Draft alife 2023 conference paper works entry

Author: mmore500

blog_efflux/_posts/2023-07-24-moreno2023toward.md

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+---
+layout: efflux
+title: "Toward Phylogenetic Inference of Evolutionary Dynamics at Scale"
+date: 2023-07-24
+permalink: "/pubs/:title"
+category: conference
+download: https://github.com/mmore500/hereditary-stratigraph-concept/releases/download/v0.3.0/hereditary-stratigraph-concept-manuscript.pdf
+authors:
+  - Matthew Andres Moreno
+  - Emily Dolson
+  - Santiago Rodriguez-Papa
+venue: The 2023 Conference on Artificial Life
+projects:
+  - hstrat
+abstract: |
+  As digital evolution systems grow in scale and complexity, observing and interpreting their evolutionary dynamics will become increasingly challenging.
+  Distributed and parallel computing, in particular, introduce obstacles to maintaining the high level of observability that makes digital evolution a powerful experimental tool.
+  Phylogenetic analyses represent a promising tool for drawing inferences from digital evolution experiments at scale.
+  Recent work has introduced promising techniques for decentralized phylogenetic inference in parallel and distributed digital evolution systems.
+  However, foundational phylogenetic theory necessary to apply these techniques to characterize evolutionary dynamics is lacking.
+  Here, we lay the groundwork for practical applications of distributed phylogenetic tracking in three ways: 1) we present an improved technique for reconstructing phylogenies from tunably-precise genome annotations, 2) we begin the process of identifying how the signatures of various evolutionary dynamics manifest in phylogenetic metrics, and 3) we quantify the impact of reconstruction-induced imprecision on phylogenetic metrics.
+  We find that selection pressure, spatial structure, and ecology have distinct effects on phylogenetic metrics, although these effects are complex and not always intuitive.
+  We also find that, while low-resolution phylogenetic reconstructions can bias some phylogenetic metrics, high-resolution reconstructions recapitulate them faithfully.
+bibtex: |-
+  @inproceedings{moreno2023toward,
+      author = {Moreno, Matthew Andres and Dolson, Emily and Rodriguez-Papa, Santiago},
+      title = "{Toward Phylogenetic Inference of Evolutionary Dynamics at Scale}",
+      volume = {ALIFE 2023: The 2023 Conference on Artificial Life},
+      series = {ALIFE 2023: The 2023 Conference on Artificial Life},
+      year = {in print},
+  }
+citation: 'Matthew Andres Moreno, Emily Dolson, and Santiago Rodriguez-Papa; in print. "Toward Phylogenetic Inference of Evolutionary Dynamics at Scale." Proceedings of the ALIFE 2023: The 2023 Conference on Artificial Life. ALIFE 2023: The 2023 Conference on Artificial Life. Online.'
+supporting_materials: |
+  - [data](https://osf.io/vtxwd/) [via Open Science Framework ❋](https://osf.io)
+  - [source code](https://github.com/mmore500/hstrat-evolutionary-inference/tree/v1.0.0) [via GitHub <i class="icon-github-1"></i>](https://github.com/)
+  - [hstrat library code](https://github.com/mmore500/hstrat/tree/v1.6.1) [via GitHub <i class="icon-github-1"></i>](https://github.com/)
+  - [evolution conference presentation](https://youtu.be/2cRbRJSA5Qw?t=3774) [via YouTube <i class="icon-video"></i>](https://youtube.com)
+  - [evolution conference slides](https://docs.google.com/presentation/d/1_e-_cCGmdavRN5RscQeml52IDXyQSjyvoJ6K9fLQhE8/) [via Google Slides](https://workspace.google.com/products/slides/)
+  - [LaTeX source](https://github.com/mmore500/hstrat-evolutionary-inference/tree/239992269f9387596d4be726eb860b733e00b6ed) [via GitHub <i class="icon-github-1"></i>](https://github.com/)
+---