A short history of humans and biodiversity
It is undeniable that humans have unprecedented environmental impacts, especially with continued global industrialization (1). Among the myriad anthropogenic transformations, greenhouse gas emissions stand as a colossal contributor to global climate change. Concurrently, alterations like deforestation, expansive urbanization, and the release of harmful chemicals have further exacerbated the environmental crisis. These shifts led to new fields of study such as conservation biology, a crisis discipline focusing on biodiversity preservation (2). Despite living in a scientific era, much of our planet’s biodiversity remains largely unknown or understudied, placing a weighty responsibility on conservation biologists to navigate anthropogenic impacts. They often formulate recommendations based on partial knowledge due to technological limitations or time constraints, while also grappling with the fear of failure (3).
New advances, new scientific fields
With industrialization came technological advances in computation and biology. One of the most notable advances was in the field of genomics, beginning with the Molecular Clock concept in the 1960s (4), followed by the complete genome sequencing of bacteria in the 1990s (5,6) and the (almost) complete sequencing of worm, fly, and human genomes rounding out the century (7–9). This transformative period exponentially expanded molecular tools available for biodiversity research. This opened the doors for inferences of genomic population structure and diversity, investigation of the molecular response of organisms to stimuli, and even a new understanding of heritability outside of the genetic sequence. Consequently, the shift from conservation genetics, which predominantly involves a few genes or selectively neutral regions, to conservation genomics, encompassing the entirety of organisms’ genomes, unfolded and provided further insights into responses to selective pressures (10,11).
‘Omics and conservation
Incorporating genomic and molecular tools into conservation biology allows investigation into questions along evolutionary timescales, such as whether a population contains the genetic diversity necessary to adaptat to new or changing environmental variables (12). Genomics facilitates a better understanding of contemporary status of a population, as well as a view of its past, such as a history of bottlenecks or selective events. This understanding of genomic history and current population status enhances predictions of persistence through selection events. It also helps assess the potential negative repercussions of limited gene flow, inbreeding depression, or genetic drift, which might lead to maladaptation or eventual extirpation. Key metrics like allelic richness, the proportion of alleles unique to a single population, relatedness/inbreeding, heterozygosity, and effective population size (Ne) estimates aid in delineating crucial populations to serve as conservation units for biodiversity preservation or even the need for evolutionary or genetic rescue or imperiled populations (13,14).
Transcriptomics
Molecular tools also play a role in discerning how individuals and populations respond to contemporary stressors over physiological timescales. Transcriptomics, the study of genome-wide RNA expression, is especially valuable as it can now be applied to both wild and laboratory populations (15). This is especially useful in linking a particular phenotype to its molecular mechanism by measuring changes in RNA expression. Importantly, the broad range of data developed from transcriptomic approaches expands our knowledge of stressors’ effects on organisms (16).
Methylomics/Epigenomics
Another molecular response is DNA methylation, where nucleotides are selectively methylated, likely altering gene function. Observations of consistent DNA methylation changes across generations contribute to the study of epigenomics, heritable changes in gene function that do not rely on DNA sequence alterations (17). It is by this feature that genome-wide DNA methylation is both a direct response at physiological timescales and potentially a heritable, population-wide change capable of affecting species along evolutionary timescales. As it becomes easier to link molecular changes to their phenotypic results, this allows for a more functional assessment of molecular data. In turn, this facilitates the scaling of phenotypic consequences of molecular findings upwards through levels of biological organization, potentially leading to evolutionary insights.
Some considerations
Given the constraints of experience, time, study viability, and finances often found in the field of conservation biology, the choice of which ‘omics method to use when addressing conservation challenges warrants careful consideration. Out of genomics, transcriptomics, and epigenomics, the most widely accessible method is genomics, especially when studying entire populations. Genomics allows for the reliable sequencing of the largest number of samples at once, especially using protocols featuring reduced representation. This method is also easily compatible with non-destructive sampling schemes, a critical aspect considering that the loss of individuals, especially in small populations, can have detrimental consequences. As stated above, genomics methods are ideal in analyses concerning the current diversity of a population.
Another key feature of genomics studies is they are equally possible for organisms lacking a reference genome as they are for organisms with more developed genomic resources. In contrast, transcriptomic and epigenomic methods are more resource-intensive on all fronts and therefore (historically) find fewer applications in conservation. Rigorous experimental designs for most transcriptomic questions necessitate multiple samples and replicates, challenging feasibility outside of laboratory conditions. DNA methylation research requires more complicated laboratory preparation that may not be readily accessible. Furthermore, the availability of high-quality genomes or transcriptomes for the species is essential for optimal data analysis using these methods.
Harnessing potential
Perhaps the most exciting feature of incorporating these various ‘omics into conservation questions is the potential for the comprehensive view. For example, after understanding the existing variation within populations using genomics, transcriptomics of those populations along altitudinal gradients could reveal differential gene expression in consistent genes or suites of genes. Following that, running a DNA methylation assay may reveal the actual mechanism behind the expression changes in the form of differential methylation along genes or regulatory regions. This framework easily generates forward-thinking questions, linking expression changes to heritable methylation and enabling hypotheses along a population’s evolutionary trajectory, whether driven by epigenomic alterations or conventional genomic changes.
Looking forward
As humans have made significant strides in both altering our environment and advancing the technology to comprehend and mitigate these changes, the complexity of anthropogenic effects continues to grow. Correspondingly, questions and hypotheses are becoming more intricate. ‘Omics stands at the forefront of biodiversity conservation, offering a glimpse of hope in an otherwise uncertain future on Earth. It is indeed thrilling to anticipate the forthcoming technologies and advancements that will further propel the field, providing a beacon of hope in an otherwise uncertain future on Earth.
Note: this post was adapted from the fourth chapter of my dissertation.
References
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'Omics in the Anthropocene 