Category: Genetic diversity

In the second of two posts, Sean Hoban completes his discussion of recent advances in the optimization of collecting strategies for ex situ conservation.

Dr McGlaughlin, a professor at the University of Northern Colorado, works on rare plant species, particularly Sibara filifolia, an annual plant restricted to two small California islands. Sampling seed can help preserve this species in case of loss of wild populations (some populations are located in a naval bombing range — thus there is a very real possibility of loss!). McGlaughlin and colleagues recently tested how to sample on the two islands, whose populations exhibit very different population dynamics: one population has high diversity and high outcrossing, while the other population is highly selfing.

The research shows that very different minimum sampling numbers are needed to get the diversity of the two populations. In fact, more than twice as many samples were needed in the former population than the later! The researchers also mention that the optimal protocol depends on the goal, e.g. to capture all the alleles, or just the ‘non-rare’ alleles. The authors point out that much variation (about one third of the variation on one island, and about half the variation on the other) is composed of rare alleles, which may be important for future evolutionary change or disease resistance. These alleles, though, are not targeted by the Brown & Marshall strategy.

As a postdoc at the University of Tennessee, and soon-to-be Conservation Biologist at the Morton Arboretum, I also test sampling strategies. My work is highly complementary to McGlaughlin’s — I use a model-based approach to test sampling strategies for different species and situations.

First, with Allan Strand, we have shown that the minimum sample size should differ for species with different reproductive biology — for example, species with low dispersal and high rates of self-pollination could need about five times as many seeds as species without these characteristics. Second, when sampling only a small portion of the population, more samples should be taken than when you are able to sample randomly (depending on the species, between two and ten times as much seed). This is important because we often do sample nonrandomly (the Brown & Marshall guideline assumes perfect random sampling), by sampling the nearest access point, or along a road or transect when hard to reach all parts of a population!

Thus far, the message generally is “we need to sample more.” For some species, a lot more! However, the third finding was that, when sampling many populations, the Brown & Marshall guideline may lead to occasional over-sampling. This is because genetic variants are often shared to some degree among populations, and thus when visiting multiple populations there are more chances to catch those variants in the sample — the Brown & Marshall guideline does not consider this possibility. So, in some cases of visiting many sites, 25 samples may be more appropriate. Furthermore, selective choice of far-flung populations can be almost as good as sampling every population (Hoban and Schlarbaum, 2014). My colleagues and I are continuing to test how robust these new recommendations are.

It is of course important to remember that all this work is on the “minimum sample” problem — the lowest sample investment to achieve a genetic variation target. However, many seed are inviable, infested, lost, or used for evaluation tests, and seed lose viability over time even under good storage conditions. The minimum sample recommendations do not account for this. Michael Way estimated that the number of seed to be collected from a population, to allow for monitoring, duplication, distribution and decline in viability, should be at least 10,000. A smaller sample of about 500 seed may be much too few to allow for this ‘active use’ of a collection. Thus, we should also keep in mind seed viability, storage and use when deciding how much seed to sample!

Overall, my work with McGlaughlin, as well as similar work (see papers by Juli Caujapé-Castells, Washington Gapare, Patrick Griffith, and Sandra Namoff), shows that a single sampling guideline for all species is not the best approach. A single guideline will lead to frequent under-sampling and sometimes over-sampling. To achieve the best conservation of genetic diversity, we should design our sampling taking into consideration what we know about a species’ biology (selfing rates, dispersal, distribution), as well as the recent ecology and demography of the population (such as recent declines, or absence of pollinators).

We think our approach — to perform a genetic survey to help us understand genetic patterns, and to use simulation models of genetics and ecology — is a really promising way to improve our sampling and thus the effectiveness of ex situ conservation.

Today we introduce a new guest blogger. Sean Hoban “uses population and genetic models as well as optimization techniques to develop practical guidelines for ex situ conservation of plants for botanic gardens, seed banks, and breeding programs.” Below, in the first of two posts, he sets the scene for us. Tomorrow, he will tell us about recent advances in how to collect maximum seed diversity as efficiently as possible. Welcome to the blog, Sean.

Climate change, species’ extinctions, loss of natural habitats, crop failures… In the new millennium we face many challenges for society and the environment. Large-scale initiatives for collecting and saving seed can help by enabling crop improvement, promotion and sharing of biodiversity, protecting rare species, and restoring ecosystems. If the right genes are in seed collections, plant breeders can make crosses to transfer traits like tolerance to disease and environmental stresses, ultimately boosting crop resilience. Or, if seeds are used for reintroduction, a diversity of genes can help a population cope with environmental change. Maximizing genetic and trait diversity is thus a key task on a seed collector’s mind. At the same time, we don’t have enough resources to visit every location in a species’ geographic range, nor to store immense quantities of seed. Thus the challenge is to get enough of the right diversity in a small-ish batch of seed. Here I’ll discuss progress on this challenge, including recent advances.

Where to sample from, and how much? We need to be efficient, because we have limited resources, but also be effective, because any variation we miss may be lost in threatened natural populations. In the 1970s, a key innovation was made by academic researchers AHD Brown and DR Marshall. They used simple probability models to determine that sampling 30-60 individuals in a population would ensure capturing alleles that were ‘not rare’ (not below 0.05 frequency in the population). The recommendation of ‘approximately 50’ samples quickly caught on, and has been a common basis of protocols ever since, including recent protocols for many botanic gardens, restoration companies, the United States Forest Service and Bureau of Land Management, and others.

Recent work has begun to revisit this decades-old recommendation, and might lead to more refined, and more effective and efficient, collections. It comes down to recognizing that ’50 samples’ may in fact be too few or too many for some species and population.

The Brown & Marshall guideline, as it is often called, has key limitations. Specifically it assumes that every sample will contain a random selection of genes from the population. However, this assumption rarely holds true! For example, when we sample adjacent plants that are relatives we are quite likely to capture some of the same genetic variants rather than new, random ones — a phenomenon called redundancy. Redundancy in a collection means fewer unique genetic variants than expected, meaning that the 50 samples guideline may capture less (or much less) variation than we expect it too. Another limitation: Brown & Marshall recommend sampling every population that can be reached. However, populations differ in size and connectivity — some populations may share a good deal of genetic variation and thus sampling nearby populations may also lead to redundancy.

These limitations have been pointed out repeatedly over the decades by authors (CPC 1991 ((Center for Plant Conservation, CPC. 1991. Genetics and conservation of rare plants, edited by D. A. Falk and K. E. Holsinger. New York: Oxford University Press.)) ; Guerrant 2004, 2014) who say we should sample differently for abundant or common species, or for species whose life history and reproductive strategies are different. After all, these characteristics affect how genetic variation is distributed in landscapes, so they will likely affect how well sampling strategies perform. We may even need to sample differently in different populations — large vs. small populations, for example. Mitchell McGlaughlin and I have recently provided evidence for such assertions, using different approaches. Our works shows precisely how limiting the generic Brown & Marshall strategy can be — and how we can improve our sampling guidelines. I’ll talk about that tomorrow.