{r}Evolving Kinship

Taxonomy and biological systematics are often viewed as cold, rigid frameworks. Evolving Kinship is a data-engineering and digital art project designed to break the roughness of traditional systematics. By receiving and transforming user-selected species into phylogenetic trees with the bioinformatic knowledge of today’s age, this project enables users to request a personalized “kinship tree” showcasing to the world the genetic proximity between us, and our favorite kin.

This pilot dataset seeks to map and visualize the phylogenetic web of Urban species in Yaanga (the historical Tongva name for the Los Angeles basin), mapping 10 iconic urban species: from the Coast Live Oak (Quercus agrifolia) to the Coyote (Canis latrans), alongside Homo sapiens to highlight our shared evolutionary chronology.

To maintain strict biofidelity, the project relies on foundational ecological and evolutionary principles. With this information we include:

Systematics & Phylogenomics: Mapping the exact evolutionary pathways and clades (e.g., Sauria, Boreoeutheria) that connect distinct urban species.
Last Common Ancestor (LCA) & Divergence Time: Utilizing chronological data to understand deep-time relationships (e.g., highlighting the 260-million-year-old divergence in the Sauria clade). [Updating screenshots soon…]
Taxonomic Standardization: Using NCBI Taxonomy IDs (TaxIDs) as the primary and immutable identifiers, to have accuracy while allowing space to share metadata that honors common names and stories across cultures.

Kinship Architecture

Behind the visual art is a robust ETL (Extract, Transform, Load) data pipeline built on Google Cloud infrastructure. The architecture was designed to scale, bypassing the rate limits of free and commercial visualization APIs by building our very own custom data processing hub:

1. Data Ingestion & Storage (BigQuery) User requests are captured and pushed into Google BigQuery. Instead of flat files, the data is structured relationally. This allows for partitioned tables where different projects (like the “LA Urban Species” batch) are managed seamlessly without overwriting historical data.

2. The Transformation Engine (Google Colab & Python)
The core processing relies on a Python script running in Google Colab.

Using the ETE3 bioinformatics library, the script downloads a local instance of the NCBI taxonomy database to memory.
It cross-references the BigQuery TaxIDs to generate an accurate topological structure.
The script programmatically traverses the tree, enriching internal node IDs with their actual scientific clade names.

3. Infrastructure as Code for Visualization (iTOL)
To visualize the data, I utilized a Split Architecture approach:

The Skeleton: The Colab script exports a lightweight Newick (.nwk) file that dictates the pure topology and branch lengths. Example:

			
((((Quercus_kelloggii:1,Chlamydophora_tridentata:1)Pentapetalae:1,Liriodendron_tulipifera:1)Mesangiospermae:1,Spondylosium_pulchrum:1)Streptophytina:1,(((Uma:1,Buteo:1)Sauria:1,((Canis_latrans:1,Puma_concolor:1)Carnivora:1,Homo_sapiens:1)Boreoeutheria:1)Amniota:1,(Apis_mellifera:1,Danaus_plexippus:1)Endopterygota:1)Bilateria:1);

The Meat: Instead of manually formatting the tree in the Interactive Tree of Life (iTOL) UI, I am currently working on a Python script to engineer “iTOL Dataset Text Files.” This would act as Infrastructure as Code that automatically maps Common Names, colors, and metadata over the base tree. For now I am doing it manually…

To request a custom {r}Evolving Kinship tree keep an eye out for our form, coming very soon!

Kinship Sonification

The newest version of Evolving Kinship involve Data Sonification, mapping evolutionary age (in mya) to MIDI pitches, and DNA GC-content to tempo or other dynamics. I want a python pipeline that can compose unique audio tracks representing the evolutionary distances of a user’s chosen species via sound. These visual and auditory elements could even be pipelined via APIs to print-on-demand services, turning this rawer biological data into more accessible, fun, and informative custom merchandise.

Here’s a sketch made for a one night activation at The Goat Farm Arts Center in Proctor Creek, Atlanta