An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles

Area of Science:

• * Evolutionary biology
• * Molecular genetics
• * Genomics

Background:

• * The temporal program of genome replication in yeast species of the *Lachancea* clade suggests replication origin dynamics drive evolutionary changes.
• * Understanding the evolutionary forces shaping replication timing is crucial for deciphering genome stability and function.

Purpose of the Study:

• * To develop and apply an evolutionary model to identify biases in replication origin dynamics.
• * To investigate the evolutionary pressures influencing the birth and death of replication origins.
• * To establish a predictive framework for studying replication timing evolution.

Main Methods:

• * Developed a birth-death process model for replication origins.
• * Utilized comparative genomic data from *Lachancea* yeast species.
• * Compared evolutionary models against empirical data to identify key pressures.

Main Results:

• * Replication origin birth and loss events are significantly influenced by evolutionary pressures.
• * Origins associated with higher double-stall probability of replication forks are disfavored.
• * Less efficient replication origins are more susceptible to evolutionary loss.

Conclusions:

• * The study provides an empirically grounded framework for evolutionary studies of replication timing.
• * Replication timing profiles are shaped by specific evolutionary biases acting on origin dynamics.
• * This model advances our understanding of genome replication evolution.