gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

The evolution of critical thermal limits of life on Earth

(2021) Joanne M. Bennett et al.   Nature Communications

Climatic effects on niche evolution in a passerine bird clade depend on paleoclimate reconstruction method

(2021) Alison Eyres et al.   EVOLUTION

Angiosperm speciation cools down in the tropics

(2020) Javier Igea et al.   ECOLOGY LETTERS

Harnessing paleo‐environmental modeling and genetic data to predict intraspecific genetic structure

(2020) Glenn Yannic et al.   Evolutionary Applications

The role of the Neotropics as a source of world tetrapod biodiversity

(2020) Andrea S. Meseguer et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Low availability of code in ecology: A call for urgent action

(2020) Antica Culina et al.   PLOS BIOLOGY

Global Cenozoic Paleobathymetry with a focus on the Northern Hemisphere Oceanic Gateways

(2020) E.O. Straume et al.   GONDWANA RESEARCH

An astronomically dated record of Earth’s climate and its predictability over the last 66 million years

(2020) Thomas Westerhold et al.   SCIENCE

A minimalist model of extinction and range dynamics of virtual mountain species driven by warming temperatures

(2019) Jonathan Giezendanner et al.   PLoS One

Non-random latitudinal gradients in range size and niche breadth predicted by spatial patterns of climate

(2019) Erin E. Saupe et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

A simple spatially explicit neutral model explains the range size distribution of reef fishes

(2019) Adriana Alzate et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

The evolution of latitudinal temperature gradients from the latest Cretaceous through the Present

(2019) Laiming Zhang et al.   EARTH-SCIENCE REVIEWS

A minimal model for the latitudinal diversity gradient suggests a dominant role for ecological limits

(2019) Rampal S. Etienne et al.   AMERICAN NATURALIST

A process‐based model supports an association between dispersal and the prevalence of species traits in tropical reef fish assemblages

(2019) Giulia Francesca Azzurra Donati et al.   ECOGRAPHY

The carrying capacity for species richness

(2019) David Storch et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes

(2019) Théo Gaboriau et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Building mountain biodiversity: Geological and evolutionary processes

(2019) Carsten Rahbek et al.   SCIENCE

Humboldt’s enigma: What causes global patterns of mountain biodiversity?

(2019) Carsten Rahbek et al.   SCIENCE

Spatio-temporal climate change contributes to latitudinal diversity gradients

(2019) Erin E. Saupe et al.   Nature Ecology & Evolution

A 450 million years long latitudinal gradient in age‐dependent extinction

(2019) Daniele Silvestro et al.   ECOLOGY LETTERS

Extinction intensity during Ordovician and Cenozoic glaciations explained by cooling and palaeogeography

(2019) Erin E. Saupe et al.   Nature Geoscience

The more-individuals hypothesis revisited: the role of community abundance in species richness regulation and the productivity-diversity relationship

(2018) David Storch et al.   ECOLOGY LETTERS

Growth-competition-herbivore resistance trade-offs and the responses of alpine plant communities to climate change

(2018) Loïc Pellissier et al.   FUNCTIONAL ECOLOGY

Mountains of diversity

(2018) Alexander Zizka et al.   NATURE

Eocene greenhouse climate revealed by coupled clumped isotope-Mg/Ca thermometry

(2018) David Evans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The biomass distribution on Earth

(2018) Yinon M. Bar-On et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves

(2018) Thiago F. Rangel et al.   SCIENCE

PLANT DIVERSITY IN OCEANIC ARCHIPELAGOS: REALISTIC PATTERNS EMULATED BY AN AGENT-BASED COMPUTER SIMULATION

(2018) Madli Jõks et al.   ECOGRAPHY

Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages

(2018) Ben H. Warren et al.   EVOLUTION

Synchronous tropical and polar temperature evolution in the Eocene

(2018) Margot J. Cramwinckel et al.   NATURE

Reconstructing the Geography of Speciation from Contemporary Biodiversity Data

(2018) Alexander Skeels et al.   AMERICAN NATURALIST

The Latitudinal Diversity Gradient: Novel Understanding through Mechanistic Eco-evolutionary Models

(2018) Mikael Pontarp et al.   TRENDS IN ECOLOGY & EVOLUTION

Closing the gap between palaeontological and neontological speciation and extinction rate estimates

