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Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

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Detecting Environment-Dependent Diversification From Phylogenies: A Simulation Study and Some Empirical

Eric Lewitus¹, Hélène Morlon¹

¹IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France.

Systematic Biology

|December 23, 2017

Summary

Macroevolutionary studies now use phylogenetic methods to assess how environmental factors influence speciation and extinction rates. This research validates these models using paleodatasets and simulations, showing their effectiveness in understanding diversification dynamics.

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Area of Science:

Macroevolutionary biology
Phylogenetics
Paleoecology

Background:

Understanding drivers of diversification is key in macroevolution.
Phylogenetic methods using time-calibrated trees and paleoenvironmental data estimate environmental influences on diversification.
Current methods effectively estimate speciation and extinction rate variations with abiotic factors like temperature and sea level.

Purpose of the Study:

To compile biotic and abiotic paleodatasets for use in macroevolutionary models.
To assess the statistical properties and performance of environment-dependent diversification models using simulations.
To infer environment-dependent diversification in empirical phylogenies (Cetacea and Ruminantia).

Main Methods:

Compilation of biotic and abiotic paleodatasets.
Simulations to test statistical properties of environment-dependent models.
Application of models to empirical phylogenies (Cetacea and Ruminantia) using temperature and $\delta^{13}C$ data.

Main Results:

Environment-dependent models accurately recover speciation and extinction parameters.
Models correctly identify the environmental drivers when speciation is environment-dependent.
Model performance is influenced by environment-dependency strength, tree size, missing taxa, and paleoenvironmental curve characteristics.

Conclusions:

Environment-dependent models are statistically robust for macroevolutionary analyses.
These models successfully infer diversification patterns linked to specific environmental variables in empirical clades.
The study provides a crucial statistical assessment for utilizing paleoenvironmental data in macroevolutionary research.