Biology subjects

McHugh, S. W.

Publications and source records attributed to McHugh, S. W..

5 recordsLinked to original sources

bioRxiv2026

Summarizing Evolutionary Trajectories from Phylogenetic Character Maps of Discrete Traits

Abstract.--When reconstructing phylogenetic character histories, biologists aim to identify distinct evolutionary trajectories, or paths of character state evolution. However, biologists typically wish to summarize the information representing large numbers of potential character histories for a single phylogeny. For discrete characters, few approaches exist for summarizing the number of unique evolutionary trajectories beyond the frequency of specific events (i.e., state transition types) or the time lineages spend in each state. Here, we introduce a framework for summarizing the evolutionary trajectories of discrete character histories by compressing them into trajectory trees, where branches represent unique character-evolution pathways rather than lineages. This framework includes a novel compressed tree representation, called a scenario tree, that retains temporal information, ensuring that each root-to-tip path represents a unique, temporally explicit evolutionary trajectory. We describe and apply several approaches to summarize phylogenetic trees into transition trees. We include visual summaries - such as consensus trajectory trees, trajectory tree tanglegrams, and"trajectory-through-time plots" - to compare how unique evolutionary trajectories accumulate across lineages and state transitions. We also include quantitative summaries, such as the time spent in unique evolutionary trajectories and the number of transitions that follow unique character-state transitions. We use our new trajectory-wise summaries to evaluate the adequacy of commonly used continuous-time Markov models of character evolution, which are memoryless and consider only the rates between pairs of states. We conducted multiple simulation-based experiments demonstrating the utility of our novel trajectory-wise approaches. We also apply our new trajectory-wise approaches to Greater Antillean Anolis lizard biogeography and ecomorph evolution, and find that Anoles evolved along considerably more unique evolutionary trajectories than expected under simulations of our best-fitting character evolution model. The number of unique evolutionary paths accumulated in an "early burst" pattern relative to simulated trajectories, with this burst being more intense than expected across all character state transition events.

evolutionary biology↗

bioRxiv2026

EMPIRE: The Ellipse Model for Phylogenetic Inference of Range Evolution

AO_SCPLOWBSTRACTC_SCPLOWMany phylogenetic models of historical biogeography exist for describing how lineages move and evolve over time. Here, we present the Ellipse Model for Phylogenetic Inference of Range Evolution (O_SCPLOWEMPIREC_SCPLOW), which models the movement and splitting of species range ellipses in continuous space, summarizing important attributes of each range, such as its position, size, and orientation. The framework allows us to reconstruct ancestral range ellipses, investigate rates governing important processes like movement, expansion, and elongation, and examine the spatial context of speciation, including asymmetric range inheritance at cladogenesis. We apply O_SCPLOWEMPIREC_SCPLOW to the Australian Sphenomorphinae, a group of skinks whose diversification has coincided with substantial climatic change over the past ~36 million years. We find that speciation events are positively associated with aridification, while daughter lineages post-speciation do not tend to show evidence of ecological partitioning.

evolutionary biology↗

bioRxiv2024

A Phylogenetic Model of Established and Enabled Biome Shifts

Where each species actually lives is distinct from where it could potentially survive and persist. This suggests that it may be important to distinguish established from enabled biome affinities when considering how ancestral species moved and evolved among major habitat types. We introduce a new phylogenetic method, called RFBS, to model how anagenetic and cladogenetic events cause established and enabled biome affinities (or, more generally, other discrete realized versus fundamental niche states) to shift over evolutionary timescale. We provide practical guidelines for how to assign established and enabled biome affinity states to extant taxa, using the flowering plant clade Viburnum as a case study. Through a battery of simulation experiments, we show that RFBS performs well, even when we have realistically imperfect knowledge of enabled biome affinities for most analyzed species. We also show that RFBS reliably discerns established from enabled affinities, with similar accuracy to standard competing models that ignore the existence of enabled biome affinities. Lastly, we apply RFBS to Viburnum to infer ancestral biomes throughout the tree and to highlight instances where repeated shifts between established affinities for warm and cold temperate forest biomes were enabled by a stable and slowly-evolving enabled affinity for both temperate biomes.

evolutionary biology↗

bioRxiv2022

Molecular early burst associated with the diversification of birds at the K-Pg boundary

Complex patterns of genome and life-history evolution associated with the end-Cretaceous (K- Pg) mass extinction event limit our understanding of the early evolutionary history of crown group birds [1-9]. Here, we assess molecular heterogeneity across living birds using a technique enabling inferred sequence substitution models to transition across the history of a clade [10]. Our approach identifies distinct and contrasting regimes of molecular evolution across exons, introns, untranslated regions, and mitochondrial genomes. Up to fifteen shifts in the mode of avian molecular evolution map to rapidly diversifying clades near the Cretaceous-Palaeogene boundary, demonstrating a burst of genomic disparity early in the evolutionary history of crown birds [11-13]. Using simulation and machine learning techniques, we show that shifts in developmental mode [14] or adult body mass [4] best explain transitions in the mode of nucleotide substitution. These patterns are related, in turn, to macroevolutionary shifts in the allometric scaling relationship between basal metabolic rate and body mass [15, 16]. In agreement with theoretical predictions, this scaling relationship appears to have weakened across the end-Cretaceous transition. Overall, our study provides evidence that the Chicxulub bolide impact [17] triggered integrated patterns of evolution across avian genomes, physiology, and life history that structured the evolutionary potential of modern birds.

evolutionary biology↗

bioRxiv2022

Jointly Modeling Species Niche and Phylogenetic Model in a Bayesian Hierarchical Framework

When studying how species will respond to climatic change, a common goal is to predict how species distributions change through time. Environmental niche models (ENMs) are commonly used to estimate a species environmental niche from observed patterns of occurrence and environmental predictors. However, species distributions are often shaped by non-environmental factors-including biotic interactions and dispersal barriers--truncating niche estimates. Though a truncated niche estimate may accurately predict present-day species distribution within the sampled area, this accuracy decreases when predicting occurrence at different places and under different environmental conditions. Modeling niche in a phylogenetic framework leverages a clades shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche estimation implemented in R called BePhyNE (Bayesian environmental Phylogenetic Niche Estimation). Under our model, species ENM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving as a multivariate Brownian motion. Through simulation analyses, we demonstrate model accuracy and precision that improve as phylogeny size increases. We also demonstrate our model on eastern United States Plethodontid salamanders and recover accurate estimates of species niche, even when species occurrence data is lacking and entirely informed by the evolutionary model. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and estimate niches of data-deficient species.

evolutionary biology↗