H. Morlon

Exploring congruent diversification histories with flexibility and parsimony

The paper introduces a new method to explore congruence classes of diversification rate trajectories in phylogenies, showing that rapid changes in speciation and extinction rates are not conserved across classes but can be narrowed by selecting parsimonious trajectories.

Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions

The paper distinguishes cophylogenetic signal from phylogenetic congruence using simulations, showing that global-fit methods detect signal without congruence, while event-based methods indicate stronger evolutionary dependency.

Telling mutualistic and antagonistic ecological networks apart by learning their multiscale structure

The paper distinguishes between mutualistic and antagonistic ecological networks using multiscale structure analysis and machine learning, finding structural differences beyond global metrics.

Recent evolutionary origin and localized diversity hotspots of mammalian coronaviruses

This study investigates the evolutionary origin and diversification of mammalian coronaviruses, finding recent origination in bats and localized diversity hotspots in East Asia and Europe.

A Comparison of Deep Learning Architectures for Inferring Parameters of Diversification Models from Extant Phylogenies

This study compares deep learning architectures for inferring diversification model parameters from phylogenies, finding that CNNs and RNNs with LTTs outperform other methods for CRBD, while BISSE requires topology and tip states.

Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota

The paper extends multivariate phylogenetic models to estimate phylosymbiosis, ancestral microbiota composition, and integration in vertebrates, finding significant conservation despite host diversification.

The build-up of the present-day tropical diversity of tetrapods

This study uses spatio-temporal phylogenetic and paleontological models to show that extra-tropical extinctions and tropical species outflow, rather than area or energy, shape present-day tetrapod diversity.

Deep Learning from Phylogenies for Diversification Analyses

This paper applies deep learning to diversification analysis using phylogenies, achieving accuracy comparable to likelihood-based methods but with significantly faster computation.

Comparing different computational approaches for detecting long-term vertical transmission in host-associated microbiota

The paper compares computational methods for detecting vertical transmission in primate gut microbiota, finding that different approaches perform better under varying sequence variation conditions and that only a small fraction of gut bacteria is vertically transmitted.

The birth-death diffusion leading to present-day Mammal diversity

This paper introduces a new model to estimate diversification rates in mammals, finding that speciation rates increased 10-20 My before the K-Pg extinction.

Estimating clade-specific diversification rates and palaeodiversity dynamics from reconstructed phylogenies

The paper automates a method to estimate clade-specific diversification rates and palaeodiversity dynamics using phylogenetic trees, detecting declines in diversity for three of four tested groups.

Structure and specialization of mycorrhizal networks in phylogenetically diverse tropical communities

The paper investigates mycorrhizal networks in tropical plant communities, finding that fungal specialization varies by lineage and that fungi are shared among phylogenetically distant plants.

Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks

The paper evaluates two methods for detecting phylogenetic signal in bipartite interaction networks and recommends using network permutations for significance testing.

Detecting the ecological footprint of selection

This study introduces a new form of competition in ecological simulations to better detect selection's impact on community structure using trait data.

Fast and accurate estimation of species-specific diversification rates using data augmentation

This paper introduces a fast inference method for estimating species-specific diversification rates using data augmentation and applies it to bird radiation data.

Global drivers of eukaryotic plankton biogeography in the sunlit ocean

The paper examines global eukaryotic plankton biogeography, revealing that diversity and body size influence distribution patterns across ocean basins and latitudes.

Global drivers of obligate mycorrhizal symbionts diversification

The paper analyzes diversification dynamics of Glomeromycotina fungi using molecular data and sensitivity analyses, finding a decline in speciation rates over the past 500 million years.

Prior hypotheses or regularization allow inference of diversification histories from extant timetrees

The paper investigates the implications of multiple congruent models with different diversification dynamics but equal likelihood for empirical trees, concluding they do not invalidate hypothesis-driven or data-driven approaches.

Tempo and mode of morphological evolution are decoupled from latitude in birds

This study examines how latitude affects the tempo and mode of morphological evolution in birds, finding weak and clade-dependent effects.

Model-based inference of punctuated molecular evolution

The paper develops a model to detect episodes of fast divergence in molecular evolution and applies it to snake venom protein genes to identify spikes in the phylogeny.

Cheating emergences in the arbuscular mycorrhizal mutualism: a network and phylogenetic analysis

The paper analyzes the evolution and specialization of mycoheterotrophic cheating plants and their fungal partners in a global network, revealing constraints on cheating emergence through fungal specialization.

Characterizing and comparing phylogenetic trait data from their normalized Laplacian spectrum

This paper introduces a non-parametric framework for analyzing phylogenetic trait data using the normalized Laplacian spectrum to cluster and characterize phenotypic patterns.

Reliable Phylogenetic Regressions for Multivariate Comparative Data: Illustration with the MANOVA and Application to the Effect of Diet on Mandible Morphology in Phyllostomid Bats

The paper develops and validates a multivariate phylogenetic regression method for high-dimensional phenotypic data, demonstrating its effectiveness in analyzing mandible morphology and diet in phyllostomid bats.

Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past

This paper develops a probabilistic method to estimate species diversity over time from phylogenetic data and applies it to frogs, finding that an ancient group declined in diversity due to reduced speciation.

Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations

This study evaluates environment-dependent diversification models using simulations and empirical phylogenies to assess their statistical performance and applicability to macroevolutionary analysis.

An assessment of phylogenetic tools for analyzing the interplay between interspecific interactions and phenotypic evolution

This study evaluates phylogenetic tools for analyzing how interspecific interactions and phenotypic evolution influence each other, finding that current methods often fail to detect interaction effects and that process-based models perform better.