Add alife phylogenies tutorial

Author: mmore500

blog_efflux/_posts/2023-07-24-phylogenies.md

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+---
+layout: efflux
+title: "Phylogenies: how and why to track them in artificial life"
+date: 2023-07-24
+category: teaching
+authors:
+  - Emily Dolson
+  - Matthew Andres Moreno
+  - Alexander Lalejini
+venue: Tutorial at ALIFE 2023
+description: |
+  Phylogenies (i.e., ancestry trees) group extant organisms by ancestral relatedness to render the history of hierarchical lineage branching events within an evolving system.
+  These relationships reveal the evolutionary trajectories of populations through a genotypic or phenotypic space.
+  As such, phylogenies open a direct window through which to observe ecology, differential selection, genetic potentiation, emergence of complex traits, and other evolutionary dynamics in artificial life (ALife) systems.
+  In evolutionary biology, phylogenies are often estimated from the fossil record, phenotypic traits, and extant genetic information.
+  Although substantially limited in precision, such phylogenies have profoundly advanced our understanding of the evolution of life on Earth.
+  In digital systems, we often have the ability to create perfect (or near perfect) phylogenies that reveal the step-by-step process by which evolution unfolds.
+  However, phylogeny tracking and phylogeny-based analyses are not yet commonplace in ALife.
+  Fortunately, a number of software tools have recently become available to facilitate such analyses, such as Phylotrackpy, DEAP, Empirical, MABE, and hstrat.
+
+  Biologists have developed many sophisticated and powerful phylogeny-based analysis techniques.
+  For example, existing work uses properties of tree topology to infer characteristics of the evolutionary processes acting on a population.
+  With an understanding of the differences between biology and artificial life, these approaches can be imported into ALife systems.
+  For example, phylodiversity metrics can be used to detect diversity-maintaining ecological interactions and ongoing generation of significant evolutionary innovations.
+
+  This tutorial will provide an introduction to phylogenies, how to record them in digital systems, and use cases for phylogenetic analyses in an artificial life context.
+  We will open with a quick discussion of prior research enabled by and based on phylogenies in digital evolution systems.
+  We will then survey existing phylogeny software tools and lead interactive tutorials on tracking phylogenies in both traditional and distributed computing environments.
+  Next, we will demonstrate measurements and data visualizations that phylogenetic data enables, including Muller plots, phylogenetic topology metrics, and annotated phylogeny visualizations.
+  Lastly, we will discuss open questions and future directions related to phylogenies in artificial life.
+supporting_materials: |
+  - [web page](https://emilydolson.github.io/alife-phylogeny-tutorial/)
+  - [slides](https://docs.google.com/presentation/d/1D6DeZo3uGUvtMLvvNt9eCslmaPWQoEgFp08FZx8orYc) [via Google Slides](https://workspace.google.com/products/slides/)
+---