Convergent evolution and predictability of gene copy numbers associated with diets in mammals

Convergent evolution, the evolution of the same or similar phenotypes in phylogenetically independent lineages, is a widespread phenomenon in nature. If the genetic basis for convergent evolution is predictable to some extent, it may be possible to infer organismic phenotypes and adaptability based on genome sequence data. While repeated amino acid changes have been studied in association with convergent evolution, relatively little is known about the potential contribution of repeated gene copy number changes. In this study, we explore whether certain gene copy number changes are linked to diet shifts in mammals and assess if trophic ecology can be inferred from the copy numbers of a specific set of genes. Using 86 mammalian genome sequences, we identified several genes with higher copy numbers in herbivores, carnivores, and omnivores, even after phylogenetic corrections. We were able to confirm previous findings on genes such as amylase, olfactory receptor, and xenobiotic metabolism g..., The publicly available data were used. The scripts for processing the data are uploaded here., , This README file was generated on 2023-11-28 by Jun Kitano.

GENERAL INFORMATION

1. Title of Dataset: Analysis of convergent evolution and predictability of gene copy numbers associated with diets in mammals

2. Author Information
Principal Investigator Contact Information
Name: Jun Kitano
Institution: National Institute of Genetics
Address: Mishima, Shizuoka, Japan
Email:

3. Date of data collection: 2022-2023

4. Geographic location of data collection: Mishima, Japan

5. Information about funding sources that supported the collection of the data: NIG Summer Internship Program, JSPS Kakenhi (23KJ0483, 22H04925, and 22H04983), JST CREST (JPMJCR19S2 and JPMJCR20S2), and MEXT (JPMXD1521474594).

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain

2. Links to publications that cite or use the data:

Wilhoit, K., Yamanouchi, S., Chen. B.Y., Yamasaki., Y.Y., Ishikawa, A., Inoue, J., Iwasaki, W., and ...