Exploring the methods and measurement of genetic diversity

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Genetic diversity is the biological wealth within species. It’s what gives species the ability to adapt when faced with environmental transformations.

Because it fosters resilience and provides a wider scope for adaptation, genetic diversity is crucial in maintaining biodiversity. However, assessing genetic diversity spans various scales — ranging from landscape to species, population, individual, and gene levels — so a multifaceted approach is needed for its measurement and evaluation.

3 dimensions of diversity

Within the framework of biodiversity, the concept of diversity manifests in 3 dimensions: taxonomic, phylogenetic, and functional.

Traditionally, emphasis on “taxonomic” diversity has centered on species diversity classified by Linnaean taxonomy, whereas recent strides have broadened the scope to include traits and phylogenetic placement.

Phylogeny, and phylogenetic diversity, considers the placement of species on the family tree that unites all living things. From this view, a diverse ecosystem will have species from many different parts of the tree, not just very closely related ones.

Functional diversity considers the variations in roles that species play in ecosystems, produced by their phenotype. Phenotypes are the ways in which genes manifest in the individual: For example, several individuals may have different gene variations (genotype) for eye color – they are genetically diverse. But, if all of these variations produce a brown eye color – they are phenotypically the same.

Often we think of functional diversity in terms of benefits for the whole ecosystem that one or several species create through their biology or activity. This could be how several trees offer shade for other species to hide in, or how several fungi fill the role of breaking down dead wood.

Even within the same species individuals may have different phenotypes, leading them to serve different functions in the ecosystem. Yet very distantly related species may converge on a similar phenotype (like bats and birds) and so serve similar functions.

Techniques for quantifying trait and phylogenetic diversity have flourished, enhancing our understanding and enabling their assessment in the alpha, beta, and gamma diversity context. These diverse indices assess richness, evenness, and turnover, allowing a comprehensive evaluation of genetic diversity in organisms.

What we can learn from genetics

Understanding the genetics of populations and of communities of species can be valuable — informing research and conservation tools. In fact, traditional conservation genetics has been essential to conservation work.

Conservation efforts for endangered species, either in species reintroduction programs or in zoos, need to ensure 2 things: that small populations do not become inbred and that genetic diseases do not spread through the small populations. Genetic material collected from multiple species can be used to identify the species found in an ecosystem, which is especially useful for identifying cryptic species that are extremely difficult to differentiate based upon morphology alone. Modern molecular ecology’s technological and computational advances have massively increased the scales at which genetic work can be conducted.

Modern genetic approaches have made it possible to process more genetic material at reduced costs. This enables us take a focused approach by rapidly sequencing the entire genetic code of multiple individuals of a species to gain a deep understanding of population genetics for the species. Alternatively, a small region of the genome (a genetic barcode) could be sequenced from many individuals, enabling us to identify the species they belong to without any traditional taxonomic expertise. This analysis of the genetic material of many species or individuals is called metagenomics.

Metagenomics is commonly employed in 1 of 2 ways in molecular ecology. The 1st, DNA barcoding, minimizes the effort needed to identify biological specimens collected using traditional survey techniques. A small amount of tissue taken from the specimen can be used to extract the specimen’s DNA. This DNA can be tagged with a genetic marker. Those can be repeated for an entire collection: The DNA can be sequenced and the species identified and matched to the specimen.

This is especially useful when different species have incredibly similar morphology (cryptic species) or when only a small amount of the individual was collected that is difficult to classify without the rest of the organism — such as a partial specimen or a hair sample. Additionally, if the genotype identified in the specimen doesn’t match any known records, a taxonomist has a great candidate for either a new species or a new addition to the genetic library. The need for a botanical survey on a site might be completely removed by barcoding the contents of a lawn mower!

The 2nd approach is used to identify species rapidly without the need to even encounter them. Environmental samples can be sequenced to identify organisms that live in the sample or that have shed environmental DNA (eDNA) into the sample. Soils, seawater, and even eDNA collected on specially designed air filters can be used to identify species. A similar approach is taken to the above, where DNA is extracted, labeled, and sequenced in a process is called DNA metabarcoding, which reflects that it concerns the metagenome of many species in a sample, rather than the identification a the genome of a single species (DNA barcoding).

DNA metabarcoding is rapidly evolving to allow practical uses. For example, unknown populations of endangered freshwater species can be identified from a series of water samples rather than through intensive manual searches across the watercourse. DNA barcoding is much faster and more powerful than traditional techniques for identifying bacteria and fungi through culturing those species in the lab. Additionally, as so many microbial species are unknown to science, phylogenetics can be used to infer the functions of bacteria, fungi, and protists by their genetic similarity to known species that are involved in cycling nutrients, photosynthesis, or other key environmental processes that support life.

Global-level approaches

The Kunming-Montreal Global Biodiversity Framework, a pivotal aspect of the Convention on Biological Diversity, aligns its Goal A with the preservation of genetic variation within populations. It aims to sustain the adaptive potential of both wild and domesticated species.

Advancements in biotechnologies have revolutionized genetic diversity estimation by leveraging genomic data, substantially reducing costs and enhancing data availability. The Food and Agriculture Organization of the United Nations (FAO), in collaboration with partners, has developed a practical guide that encompasses genomic methods for estimating genetic diversity, a part of biodiversity measurement. This guide underscores the importance of using genomic and demographic/pedigree data to complement population size data, offering enhanced precision in monitoring genetic diversity within livestock breeds.

Small and large-scale approaches

A notable application of these assessment approaches is observed in microbial systems, driven by advancements in molecular technology. Microorganisms’ essential roles in supporting ecosystems have propelled the need to quantify their diversity akin to fish diversity in the Amazon’s flooded forest. Techniques such as rarefaction are employed to counter sampling effects and ensure robust findings.

Large-scale analyses of biodiversity changes across the globe have revealed significant shifts in species composition, highlighting the importance of the alpha/beta/gamma perspective in interpreting ecosystem restructuring. Maintaining genetic diversity becomes paramount, as it bolsters ecosystem resilience, allowing species to adapt and survive in a rapidly changing environment.

Genetic diversity plays a pivotal role in the adaptive potential of species and ecosystem functioning. By leveraging sophisticated genomic methods and incorporating diverse indices, we can better understand, monitor, and conserve genetic diversity, fostering the resilience of species and ecosystems in an ever-changing world.

References

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