Phylogenetic Patterns of Diversification and Extinction

Phylogenetic patterns of diversification and extinction reveal the mechanisms by which life radiates into novel forms and, conversely, succumbs to environmental or competitive pressures. Analyses of time-calibrated phylogenetic trees have uncovered heterogeneous rates of species formation (speciation) and disappearance (extinction) across clades, through geological time and in response to abiotic and biotic factors. Key themes include density-dependent processes, in which speciation slows as ecological niches fill; trait-dependent dynamics, where particular characteristics influence diversification trajectories; and the recognition of survivorship biases that can mask true macroevolutionary trends. Integrating molecular phylogenies with the fossil record has further refined our understanding of speciation modes, revealing that perceived discrepancies often stem from differing assumptions rather than fundamental conflicts in the data. Contemporary research employs increasingly sophisticated statistical and computational tools to disentangle complex mixtures of diversification regimes, quantify rate shifts across lineages and time, and test hypotheses regarding ecological limits to biodiversity. Such approaches illuminate not only the history of life on Earth but also the potential resilience or vulnerability of clades in the face of ongoing environmental change.

Research from Nature Portfolio

Recent studies have applied cladogenetic state-dependent models to demonstrate that changes in geographic range size during speciation are ubiquitous and that, contrary to some earlier observations, species with smaller ranges often diversify more slowly once range dynamics are properly accounted for. These findings reconcile theoretical expectations with empirical patterns by showing how localised events such as island colonisation can override broad-scale range influences.

A conceptual framework known as the “birth–death chronospecies” model has been developed to reconcile disparate estimates of speciation and extinction rates from fossil and molecular datasets. This model clarifies the definitions of speciation and extinction processes, allowing a coherent joint analysis that explains much of the apparent incongruence and highlights how differences in rate estimates inform on speciation modes.

Global sampling of a soil protist complex has revealed an exceptional radiation of microscopic diatoms since the Eocene–Oligocene transition, driven largely by colonisation of new regions followed by isolation. This study underscores the role of allopatric speciation in micro-organisms and illustrates that large-scale radiations are not confined to macro-organisms but extend across the tree of life.

Phylogenetic Patterns of Diversification and Extinction publication trend

The graph below shows the total number of articles in phylogenetic patterns of diversification and extinction across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogeny: A branching diagram that represents the evolutionary relationships among species or other taxonomic units based on shared ancestry.

Speciation: The process by which one lineage splits into two or more genetically distinct lineages, leading to the formation of new species.

Extinction: The termination of a lineage, resulting in the permanent loss of one or more species from the tree of life.

Diversification rate: The net outcome of speciation and extinction processes, typically expressed as the difference or ratio between speciation and extinction rates over time.

Birth–death model: A mathematical framework modelling speciation (birth) and extinction (death) events through time, used to infer diversification dynamics from phylogenetic data.

Density dependence: A process by which diversification rates change as a function of existing species richness, often leading to a deceleration of speciation as ecological niches become occupied.

References

1. The relationship between geographic range size and rates of species diversification. Nature Communications (2023).
2. Closing the gap between palaeontological and neontological speciation and extinction rate estimates. Nature Communications (2018).
3. Global radiation in a rare biosphere soil diatom. Nature Communications (2020).
4. RPANDA: an R package for macroevolutionary analyses on phylogenetic trees. Methods in Ecology and Evolution (2016).
5. History is written by the victors: The effect of the push of the past on the fossil record. Evolution (2018).
6. Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees. PLOS ONE (2014).