Phew! Time seems to have flown by more quickly, and I finally have some quiet time to write the second part of my conservation of giant clams post series… My days are now split into two halves: my day job as a researcher and my ‘night’ job as a TED Fellow – hahaha! So here we are, and today’s topic is Population Genetics.

American Museum of Natural History

Part 2: Population Genetics

Wikipedia sources describe population genetics as “a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology.

This simply means that we can use molecular tools to distinguish individuals coming from a single population or from multiple populations, and attempt to infer how these populations may or may not be ‘related to each other’. The reason for my quotation marks is because the individuals may be related on a sibling level or on a parental level.

How does the giant clams fit in?

Populations of giant clams have been examined using population genetics since the early 1970s, where studies initially used allozymes (i.e. enzyme systems) to find out how populations are genetically structured – either similar or different (Valentine, 1973; Ayala et al., 1973). Later, it was argued that using allozymes was not good enough for a various reasons such as limited gene coverage, labour intensive, and considered old-fashioned markers.

Since late 2000s, the first paper published by DeBoer et al. (2008) demonstrated the feasibility of using mitochondrial marker – mtCOI to study the population structures of the boring giant clam (Tridacna crocea). Subsequent studies have since persisted in using mtCOI for comparative studies with the existing database.

Giant clams are perfect for such studies as 1) they are immobile for life, 2) the smaller species are still in abundant for sampling populations, and 3) they are endangered marine life. Much of the information are useful in the downstream pipeline of applying it to management of reserves and parks.

So how do we interpret the results from tons of molecular analyses?

Let’s take a look at the figure below. The figure below shows the results of a large study conducted on three species of giant clam populations. On the left column comprising the map, it is marked with numerous circles of different colours and sizes. A quick explanation below:

  • Each circle represents a group of clams collected from each site.
  • The size of circle represents number of clams.
  • The colour of circle represents a particular type of haplotype – that is, the representative set of genes inherited by the clam!

Next, we look at the right column, with the wriggly lines. These are called haplotype networks, which represents how each haplotype is connected (or related in this case) to one another. Similar to the earlier descriptors:

  • Each circle is also representative of a unique haplotype.
  • The length of connecting lines represents the number of mutation steps between two haplotypes. This means how many times the genes changed to become the other haplotype, and vice versa.
  • The further the haplotype, the less related it is to the central haplotypes.
Tridacna spp. IND
Figure extracted from DeBoer et al. (2014)

Erm… Are you lost yet?

hahaha! Don’t worry if you got lost, as the mechanics of interpreting the results are much more technical, but the above outlines the gist of the story. I will use a personal example – population structures of two species of giant clams in Singapore. In a very similar way of presentation, but with colours!

The objective of my study was to find out how our giant clams are genetically related (or not) by sequencing their mtCOI. I spent a full year sampling various sites in Singapore to amass a dataset of ~30 samples per species. Each species showed a completely different result!

The boring giant clam, Tridacna crocea was found to be genetically different between individuals, which means that there exists a high genetic variation. This can be inferred by the number of haplotypes represented by individual colours. The map complements by indicating where these individuals are found, i.e. haplotype 1 (green) can be found at Pulau Salu, Pulau Senang and Pulau Semakau – suggesting that the clams are related to each other, despite the geographic distances!

Figure extracted from Neo & Todd (2012)

On the contrary, the fluted giant clam, Tridacna squamosa showed a different picture. Almost half of the individuals sampled are genetically similar (haplotype 13 in light blue), suggesting that they are related and the species connectivity between reefs is higher than that of Tridacna crocea (earlier figure). Another interesting take-home here is that Tridacna squamosa is genetically less diverse, given the fewer haplotypes detected.

Figure extracted from Neo & Todd (2012)

So how is population genetics useful then?

The power of population genetics is its ability to tell us how individuals of a species population are related or not, and this has implications for demarcating areas of conservation. With the knowledge of how populations are connected, we can thus better define specific reefs for protection with respect to the giant clams, such as marine reserves and marine parks.

This is especially critical when some giant clam populations in certain areas come under high levels of exploitation pressure, which can potentially wipe out the entire genetic diversity as well. When this happens, the genetic diversity of species is not only lost but unable to be passed on and spread to other reefs. In addition, there is an increasing number of studies that defines species by its unique evolutionary history and lineage, and that conservation should also account for these traits (Huang, 2012; Huang & Roy, 2014).

Unfortunately a caveat in current population genetics studies is that we may already be sampling the remnant individuals that were missed out during exploitation or other impacts. Thus, the current gene pool may already have reduced to very low levels, but undetectable in these studies because we cannot compare with non-existent past data.

Additional remarks

While the techniques used to aid in conservation has been useful such as mariculture of giant clams and using molecular tools, there is the need to complement the science with policy and legislations. In the next part, I will share the most recent knowledge of laws and legislations that have helped keep giant clams safe from humans.

Reference List:

Ayala et al. (1973) Genetic variation in Tridacna maxima, an ecological analog of some unsuccessful evolutionary lineages. Evolution 27: 177-191.

DeBoer et al. (2008) Phylogeography and limited genetic connectivity in the endangered boring giant clam across the Coral Triangle. Conservation Biology 22: 1255-1266.

DeBoer et al. (2014) Concordance between phylogeographic and biogeographic boundaries in the Coral Triangle: conservation implications based on comparative analyses of multiple giant clam species. Bulletin of Marine Science 90: 277-300.

Huang (2012)  Threatened reef corals of the world. PLoS ONE 7: e34459. doi:10.1371/journal.pone.0034459

Huang & Roy (2015) The future of evolutionary diversity in reef corals. Philosophical Transactions of the Royal Society B-Biological Sciences 370: 20140010.

Neo & Todd (2012) Population density and genetic structure of the giant clams Tridacna crocea and T. squamosa on Singapore’s reefs. Aquatic Biology 14: 265-275.

Valentine (1973) Mass extinctions and genetic polymorphism in the ‘killer clam’, Tridacna. Geological Society of America Bulletin 84: 3411-3414.