Conservation Genomics

Conservation Genomics is the use of genomic study to aide in the preservation and viability of different and diverse organisms and populations. Genomics can be utilized in order to classify or argue diversity, hybridization, and history as well as identity different and similar species. Genomics can evaluate how these measures relate to effective population size as well as other ideas under the umbrella of conservation genetics, and overall biological conservation.[1] Genomic analysis can evaluate the extent to which alleles at certain loci interact with one and other to display nuanced ways which the genome may be intertwined.[2]

## Genetic diversity[edit]

Genetic diversity is a measure of the number of different alleles or combinations of alleles present in a population. This may be measured by the amount of heterozygosity measured compared to the expected amount of heterozygosity predicted by Hardy-Weinberg Equilibrium. Evaluating genetic diversity in the genomes of populations can inform us about levels of biodiversity and allele frequencies. Genetics play a large role in the extinction of species [3] and understanding how certain alleles accumulate and interact at the genome level is crucial to the preservation of those species.

## Heterozygosity[edit]

One of the most important measures of genomic health is the ratio of expected heterozygosity to measured heterozygosity. Generally, an individual or species with more heterozygous alleles have a higher chance of survival. This is known as heterosis [4]. Low levels of heterozygosity is a sign of possible concern for a species or organism. Evaluating the genomes of organisms that exist in an endangered species or population segment can provide insight to the severity of their endangerment. This method can be used to classify and rank species as well. A high level of genomic heterozygosity may not only be a bad marker for the survivability of a species, but it also may have negative effects on the genetic diversity created through crossing over and linkage disequilibrium.

## Linkage disequilibrium[edit]

Linkage disequilibrium is a concept that defines the non-random bond between two alleles in the genome. Measures of linkage disequilibrium are useful tools for gene and genome mapping [5]. A linkage between two genes may be due to their positions relative to each other in the genome or it may be due to selection acting to favor certain combinations of alleles. On a genomic scale, linkage disequilibrium plays a large analytical role. The term linkage disequilibrium concedes that there may also be a disruption or lack of linkage between two alleles. Any sort of deviation from the expected linkage between two alleles is considered linkage disequilibrium. In the age of genetic analysis in the use of conservation, understanding how alleles interact with each other to build genomes is imperative to understanding how genomic diversity, and conservation of such, can be aided.

## Applications[edit]

Genomics and genomic analysis provide a bigger picture explanation of aggregate smaller genetic evaluations. Different relationships and reasoning can be drawn from the data presented by genomics than compared to that data that can be drawn from genetics. Genomics is beginning its use in the field of invasive species where it is thought that understanding how genomes drive invasive processes can help better protect native species from their devastating effects[6]. These studies are aimed at tackling the major issue of habitat damage and disrupted ecosystems that invasive species have caused.

Under historical contexts, understanding genomic analysis can teach us much about patterns and effects of natural processes. Historical genomic evaluations have been performed on animals like Hominids[7], and even diseases like Multiple Sclerosis[8] and the Black Death[9] in order to determine their origins and evolutionary histories. In the case of diseases this information is often used in eradication efforts, as it would be used with invasive species. However, this data can be used in the preservation of species as well. Understanding the history of the genomics in a population is an important step in making decisions about how to correctly interpret and apply genomic analysis for conservation today.

In conservational contexts specifically, genomics can be used to research and understand how the relationships amongst the factors listed above effect an organisms fitness. The study of organisms through a genomic lens can lead to knowledge about their history that can be applied today.

### Hybridization[edit]

Hybridization practices, as they become a larger player in conservation may be impacted by genomic research. Hybridization can create entirely new allelic relationships and disequilibria. Understanding these factors is important in the interests of effective conservation efforts. Furthermore, studying these new relationships in hybrids can continue to provide insight in the efforts to conserve species. Hybridization still has many critics and has been shown to cause reduced fitness amongst natural populations. There are still many questions about the consequences of hybridization on evolution and genetic health of species[10]. Genomic studies may help to draw conclusions about new allelic relationships and how they may effect the outcomes for those species.

## Current Landscape[edit]

The current landscape of conservation genomics is still in its infancy. New ways to apply and understand genomics for the use of conservation are arising, and there is much thought that the understanding of gene interactions plays an important role in conservation. Currently, despite genomics being valuable to the conservation sphere, there is not enough of a connection between the researchers who study it and those with the means to apply it[11].

## References[edit]

1\. https://www.nature.com/subjects/conservation-genomics

2\.  Stange, M., Barrett, R.D.H. & Hendry, A.P. The importance of genomic variation for biodiversity, ecosystems and people. Nat Rev Genet 22, 89–105 (2021). https://doi.org/10.1038/s41576-020-00288-7

3\. Richard Frankham,Genetics and extinction,Biological Conservation,Volume 126, Issue 2,2005,Pages 131-140,

ISSN 0006-3207,https://doi.org/10.1016/j.biocon.2005.05.002.

