Recent Evolution in Rattus norvegicus Is Shaped by Declining Effective Population Size

Area of Science:

• Genomics
• Evolutionary Biology
• Mammalian Genetics

Background:

• The brown rat (Rattus norvegicus) is a significant pest and a crucial model organism in biomedical research.
• Understanding the genetic variation and evolutionary forces in wild rat populations is essential for both pest control and research applications.

Purpose of the Study:

• To investigate the selective and demographic forces shaping genome variation in wild brown rats.
• To compare genomic patterns between brown rats and house mice to understand the role of genetic drift in mammalian evolution.

Main Methods:

• Genome sequencing of 12 wild-caught brown rats from their ancestral range in Northeast China.
• Comparative genomic analysis with Rattus rattus and Mus musculus castaneus (house mouse).
• Pairwise Sequentially Markovian Coalescent (PSMC) analysis to infer demographic history.

Main Results:

• Estimated a recent effective population size (Ne) for brown rats based on silent site diversity.
• Inferred a population size bottleneck in wild rats approximately 20,000 years ago.
• Observed an increased frequency of mildly deleterious mutations and negative estimates for the rate of adaptive evolution (α) in rats compared to mice.
• Documented a slower decay of linkage disequilibrium in wild rats post-bottleneck.

Conclusions:

• Genetic drift plays a significant role in mammalian genome evolution, particularly in species with smaller effective population sizes.
• The recent population bottleneck in brown rats has led to an accumulation of deleterious mutations and reduced adaptive potential.
• These findings provide insights into the evolutionary trajectory of Rattus norvegicus and its implications for its role as a pest and research model.