M. Steel

The probability of a unique gene occurrence at the tips of a phylogenetic tree in the absence of horizontal gene transfer (the last-one-out)

The paper calculates the probability of last-one-out gene distributions under a Markovian loss model and shows gene loss can explain observed patterns resembling horizontal gene transfer.

Self-generating autocatalytic networks: structural results, algorithms, and their relevance to evolutionary processes

This paper presents new structural and algorithmic results for autocatalytic reaction networks, focusing on complex catalysis and minimal RAF sets.

Labellable phylogenetic networks

This paper introduces a new class of phylogenetic networks called labellable and establishes a bijection with expanding covers of finite sets, generalizing phylogenetic forest encodings.

Spaces of phylogenetic diversity indices: combinatorial and geometric properties

The paper defines phylogenetic diversity indices on rooted trees, showing they form a convex space with extremal points determined by tree shape and generalizing existing indices.

The expected loss of feature diversity (versus phylogenetic diversity) following rapid extinction at the present

The paper derives mathematical expressions for feature diversity loss after extinction events, showing it differs from phylogenetic diversity loss when features can be lost.

Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage

This paper introduces EvoHeritage, a new phylogenetic biodiversity metric that accounts for both accumulation and attrition of evolutionary features, showing it better predicts community productivity and identifies living fossils than traditional metrics.

EDGE2: advancing the prioritisation of threatened evolutionary history for conservation action

The paper introduces EDGE2, an updated metric for prioritizing species with threatened evolutionary history, showing it prioritizes species with fewer close relatives more than the original EDGE method.

Gene Transfer based Phylogenetics: Analytical Expressions and Additivity via Birth/Death Theory

This paper develops a new method for phylogenetics using gene transfer models and birth-death theory, achieving additivity and accurate results in both simulations and real data.

The probability of joint monophyly of all species in an arbitrary species tree.

The paper derives the probability of joint monophyly for arbitrary numbers of groups in arbitrary species trees, generalizing previous results and providing bounds.

Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference

The paper analyzes the expected lengths of pendant edges in phylogenetic trees under birth-death processes and applies findings to biodiversity and tree inference.

Accuracy in near-perfect virus phylogenies

The paper analyzes accuracy in phylogenetic trees under near-perfect conditions, showing that false positive rates are low even with short edges.

Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events

The paper examines conditions under which edge length ratios on phylogenetic trees can order evolutionary events, highlighting limitations of molecular clock assumptions.

An Evolutionary Process Without Variation and Selection

The paper proposes a new evolutionary process, Self-Other Reorganisation (SOR), that explains cumulative adaptive change in domains where acquired traits are retained, contrasting with Darwinian evolution.

Formal Links between Feature Diversity and Phylogenetic Diversity

This paper establishes a mathematical condition under which phylogenetic diversity and feature diversity coincide and explores their relationship through cooperative game theory concepts.

A Model of the Transition to Behavioural and Cognitive Modernity using Reflexively Autocatalytic Networks

The paper models the transition to behavioral and cognitive modernity using autocatalytic networks, suggesting genetic mutations enabled more flexible and unified semantic networks.

The structure of autocatalytic networks, with application to early biochemistry

This paper extends RAF theory to analyze autocatalytic networks in archaeal and bacterial metabolism, introducing new algorithms for visualizing and understanding early biochemistry structures.

Terraces in Gene Tree Reconciliation-Based Species Tree Inference

The paper analyzes terraces in gene tree reconciliation-based species tree inference, showing how incomplete gene trees can lead to multiple optimal species trees with identical scores.

Autocatalytic chemical networks preceded proteins and RNA in evolution

The paper identifies autocatalytic networks in ancient microbial metabolism, showing small-molecule catalysis preceded polymers in biochemical evolution.

Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models

This paper identifies and formalizes symmetries in birth-death models by swapping birth and death rates, showing their preservation under sampling and relevance to phylodynamic inference methods.

A Darwinian Uncertainty Principle

This paper demonstrates that accurately estimating both ancestral states and state change rates in phylogenetic trees is generally impossible from tip data, highlighting an inherent uncertainty in evolutionary reconstruction.

Evolutionary Isolation And Phylogenetic Diversity Loss Under Random Extinction Events

The paper shows that phylogenetic diversity loss under random extinction can be predicted from isolation value loss using a non-linear transformation, with error converging to zero as tree size increases.