How genes and genomes play a role in the future of conservation
The following is based on the article 'The importance of genomic variation for biodiversity, ecosystems and people' by M. Stange, D. Barrett and A. Hendry, first published in Nature Reviews Genetics on October 16 2020. Links to that article and other relevant reads can be found in the 'Read more' section below this post.
A 2019 UN global assessment report on biodiversity estimated that approximately one million species of living things are at risk around the world of extinction, and that it was mostly our fault. Biodiversity is a word that’s thrown around enough that most people are likely to have heard it. Most people are fairly cognisant of the fact that more biodiversity is a good thing, less biodiversity is a bad thing, and biodiversity is related to the diversity of living things. Biodiversity is, like a lot of concepts in ecology, a deceptively complex and multi-layered word, and today I’ll be talking about the role of genetics in the future of biodiversity management and sustenance.
Types of biodiversity
Biodiversity can be thought of as a number of categories all contributing to one overall measure. These categories include species identity (the presence or absence of a particular species in a community), species diversity (the number of species in a community), functional diversity (the variation of physical traits within a community), evolutionary diversity (how long ago members of a community diverged from each other on an evolutionary tree), and intraspecific genetic variation (variation in genomes within a single species population in a community). All of these categories are, worldwide, in decline. For our purposes, we will be focusing on the last of these categories, intraspecific genetic variation (which we will call, from now on, genetic diversity), and its relationship with contemporary evolution and ecosystem services.
Makes sense, but what are contemporary evolution and ecosystem services?!?!
We’ll get to ecosystem services in a hot second. Contemporary evolution, also known as rapid evolution, is a type of evolution which occurs (you guessed it) rapidly. On the evolutionary timescale, we’ll define rapid as taking place over less than a few hundred years. Contemporary evolution assists in increasing the genetic diversity within a population in a species, as the faster evolution works its magic, the more genetic differences appear within a population in a given amount of time. There are a number of ways contemporary evolution and genetic diversity can be accelerated artificially. These include deliberate breeding programs, aimed at breeding relatively unrelated individuals in populations so genes become more diverse, translocations (bringing in individuals from outside the population), and migration (usually not artificial in ecosystems, but can be, and creates a larger, more diverse gene pool).
Before we get to ecosystem services, it’s worth asking (and answering) a quick question.
Why do we even want more biodiversity? Enter the banana
Ah, the banana. So delicious in overpriced breakfast smoothies. And yet in our lifetime, liable to go completely extinct. This may not be news to you, but in case you were unaware, all our bananas (at least in Western countries) are part of what’s known as a monoculture. This means they are all genetically identical (give or take a base pair here or there), and clones of each other. There are advantages to this: bananas have consistent textures and flavours, you have less chance of growing a failed banana tree, you can brag about eating clones for breakfast, the list goes on. However, it means that if a disease were to ravage a banana population, they would be doomed, because they all have the exact same susceptibilities. In fact, such a disease already does exist, and it’s called Panama disease. And it’s caused absolute chaos for banana communities across the world. If it manages to infiltrate banana populations where it isn’t already found, that may be curtains for the humble banana.
The answer to this problem is genetic diversity. If we have a population of four thousand people, and five of them is naturally, genetically immune to Dragonfyre*, if Dragonfyre swept through the population, the five individuals with immunities would survive and could start their town afresh (or engage in a Battle Royale style survivor showdown, which would make for better television but weaker biology). These genetic immunities will have likely arisen as a part of a random mutation in the population’s genome, and only been useful by complete chance. Genetic diversity makes populations more robust to varying threats, both diseases, and changing environmental conditions.
Now to ecosystem services
Ecosystem services, or Nature’s Contributions to People (NCPs) are the ways in which natural ecosystems assist us (humans) in living in the world. It’s a very anthropocentric way of viewing nature, but it is also historically the way of viewing nature that’s attracted the most funding to conservation programs, so it’s something we’d probably better get used to if we want our natural world to thrive. The paper identifies eighteen categories of ecosystem services, which are listed below.
Habitat creation and maintenance
Pollination dispersal
Regulation of air quality
Regulation of climate
Regulation of ocean acidification
Regulation of freshwater quantity, location and timing
Regulation of freshwater and coastal water quality
Formation, protection and decontamination of soils and sediments
Regulation of the impacts and hazards of extreme events
Pest, disease and stress regulation
Energy
Food and feed
Materials and assistance
Medicinal, biochemical and genetic resources
Learning, artistic, scientific and technological inspiration
Physical and experiential interactions with nature
Supporting identities (religious and spiritual connection to the land)
Maintenance of options
Now we’ve covered exactly why diversity is important, we can talk about how we can use scientific techniques to measure (and potentially regulate) diversity.
