The Genomic Imprint of Evolution

 

Over a century ago, scientists relied on physical and anatomical evidence for the reconstruction of the evolutionary past, namely in the form of transitional fossils in geology/paleontology and vestigial structures in anatomy. It wasn't until the late 1960's and early 1970's that biologist Allan Wilson and colleagues utilized protein electrophoresis to analyze genetic variation among different populations, which led to a better understanding of human origins, including the "Out of Africa" hypothesis, which suggests that modern humans originated in Africa. This continues to be the consensus among scientists today.

Whole Genome Sequencing (WGS)

Whole Genome Sequencing (WGS) is a technique utilized in order to obtain complete DNA sequence of an organism's genome. In order for this to be done, all the genetic material of said organism must be analyzed, including both coding and non-coding regions. The first step of WGS involves collection some form of DNA from an organism, which could be blood, tissue, or other kind of sample. Genomic DNA is then isolated from the sample using DNA extraction methods. Following preparation, the DNA fragments undergo sequencing using high-throughput platforms such as Illumina, PacBio, or Oxford Nanopore. These platforms employ diverse sequencing technologies and methodologies, and generally involve decoding the sequence of nucleotides (A, T, C, and G) within each DNA fragment. Upon completion of sequencing, raw sequence data undergoes analysis through bioinformatics tools and algorithms. This process encompasses quality assessment, aligning sequence reads with a reference genome (if available), detecting genetic variations like single nucleotide polymorphisms (SNPs) and structural variants, and annotating genomic attributes.

Genome Sequencing: Evolutionary Relationships & Evolutionary Past 

Once a genome of a species is sequenced, it can be compared with the genome of another, which aids in the construction of phylogenetic trees which show how the two (or more) species are related to one another, including tracing evolutionary splits. The sequences can also uncover genetic changes throughout lineages, such as crucial mutations, gene duplications, and gene losses; all important processes that helped shape the current genome. Genomic data in addition to fossils found in a certain region can help reveal and pinpoint adaptations that assisted in an organisms survival in that specific period and environment. Instances of horizontal gene transfer, in which genetic material is exchanged between species, can also be detected. Analyzing the genetic diversity within a population of a species can illuminate the dynamics of its evolution, encompassing phenomena like genetic drift, natural selection, and gene flow. This knowledge plays a pivotal role in comprehending the evolutionary trajectories of populations across successive generations.

Genomic Fossils

Genomic fossils are remnants of ancient genetic material or sequences that have been preserved within the genomes of modern organisms. Transposable elements (TEs), also called jumping genes, represent a category of genomic fossils. These DNA sequences possess the ability to relocate or "jump" within a genome, occasionally integrating into fresh positions. As time elapses, certain TEs lose functionality, resulting in preserved "fossilized" duplicates within the genome. Investigation of these vestiges unveils the varieties of TEs that were operative in progenitor species, shedding light on their influence on genome organization and operation. Pseudogenes are gene duplicates that have accumulated mutations, causing them to lose their original functionality. These sequences act as genomic relics, mirroring the evolutionary journey of genes and gene families. Through cross-species comparison of pseudogenes, scientists can deduce instances of gene loss, duplication events, and alterations in function that have transpired throughout evolutionary processes. Occasionally, alleles or genetic variations that were previously beneficial can persist as "fossilized" remnants in the genome despite losing their selective advantage. These (known as ancient alleles) offer insights into past adaptations, selective pressures, and evolutionary shifts prompted by changes in the environment. Also, Certain non-coding DNA sequences, such as regulatory elements or sequences involved in genome organization, can be highly conserved across species. 

References

Darwinian genomics and diversity in the tree of life