Native and endangered species

Microsatellites as population genetic markers

The tools of genomic research have also been applied to native species of high conservation priority. As part of a collaboration with the Royal Botanic Garden in Edinburgh we have evaluated the information content and practical utility of different types of genetic markers (SSRs, AFLPs and SNPs) over different scales of population differentiation from local small scale separation, to where gene flow is probable (ca 1 km and ca 10 km), and where gene flow is highly unlikely (global inter-continental disjunctions).

As our aim was to evaluate marker performance for biodiversity studies we have included species with no previous genomic knowledge and those that are likely to be representative of the challenges often encountered in biodiversity research in terms of tissue sampling and broad taxonomic scope (a fern, a diminutive selfing angiosperm, and a liverwort). By way of comparison, with have also studied an outcrossing relative of the model organism Arabidopsis thaliana (highlighted in the Figure below)

The marker systems examined in this project included genomic-SSRs, EST-derived SSRs, AFLPs, cpDNA sequences from non-coding DNA and introns, nuclear sequence variation from non-coding and coding regions and are summarised in the Table below.

In summary EST-SSRs provided robust and easy to score markers, and in taxa where large amounts of growing tissue are available, they represent a useful source of markers. They posses some advantages over traditional genomic SSRs in terms of stability and at least some degree of enhanced conservation of priming sites. The overall picture of population differentiation from the two classes of SSRs was strongly consistent. When diversity estimates from SSRs and AFLPs were compared there was a general lack of congruence in the two marker systems, although broadly congruent estimates of population divergence were obtained from both AFLPs and SSRs.  Insights into the species biology revealed strong evidence for recent genetic communication between populations that are currently separated by massive geographical distances. For example, populations of liverworts in Scotland show high levels of genetic similarity with extreme disjunct populations in the Himalaya.

Conservation of rare and endangered sub-arctic willow scrub

Conservation action requires underpinning scientific research, and as part of a large collaborative research project we were funded to research the one of the UK’s rarest and most endangered habitats, that of Sub-arctic willow scrub. This multi-disciplinary project aimed to address the outstanding research requirements for sub-arctic willow communities in Scotland by investigating the relationship between species diversity, genetic diversity and ecological interactions. Our aims were to assess how willows reproduce, and to establish whether fragmentation has led to a series of genetically impoverished and isolated populations.

To evaluate patterns of reproduction in montane willows, microsatellite markers were used to assess the extent of individual clones.  The first study site was a steep sided valley containing the rare S. lanata and sparce S. lapponum. Genetic analyses showed genotypic diversity and low levels of clonal growth, suggesting that sexual reproduction is the major mode of reproduction, and that the contribution of vegetative spread is limited, despite limited seed production being observed during the course of the project and a general lack of evidence for extensive sexual reproduction in sub-arctic willow populations. The second study site focused on the more common S. herbacea, growing in a open ridge-top habitat. In contrast to the results from S. lanata and S. lapponum, higher levels of clonal growth were observed in S. herbacea, with the same genotype being recovered from samples up to 8 m apart.

To assess the amounts and partitioning of genetic diversity in sub-arctic willow scrub in Scotland, populations of three species of montane willow (S. herbacea, S. lanata and S. lapponum) have been screened for genetic variation using nuclear microsatellites.

By sampling populations of varying sizes and degrees of spatial isolation it is possible to examine the extent to which geographical isolation and population size is correlated with diversity and differentiation. There was little difference in diversity levels between the rare S. lanata, the scarce S. lapponum, and the common S. herbacea, and no evidence for genetic depauperacy associated with rarity.

In summary, whilst there is some evidence for population differentiation in all species, there is no clear relationship between this and geography, or rarity and population sizes. Likewise, there is no strong evidence for genetic depauperacy associated with small population sizes or rarity. The most likely explanation for this is that a limited number of generations have occurred since the species were more abundant.

Allanblackia in agroforestry systems: developing the tools to manage a new tree crop for small-scale farmers in Africa

Recently with funding from Rothamsted International in collaboration with the World Agroforestry Centre (ICRAF) we have examined diversity in fragmented forests in Sub-Saharan Africa, where farmers rely on tree products for an important portion of their income. Allanblackia, a fruit tree native to highly bio-diverse humid forests of sub-Saharan Africa, is the subject of increased interest for edible oil production for the global food market. Until recently, however, Allanblackia has been an overlooked wild tree and very little is known about the biology of the genus to guide conservation and use in a transition from wild harvesting to cultivation. Here, we applied AFLP markers to assess the genetic composition of populations of five Allanblackia species. Data indicated significant differentiation between some taxa and occasional misidentification of species during field collection, suggesting care is required during sampling, especially if basing a domestication strategy on a single species in areas where distributions overlap. Genetic relatedness between species and geographic proximity sometimes but did not always correspond, likely reflecting complex evolutionary processes related to migration and dispersal in the genus. AFLPs suggested that Cameroon presents particular challenges for conservation and opportunities for domestication of the genus.