4\. "Effective Population Size - an overview | ScienceDirect Topics" . Retrieved 2023-02-11

5\. latkin M. Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. Nat Rev Genet. 2008 Jun;9(6):477-85. doi: 10.1038/nrg2361. PMID: 18427557; PMCID: PMC5124487

6\.  Matheson, P., McGaughran, A. Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates. Sci Rep 12, 13987 (2022). https://doi.org/10.1038/s41598-022-17937-y

7\.  Allentoft, M.E., Sikora, M., Fischer, A. et al. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. Nature 625, 329–337 (2024). https://doi.org/10.1038/s41586-023-06862-3

8\.  Samira Asgari et al. Nature, Springer Nature, Jan 10, 2024,Nature 625, 247-249 (2024). doi: https://doi.org/10.1038/d41586-023-03977-5

9\.  Spyrou, M.A., Musralina, L., Gnecchi Ruscone, G.A. et al. The source of the Black Death in fourteenth-century central Eurasia. Nature 606, 718–724 (2022). https://doi.org/10.1038/s41586-022-04800-3

10\. (1)  Benjamin M Moran, Cheyenne Payne, Quinn Langdon, Daniel L Powell, Yaniv Brandvain, Molly Schumer (2021) The genomic consequences of hybridization. https://doi.org/ eLife 10:e69016

11\. Hogg, C.J. Translating genomic advances into biodiversity conservation. Nat Rev Genet(2023).https://doi.org/10.1038/s41576-023-00671-0

1. ^ "Conservation Genomics". Nature Portfolio. Retrieved 03/12/2024. `{{cite web}}`: Check date values in: `|access-date=` (help)
2. ^ Stange, Madlen; Barrett, Rowan D. H.; Hendry, Andrew P. (February 2021). "The importance of genomic variation for biodiversity, ecosystems and people". Nature Reviews Genetics. 22 (2): 89–105. doi:10.1038/s41576-020-00288-7. ISSN 1471-0064. PMID 33067582. S2CID 223559538.
3. ^ Frankham, Richard (2005-11-01). "Genetics and extinction". Biological Conservation. 126 (2): 131–140. Bibcode:2005BCons.126..131F. doi:10.1016/j.biocon.2005.05.002. ISSN 0006-3207.
4. ^ "Effective Population Size - an overview | ScienceDirect Topics". www.sciencedirect.com. Retrieved 2024-03-12.
5. ^ Slatkin, Montgomery (June 2008). "Linkage disequilibrium — understanding the evolutionary past and mapping the medical future". Nature Reviews Genetics. 9 (6): 477–485. doi:10.1038/nrg2361. ISSN 1471-0056. PMC 5124487. PMID 18427557.
6. ^ Matheson, Paige; McGaughran, Angela (2022-08-17). "Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates". Scientific Reports. 12 (1): 13987. Bibcode:2022NatSR..1213987M. doi:10.1038/s41598-022-17937-y. ISSN 2045-2322. PMC 9385848. PMID 35977991.
7. ^ Allentoft, Morten E.; Sikora, Martin; Fischer, Anders; Sjögren, Karl-Göran; Ingason, Andrés; Macleod, Ruairidh; Rosengren, Anders; Schulz Paulsson, Bettina; Jørkov, Marie Louise Schjellerup; Novosolov, Maria; Stenderup, Jesper; Price, T. Douglas; Fischer Mortensen, Morten; Nielsen, Anne Birgitte; Ulfeldt Hede, Mikkel (January 2024). "100 ancient genomes show repeated population turnovers in Neolithic Denmark". Nature. 625 (7994): 329–337. Bibcode:2024Natur.625..329A. doi:10.1038/s41586-023-06862-3. ISSN 1476-4687. PMC 10781617. PMID 38200294.
8. ^ Asgari, Samira; Pousaz, Lionel A. (January 2024). "Prehistoric events might explain European multiple sclerosis risk". Nature. 625 (7994): 247–249. Bibcode:2024Natur.625..247A. doi:10.1038/d41586-023-03977-5. PMID 38200304. S2CID 266931476.
9. ^ Spyrou, Maria A.; Musralina, Lyazzat; Gnecchi Ruscone, Guido A.; Kocher, Arthur; Borbone, Pier-Giorgio; Khartanovich, Valeri I.; Buzhilova, Alexandra; Djansugurova, Leyla; Bos, Kirsten I.; Kühnert, Denise; Haak, Wolfgang; Slavin, Philip; Krause, Johannes (June 2022). "The source of the Black Death in fourteenth-century central Eurasia". Nature. 606 (7915): 718–724. Bibcode:2022Natur.606..718S. doi:10.1038/s41586-022-04800-3. ISSN 1476-4687. PMC 9217749. PMID 35705810.
10. ^ Moran, Benjamin M; Payne, Cheyenne; Langdon, Quinn; Powell, Daniel L; Brandvain, Yaniv; Schumer, Molly (2021-08-04). Wittkopp, Patricia J (ed.). "The genomic consequences of hybridization". eLife. 10: e69016. doi:10.7554/eLife.69016. ISSN 2050-084X. PMC 8337078. PMID 34346866.
11. ^ Hogg, Carolyn J. (2023-11-27). "Translating genomic advances into biodiversity conservation". Nature Reviews Genetics: 1–12. doi:10.1038/s41576-023-00671-0. ISSN 1471-0064. PMID 38012268. S2CID 265465265.