(2018) Daniele Silvestro et al.   Nature Communications

Inferring community assembly processes from macroscopic patterns using dynamic eco-evolutionary models and Approximate Bayesian Computation (ABC)

(2018) Mikael Pontarp et al.   Methods in Ecology and Evolution

Evolving biodiversity patterns in changing river networks

(2018) Rachata Muneepeerakul et al.   JOURNAL OF THEORETICAL BIOLOGY

Linking species diversification to palaeo-environmental changes: A process-based modelling approach

(2017) Patrice Descombes et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Spatial imprints of plate tectonics on extant richness of terrestrial vertebrates

(2017) Patrice Descombes et al.   JOURNAL OF BIOGEOGRAPHY

R Package gdistance: Distances and Routes on Geographical Grids

(2017) Jacob van Etten   Journal of Statistical Software

Speciation gradients and the distribution of biodiversity

(2017) Dolph Schluter et al.   NATURE

Process, Mechanism, and Modeling in Macroecology

(2017) Sean R. Connolly et al.   TRENDS IN ECOLOGY & EVOLUTION

Progress in climate modelling

(2017) Graham Simpkins   Nature Climate Change

Global determinants of zoogeographical boundaries

(2017) Gentile Francesco Ficetola et al.   Nature Ecology & Evolution

Impacts of Niche Breadth and Dispersal Ability on Macroevolutionary Patterns

(2016) Huijie Qiao et al.   AMERICAN NATURALIST

Mechanistic simulation models in macroecology and biogeography: state-of-art and prospects

(2016) Juliano Sarmento Cabral et al.   ECOGRAPHY

A neutral-metabolic theory of latitudinal biodiversity

(2016) Derek P. Tittensor et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Niche width impacts vertebrate diversification

(2016) Jonathan Rolland et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

The origin of species richness patterns along environmental gradients: uniting explanations based on time, diversification rate and carrying capacity

(2016) Mikael Pontarp et al.   JOURNAL OF BIOGEOGRAPHY

Late Cenozoic onset of the latitudinal diversity gradient of North American mammals

(2016) Jonathan D. Marcot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plate tectonics drive tropical reef biodiversity dynamics

(2016) Fabien Leprieur et al.   Nature Communications

RPANDA: an R package for macroevolutionary analyses on phylogenetic trees

(2016) Hélène Morlon et al.   Methods in Ecology and Evolution

Origins of Biodiversity

(2016) Michael J. Benton   PLOS BIOLOGY

Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities

(2016) Paula Villa Martín et al.   PLoS Computational Biology

Ecological and Evolutionary Drivers of Geographic Variation in Species Diversity

(2015) Paul V.A. Fine   Annual Review of Ecology Evolution and Systematics

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments

(2015) Constantinos Tsirogiannis et al.   ECOGRAPHY

Phylogenies support out-of-equilibrium models of biodiversity

(2015) Marc Manceau et al.   ECOLOGY LETTERS

The general dynamic model: towards a unified theory of island biogeography?

(2015) Michael K. Borregaard et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis

(2015) Jeet Sukumaran et al.   SYSTEMATIC BIOLOGY

Age-Dependent Speciation Can Explain the Shape of Empirical Phylogenies

(2015) Oskar Hagen et al.   SYSTEMATIC BIOLOGY

Ecological and evolutionary perspectives on community assembly

(2015) Gary G. Mittelbach et al.   TRENDS IN ECOLOGY & EVOLUTION

Approximate Bayesian Computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT

(2015) Thijs Janzen et al.   Methods in Ecology and Evolution

When should species richness be energy limited, and how would we know?

(2014) Allen H. Hurlbert et al.   ECOLOGY LETTERS

Phylogenetic approaches for studying diversification

(2014) Hélène Morlon   ECOLOGY LETTERS

The role of ocean gateways on cooling climate on long time scales

(2014) Willem P. Sijp et al.   GLOBAL AND PLANETARY CHANGE

Is diversification rate related to climatic niche width?

