Haplotype Analysis

 

From spotting species to measuring genetic diversity

Every living thing leaves tiny traces of DNA in its surroundings through skin cells, scales, mucus, waste, or decomposing tissue. This “environmental DNA,” or eDNA, can be collected from water, soil, or sediment without ever catching, handling, or disturbing the animals themselves. Scientists filter a sample, extract the DNA it contains, and use it to work out what species have been present, often just from a few litres of water. Using eDNA to detect which species are present is a technique called metabarcoding and it is now a well-established, widely used tool in biodiversity monitoring. This document is concerned with a newer and more ambitious extension of that idea: using eDNA not just to say “this species is here,” but to say something about the genetic diversity within that species’ population. This information has traditionally required catching and physically sampling tissue from many individual animals.This distinction matters because genetic diversity (the variety in genetic makeup across individuals in a population) is a strong indicator of long-term resilience. A population can look numerically healthy while carrying very little genetic diversity, leaving it vulnerable to disease, environmental change, or sudden decline. Counting animals tells you about the present; genetic diversity tells you something about a population’s future prospects. One long-term study of wild fish found that losses in genetic diversity destabilised biomass production within just a few generations. This is an early warning sign that simple headcounts would have missed entirely (Prunier et al., 2020).

What is a haplotype?

A haplotype is a distinct genetic “signature”; a small cluster of genetic variations, or polymorphisms, that sit close together on a chromosome and so tend to be inherited as a single block, rather than being shuffled apart by the usual reshuffling of genes between generations (Nature Education, 2014). Because a haplotype is passed down largely intact, individuals who share a recent common ancestor such as a mother and her offspring often carry the exact same haplotype. Counting how many different haplotypes exist within a population, and how they’re distributed, therefore gives geneticists a workable proxy for how genetically diverse that population’s breeding individuals actually are.In practice, haplotypes are identified by sequencing a short, specific stretch of DNA known as a “barcode” region. These are the same regions used for species identification, but read closely enough to pick out small differences between individuals of the same species rather than just differences between species. Genes carried in mitochondria (the energy-producing structures within cells, inherited only from the mother) are especially useful for this because they mutate faster than most of the rest of the genome, giving more distinct variants to work with, and because every cell carries many copies of mitochondrial DNA, making it easier to detect in trace amounts from the environment.

How is haplotype currently used?

Historically, haplotype and broader intraspecific genetic diversity studies relied entirely on physical tissue samples (a fin clip, a blood sample, a swab) collected from individual animals one at a time. This remains the gold-standard, most precise approach, and is still the basis of most population genetics work today (Wright, 1937; Billington & Hebert, 1991). However, these approaches are highly invasive, challenging to scale and introduce additional permitting and exportation challenges.Over roughly the last decade, researchers have begun applying the same haplotype-reading techniques directly to eDNA extracted from water or sediment, rather than from individual tissue. Early work by Ardura et al. (2011) demonstrated the basic feasibility of characterising haplotypes from a widely used marker gene, and Sigsgaard et al. (2016) provided one of the first direct comparisons between haplotypes recovered from seawater eDNA and those obtained from tissue samples of the same whale shark population, finding an 100% agreement between the two.

Since then, the approach has been applied to a range of settings:

  • Tracking seasonal movement of native versus non-native carp populations through differences in their eDNA haplotype signatures (Uchii et al., 2017)
  • Detecting population structure in harbour porpoises from seawater samples collected near their known surfacing points (Parsons et al., 2018)
  • Assessing genetic diversity across entire freshwater invertebrate communities from a single sample, rather than one species at a time (Elbrecht et al., 2018; Zizka et al., 2020)
  • Monitoring genetic diversity across whole kelp forest communities as an indicator of ecosystem status (Shum & Palumbi, 2021)

    Because a single water sample can contain traces from an entire community of species, this community-wide capability is one of the most distinctive features of the eDNA approach. It opens the door to tracking genetic diversity trends across many species simultaneously, at a fraction of the cost and disturbance of traditional tissue-based surveys.

Why this matters for monitoring and management

For conservation bodies and resource managers, the appeal is straightforward: haplotype diversity trends, tracked over time and across a whole community, could offer an early warning system for problems like overexploitation, habitat degradation, or biodiversity loss. This offers and early warning potential before those problems become visible through conventional abundance-based monitoring (Ovenden, 1990; Billington & Hebert, 1991; Adams et al., 2019).
Basic Content

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Key References

Adams, C.I., Knapp, M., Gemmell, N.J., Jeunen, G.J., Bunce, M., Lamare, M.D., & Taylor, H.R. (2019). Beyond biodiversity: can environmental DNA (eDNA) cut it as a population genetics tool? Genes, 10(3), 192.

Ardura, A., Planes, S., & Garcia-Vazquez, E. (2011). Beyond biodiversity: fish metagenomes. PLoS One, 6(8), e22592.

Billington, N., & Hebert, P.D. (1991). Mitochondrial DNA diversity in fishes and its implications for introductions. Canadian Journal of Fisheries and Aquatic Sciences, 48(S1), 80–94.

Elbrecht, V., Vamos, E.E., Steinke, D., & Leese, F. (2018). Estimating intraspecific genetic diversity from community DNA metabarcoding data. PeerJ, 6, e4644.

Nature Education (2014). Definition: Haplotype / Haplotypes. Retrieved from nature.com/scitable/definition/haplotype-haplotypes-142/

Ovenden, J.R. (1990). Mitochondrial DNA and marine stock assessment: a review. Marine and Freshwater Research, 41(6), 835–853.

Parsons, K.M., Everett, M., Dahlheim, M., & Park, L. (2018). Water, water everywhere: environmental DNA can unlock population structure in elusive marine species. Royal Society Open Science, 5(8), 180537.

Prunier, J.G., Chevalier, M., Raffard, A., Loot, G., Poulet, N., & Blanchet, S. (2020). Contemporary loss of genetic diversity in wild fish populations reduces biomass stability over time. BioRxiv, 2019-12.

Shum, P., & Palumbi, S.R. (2021). Testing small-scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding. Molecular Ecology.

Sigsgaard, E.E., Nielsen, I.B., Bach, S.S., Lorenzen, E.D., Robinson, D.P., Knudsen, S.W., ... & Thomsen, P.F. (2016). Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nature Ecology & Evolution, 1(1), 1–5.

Uchii, K., Doi, H., Yamanaka, H., & Minamoto, T. (2017). Distinct seasonal migration patterns of Japanese native and non-native genotypes of common carp estimated by environmental DNA. Ecology and Evolution, 7(20), 8515–8522.

Wright, S. (1937). The distribution of gene frequencies in populations. Proceedings of the National Academy of Sciences of the United States of America, 23(6), 307.

Zizka, V.M., Weiss, M., & Leese, F. (2020). Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics, 4, 23–34.

 

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