The genome of the most recent common ancestor is generally not available but can greatly facilitate the inference of demographic history and the detection of local adaptations. Here, we present a protocol for applying local ancestry inference in present-day samples to reconstruct ancestral genomes. We describe steps for estimating haplotypes, inferring local ancestry, and assembling ancestral haplotypes. This protocol describes the analytic steps of reconstructing ancestral genomes using the example data of the Miao and She target populations. For complete details on the use and execution of this protocol, please refer to Gao et al..
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.xpro.2024.103580 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Protocol for reconstructing ancestral genomes from present-day samples by applying local ancestry inference.
STAR Protoc
January 2025
State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China. Electronic address:
The genome of the most recent common ancestor is generally not available but can greatly facilitate the inference of demographic history and the detection of local adaptations. Here, we present a protocol for applying local ancestry inference in present-day samples to reconstruct ancestral genomes. We describe steps for estimating haplotypes, inferring local ancestry, and assembling ancestral haplotypes.
View Article and Find Full Text PDF"Chance and Necessity" on the Molecular Evolution of REV3 (a Catalytic Subunit of DNA Polymerase ζ)-The Dual Roles of Translesion and Neuronal Extension.
Genes Cells
January 2025
Department of Genetic Biochemistry, The National Institutes of Biomedical Innovation, Health and Nutrition, Shinjuku-ku, Tokyo, Japan.
Catalytic subunit of DNA polymerase ζ (REV3), involved in translesion-replication is evolutionarily conserved from yeast and plants to higher eukaryotes. However, a large intermediate domain is inserted in REV3 of humans and mice. The domain has "DUF4683" region, which is significantly similar to human neurite extension and migration factor (NEXMIF).
View Article and Find Full Text PDFEvolution and Functional Diversification of Serine Racemase Homologs in Bacteria.
J Mol Evol
January 2025
Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY, 40546-0312, USA.
Amino acid racemases catalyze the interconversion of L- and D-amino acids, maintaining intracellular levels of both D- and L-amino acids. While alanine and glutamate racemases are widespread in bacteria, serine racemase (SerR) is predominantly found in animals. Recently, homologs of animal SerR were reported in some bacterial genomes, but their evolutionary distribution and functional roles remain poorly understood.
View Article and Find Full Text PDFCommon Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities.
J Mol Evol
January 2025
Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
The diversity in dermal pigmentation and plumage color among domestic chickens is striking, with Black Bone Chickens (BBC) particularly notable for their intense melanin hyperpigmentation. This unique trait is driven by a complex chromosomal rearrangement on chromosome 20 at the Fm locus, resulting in the overexpression of the EDN3 (a gene central to melanocyte regulation). In contrast, the inhibition of dermal pigmentation is regulated by the Id locus.
View Article and Find Full Text PDFThe ancestral genome's tale University of Chicago Press, 2025. 160 pp.
Science
January 2025
The reviewer is at the Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Narratives that invoke ancient DNA must be crafted with care, argues an archaeologist.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!