The old and the new: Genetic techniques used to measure genetic diversity
Traditionally, methods used to quantify and analyse genetic diversity can be categorised under the umbrella term ‘classical genetics’. These have included analysing variation in populations of the nucleic acid at one specific location on the genome (single-locus variation) or quantitative genetic tools such as measuring the variation in average phenotypes in a population. This also involves measuring heritability, which is the proportion of variation in a population that can be attributed to genetic diversity and not to other environmental factors. These methods can be highly useful when attempting to locate ‘keystone genes’ in an ecosystem. A keystone gene is a gene which exists in an organism in an ecosystem which has a disproportionate effect on the nature of that ecosystem. An example is in the cottonwood tree, where variation in a single gene leads to variation in levels of tannins produced which in turn affects the species that will thrive in the surrounding soil.
Recently, more modern ‘genomic’ techniques have been used in assessing genetic diversity in ecosystems. This is a more holistic approach than the classical methods, which tend to focus on individual genes and locations on organisms’ genomes. Genomic techniques instead accept the complex interconnectedness of the genome, and how ecosystem-affecting phenotypes probably often occur from a range of different interactions within the genome. These complexities can be understood on two levels: the population (intraspecific) level, and the community (interspecific) level.
Population genomics in ecology
There are complexities within genomes which dictate the phenotypes of organisms which are still beginning to be understood by modern genetic science. A key example of this is epistasis. Epistasis is common in genetics, and is an interaction between two or more genes whereby one of the genes (the epistatic gene) blankets the functioning of another gene. Of course, whether there is epistasis will depend on the structure of each of the genes and their specific combination of nucleotides (their genotype). Another example of genetic complexity within a species is structural genomic variation. This is variation not in the genotype of a particular gene, but its location or direction. This may not be obvious at first, but the location and direction of a gene within the genome can heavily influence its functioning. For instance, the direction of a specific gene within Atlantic cods contributes significantly to whether the individual cod is capable of migrating to colder waters. Another key consideration is, as always, epigenetics. Epigenetics refers to characteristics of the chromosome which aren’t visible in the DNA sequence alone, and depend on variations in the chromosome-associated proteins, and the level and nature of extra molecules attached to the DNA. Variations in epigenetic structure strongly affect phenotypes which can shape and influence ecosystems.
Community genomics in ecology
If things weren’t complex enough with the single genome of a single species, to understand the extent of the influence of genetics in biodiversity requires considering the interactions of many genomes within many species. This includes factors like interspecific epistasis, where a particular allele (genotype) being expressed by one species in an ecosystem will result in an allele of another species going unexpressed. For instance, if the allele in the first species allowed that species to monopolise a certain resource, an allele in another species which usually helped in the processing of that resource would be useless and would likely end up unexpressed. Related to this, alleles of certain species have been shown to evolve in tandem with alleles of other species they come into contact with them in the environment (and both are affected, possibly in different ways, by the environment itself…and probably other species too). And all of that runs equally true for interspecific epigenetic variation as well. Sound complicated yet? It should. The relationships between genes within ecosystems is influenced by so many factors (including, possibly, factors we are totally unaware of) that it’s very hard to conceptualise, let alone actually begin to measure. However, understandings in these interactions are fast moving beyond anecdotal examples into the realm of nuanced and complex understandings, with astounding amounts of data being developed on organisms’ genomes every year. So once we have the power of knowledge, what comes next?
The future
Genetic engineering is a term thrown around probably too much without enough understanding for my liking, and is a very powerful and perhaps dangerous biotechnological tool we now wield. Furthermore, it is currently being contemplated as a tool to be used in the improvement of our conservation and biodiversity efforts moving forward. Gene editing tools such as CRISPR have made gene editing much simpler and much more accurate, with developments being made on what seems like a weekly basis. Genes necessary for survival in dwindling species may be able to be inserted and known genes may be tweaked for improvements in existing species. Actually, alterations for this purpose are known as gene drives and are already taking place (gene drives made in an attempt to prevent extinction of a species are heroically termed ‘rescue drives’). We even have tools to alter the epigenetic structure of the genome. But without full understanding of a lot of the complexities of intra and interspecific genomic interactions, this may be a double-edged sword. Without holistic understandings, we are unaware of the full consequences of genetic engineering in ecosystems, and may end up being at the mercy of a new nature of our own accidental design.
Or maybe, we’ll just have more bananas! Time will tell.
Read more:
https://www.nature.com/articles/s41576-020-00288-7 - Original article
https://fruitworldmedia.com/index.php/featured/banana-disaster-example-history-repeating/ - More info on bananas
*Dragonfyre is, unfortunately, fictional. Immunities to Dragonfyre doubly so.
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