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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...

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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.

Gene Evolution - Fast or Slow?

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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...

Gene Evolution - Fast or Slow?

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Reticulation, divergence, and the phylogeography-phylogenetics continuum.

Scott V Edwards¹, Sally Potter², C Jonathan Schmitt³

¹Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138; sedwards@fas.harvard.edu.

Proceedings of the National Academy of Sciences of the United States of America

|July 20, 2016

Summary

Next-generation sequencing reveals that reticulation, including recombination and introgression, complicates phylogeography. Gene trees remain crucial for understanding population divergence and speciation, even with complex evolutionary histories.

Keywords:

coalescent theory comparative phylogeography introgression monsoon tropics species trees

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A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

Evolutionary Biology
Genetics
Bioinformatics

Background:

Phylogeography traditionally relied on animal mitochondrial DNA (mtDNA) due to its nonrecombining nature and rapid evolution.
The advent of next-generation sequencing (NGS) has highlighted the prevalence of reticulation (recombination and introgression) within and across genomes.
Understanding reticulate evolution is critical for accurate phylogeographic and speciation analyses in the NGS era.

Purpose of the Study:

To explore the impact of reticulation on comparative phylogeography, speciation analysis, and phylogenomics using NGS data.
To assess the continued relevance of gene trees in phylogeographic studies amidst increasing complexity.
To examine phylogeographic patterns across the Carpentarian Barrier in northern Australia as a case study.

Main Methods:

Analysis of multilocus phylogeographic data across the Carpentarian Barrier.
Review of forces contributing to reticulate patterns in phylogeography, including introgression and contact zones.
Discussion of demographic modeling approaches incorporating reticulation at genomic and population levels.

Main Results:

Divergence across the Carpentarian Barrier is common but temporally and demographically heterogeneous, often correlating with taxonomic distinctness.
Reticulate patterns are generated by various factors, including introgression, contact zones, and potential selection on molecular markers.
NGS data reveal a greater prominence of reticulation than previously appreciated from PCR-based nuclear gene studies.

Conclusions:

Gene trees, whether explicit or implicit, remain fundamental to phylogeography, even with complex evolutionary histories.
Demographic models must incorporate reticulation at both genomic and population levels for robust inferences.
The centrality of gene trees in phylogeography persists in the NGS era, necessitating advanced analytical frameworks.