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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...

Lineage Commitment

Lineage Commitment

Commitment is the process whereby stem cells:

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

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.
In contrast, regions which code...

Synteny and Evolution

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...

Phylogeny

Phylogeny

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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Related Experiment Video

Updated: Jun 26, 2025

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM

Lineage Tracing and Clonal Analysis in Developing Cerebral Cortex Using Mosaic Analysis with Double Markers MADM

Published on: May 8, 2020

Scuphr: A probabilistic framework for cell lineage tree reconstruction.

Hazal Koptagel^1,2, Seong-Hwan Jun³, Joanna Hård⁴

¹School of EECS, KTH Royal Institute of Technology, Stockholm, Sweden.

Plos Computational Biology

|May 9, 2024

Summary

This summary is machine-generated.

Scuphr reconstructs cell lineage trees using DNA sequencing data, offering faster and more accurate analysis. This method addresses common challenges in single-cell sequencing for developmental and cancer research.

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Published on: December 18, 2015

Area of Science:

Genomics
Computational Biology
Developmental Biology

Background:

Cell lineage tree reconstruction is crucial for understanding development, differentiation, and cancer.
Single-cell sequencing technologies offer high-resolution insights into cellular processes.
Existing methods face challenges with noise and accuracy in complex biological systems.

Purpose of the Study:

To introduce Scuphr, a novel computational method for cell lineage tree reconstruction.
To utilize both bulk and single-cell DNA sequencing data for improved accuracy.
To address and incorporate common errors in single-cell DNA sequencing data.

Main Methods:

Scuphr employs a distance-based approach to infer relationships between cells.
It utilizes the neighbor-joining algorithm for phylogenetic tree reconstruction.
The method incorporates handling of allelic dropouts and amplification errors inherent in single-cell DNA sequencing.

Main Results:

Scuphr demonstrates faster analysis compared to state-of-the-art methods due to its parallel design.
The method achieves higher accuracy in reconstructing cell lineage trees.
Robustness was validated using diverse synthetic datasets and a biological dataset of 18 cells.

Conclusions:

Scuphr provides an efficient and accurate solution for cell lineage tree reconstruction.
The method is robust and capable of handling technical challenges in single-cell DNA sequencing.
Scuphr advances the analysis of cellular development and disease progression using genomic data.