Raster coordinate information is read from the GeoTIFF metadata.

When combining geographic data from several sources, coordinate reference systems should be checked before visualization.

See Troubleshooting for common spatial-data issues.