The biodiversity we see around us is the product of millions of years of evolution on Earth. To understand how plants and animals evolve or exist on this planet, one can use the deoxyribonucleic acid (DNA) molecules present in the cells of most living organisms. DNA provides biological instructions passed from one generation to the next, also known as the “process of modifying descendants.” The ability to use this history stored in DNA is an important part of the biologist’s toolkit. It enables us to understand the tree of life-the origin of species, the process of speciation, the evolution of form and function, the relationship between organisms and their response to environmental changes (evolutionary adaptation).
Certain mutations in genes (changes in DNA sequence) can be transformed into changes in the proteins they encode, resulting in variants of isoenzymes called enzyme proteins. In the 1970s, researchers used isozyme analysis, which can use its charge to detect protein variants as an agent for studying genetic variation. By the 1980s, more than a thousand animals had been screened on dozens of isozyme loci, allowing comparisons between different groups. A study found that due to the recent sharp decline in the population of South Africa, the genetic variation of cheetahs in South Africa is very low. The loss of individuals and subsequent inbreeding results in their low genetic diversity.
The development of Sanger sequencing in the late 1970s and the polymerase chain reaction (PCR) in the mid-1980s revolutionized molecular biology. It allowed us to copy DNA from a small number of samples and determine the sequence of units that formed the DNA sequence. Using these technologies to generate DNA sequences spanning multiple individuals and species, scientists can directly view genetic material, detect mutations, and measure genetic variation. In one of the earliest studies using DNA sequence data, researchers compared individual genes in an entire species to construct an evolutionary tree that divided living organisms into three major categories. Since then, multiple genes and non-protein coding DNA sequences have been combined and analyzed to establish relationships between species. For example, a large global flowering plant evolutionary tree helped us understand the characteristics that help certain groups expand in novel environments. DNA sequence data is particularly useful in identifying morphologically secretive species, which cannot be distinguished based on their appearance.
In addition to understanding the evolutionary relationship between different species, DNA sequences are also used to understand how genetic variation is geographically distributed in species or closely related species. Since the 1970s and 1980s, maternally inherited genes have been widely used in these studies. For example, they found that with the closure of the Isthmus of Panama, populations of several marine species spread between the Atlantic and Pacific Oceans. Such gender-related markers have also been used to study the social structure of animals. They indicate that female humpback whales follow specific migration routes in different generations across ocean basins. In addition to the use of gene sequences, non-protein coding regions of DNA (such as microsatellites) have been widely used to understand the relationships between individuals within a species. A recent study used DNA obtained from fecal samples to study the impact of forest fragmentation on the genetic connectivity of four mammals in central India. Microsatellite data found that the impact of human factors on a species depends on its biology, with tigers having the greatest impact, followed by leopards, lazy bears and jungle cats.
The rapid development of sequencing technology now allows us not only to sequence genes, but also to sequence large fragments of DNA in the entire genetic material of organisms. These genomic methods use parallel sequencing to generate hundreds of gigabytes of DNA sequence data, which brings analysis problems related to high computing power and complex mathematical models. Many of these techniques can also use trace amounts of DNA in the natural environment, which allows researchers to quickly investigate the biodiversity of poorly studied areas and taxa. For example, thousands of DNA sequences in soil samples allow scientists to estimate the invertebrate diversity of a remote island in New Zealand. High-resolution genomic data can help researchers distinguish closely related species when traditional genetic markers have failed, just as the cichlid fish of Lake Victoria in Africa did. Advances in technology have also allowed researchers to use poor quality DNA, such as the case of the eastern lowland gorilla, where old museum specimens have helped scientists understand the genetic effects of the rapid population decline in recent history.
Bharti Dharapuram is a postdoctoral researcher at the CSIR Center for Cellular and Molecular Biology. She is interested in the processes that drive the patterns of species distribution and genetic diversity, especially when there is insufficient research on terrestrial and marine invertebrates.
Jahnavi Joshi is an assistant professor at the CSIR Cell and Molecular Biology Center in Hyderabad, India. She mainly uses arthropods as a model system to study Asian tropical forest systems, biogeography, diversity and community gathering.
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