Related Experiment Video
Updated: Nov 4, 2025
10:23
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
347
Why extinction estimates from extant phylogenies are so often zero
Stilianos Louca1, Matthew W Pennell2
1Department of Biology, University of Oregon, 1210 University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR 97403, USA.
Current Biology : CB
|May 21, 2021
Summary
Phylogenetic studies often report zero extinction rates due to congruent diversification scenarios. This mathematical artifact, not biological reality, explains why extinction rate estimates are zero-inflated in phylogenetic analyses.
Area of Science:
- Evolutionary Biology
- Phylogenetics
- Computational Biology
Background:
- Time-calibrated phylogenies (extant timetrees) are used to estimate speciation and extinction rates via birth-death models.
- Previous studies often report zero extinction, contradicting fossil records and the high historical extinction rates.
Purpose of the Study:
- To provide a novel explanation for the "zero-inflated" extinction rate estimates in phylogenetic studies.
- To resolve the long-standing discrepancy between phylogenetic estimates and fossil-based extinction rates.
Main Methods:
- Investigated the impact of congruent diversification scenarios on birth-death model fitting.
- Analyzed simulated phylogenetic trees and 121 empirical trees to test predictions.
Main Results:
- Identified "congruent" diversification scenarios that are statistically indistinguishable from true scenarios using extant timetrees.
- Demonstrated that estimation methods can converge to biologically unrealistic scenarios with negative extinction rates, leading to zero-inflated estimates.
- Confirmed predictions using both simulated and empirical phylogenetic data.
Conclusions:
- Model congruencies, not necessarily model violations, explain zero-inflated extinction rate estimates in phylogenetics.
- This finding resolves a major controversy in estimating historical extinction rates from extant timetrees.
- Highlights the practical consequences of model congruencies in phylogenetic inference.
Related Concept Videos
03:21Phylogenetic Trees
48.4K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
48.4K
02:07Conservation of Declining Populations
11.7K
Conservation of declining population focuses on ways of detecting, diagnosing, and halting a population decline. The approach uses methods to prevent populations from going extinct.
11.7K
02:55The Evidence for Evolution
45.5K
Genetic variations accumulating within populations over generations give rise to biological evolution. Evolutionary changes can result in the formation of novel varieties and entire new species. These changes are responsible for the diverse forms of life inhabiting the planet. The evidence for evolution suggests that all living organisms descended from common ancestors.
45.5K
02:54Evolutionary Relationships through Genome Comparisons
6.5K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.5K
01:50Threats to Biodiversity
25.1K
There have been five major extinction events throughout geological history, resulting in the elimination of biodiversity, followed by a rebound of species that adapted to the new conditions. In the current geological epoch, the Holocene, there is a sixth extinction event in progress. This mass extinction has been attributed to human activities and is thus provisionally called the Anthropocene. In 2019 the human population reached 7.7 billion people and is projected to comprise 10 billion by...
25.1K
02:04Conservation of Small Populations
15.7K
Small population sizes put a species at extreme risk of extinction due to a lack of variation, and a consequent decrease in adaptability. This weakens the chances of survival under pressures such as climate change, competition from other species, or new diseases. Large populations are more likely to survive pressures such as these, as such populations are more likely to harbor individuals that have genetic variants that are adaptive under new stresses. Small populations are much less...
15.7K