(2014) Carola Gómez-Rodríguez et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Functional trait space and the latitudinal diversity gradient

(2014) C. Lamanna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Best Practices for Scientific Computing

(2014) Greg Wilson et al.   PLOS BIOLOGY

Rates of projected climate change dramatically exceed past rates of climatic niche evolution among vertebrate species

(2013) Ignacio Quintero et al.   ECOLOGY LETTERS

Early origin of viviparity and multiple reversions to oviparity in squamate reptiles

(2013) R. Alexander Pyron et al.   ECOLOGY LETTERS

WHAT CAN MULTIPLE PHYLOGENIES SAY ABOUT THE LATITUDINAL DIVERSITY GRADIENT? A NEW LOOK AT THE TROPICAL CONSERVATISM, OUT OF THE TROPICS, AND DIVERSIFICATION RATE HYPOTHESES

(2013) Roland Jansson et al.   EVOLUTION

Where am I and why? Synthesizing range biology and the eco-evolutionary dynamics of dispersal

(2013) Alexander Kubisch et al.   OIKOS

Global patterns of terrestrial vertebrate diversity and conservation

(2013) C. N. Jenkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale phylogenetic analyses reveal the causes of high tropical amphibian diversity

(2013) R. A. Pyron et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The origins of tropical marine biodiversity

(2013) Brian W. Bowen et al.   TRENDS IN ECOLOGY & EVOLUTION

An empiricist's guide to theoretical predictions on the evolution of dispersal

(2013) A. Duputie et al.   Interface Focus

The role of biotic interactions in shaping distributions and realised assemblages of species: implications for species distribution modelling

(2012) Mary Susanne Wisz et al.   BIOLOGICAL REVIEWS

Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

(2012) Nathan G. Swenson et al.   ECOLOGY

Linking ecological niche, community ecology and biogeography: insights from a mechanistic niche model

(2012) Juliano Sarmento Cabral et al.   JOURNAL OF BIOGEOGRAPHY

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide

(2012) W. D. Kissling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Update of Wallace's Zoogeographic Regions of the World

(2012) B. G. Holt et al.   SCIENCE

The evolution of species interactions across natural landscapes

(2011) Mark C. Urban   ECOLOGY LETTERS

Statistical inference for stochastic simulation models - theory and application

(2011) Florian Hartig et al.   ECOLOGY LETTERS

Warm, not super-hot, temperatures in the early Eocene subtropics

(2011) C. R. Keating-Bitonti et al.   GEOLOGY

Can stochastic geographical evolution re-create macroecological richness-environment correlations?

(2011) J. Sebastián Tello et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Thermal adaptation and ecological speciation

(2011) I. KELLER et al.   MOLECULAR ECOLOGY

Pattern-oriented modelling: a 'multi-scope' for predictive systems ecology

(2011) V. Grimm et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reconciling molecular phylogenies with the fossil record

(2011) H. Morlon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian phylogeny reveals recent diversification rate shifts

(2011) T. Stadler   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Influence of Late Quaternary Climate-Change Velocity on Species Endemism

(2011) B. Sandel et al.   SCIENCE

A simple polytomy resolver for dated phylogenies

(2011) Tyler S. Kuhn et al.   Methods in Ecology and Evolution

Spatial patterns of phylogenetic diversity

(2010) Hélène Morlon et al.   ECOLOGY LETTERS

Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist

(2010) Marti J. Anderson et al.   ECOLOGY LETTERS

The virtual ecologist approach: simulating data and observers

(2010) Damaris Zurell et al.   OIKOS

Deterministic tropical tree community turnover: evidence from patterns of functional beta diversity along an elevational gradient

(2010) N. G. Swenson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Shape and Temporal Dynamics of Phylogenetic Trees Arising from Geographic Speciation

(2010) Alex L. Pigot et al.   SYSTEMATIC BIOLOGY

Is There a Latitudinal Gradient in the Importance of Biotic Interactions?

(2009) Douglas W. Schemske et al.   Annual Review of Ecology Evolution and Systematics

Patterns and causes of species richness: a general simulation model for macroecology

(2009) Nicholas J. Gotelli et al.   ECOLOGY LETTERS

Advancing the metabolic theory of biodiversity

(2009) James C. Stegen et al.   ECOLOGY LETTERS

Estimating demographic models for the range dynamics of plant species

(2009) Juliano S. Cabral et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

(2008) Catherine H. Graham et al.   ECOLOGY LETTERS

Spatial species-richness gradients across scales: a meta-analysis

(2008) Richard Field et al.   JOURNAL OF BIOGEOGRAPHY