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Next generation conservation genetics at sea: detecting and conserving adaptive potential

Project Description

Background: There is a long tradition in conservation genetics of using neutral genetic markers to assess demographic patterns and processes relevant to conservation. For example, the identification of the units of conservation requires information on population genetic structure and patterns of connectivity. These analyses assume differentiation by neutral processes. Neutral markers also provide information on effective population size and historical population dynamics, and reflect inbreeding (and can therefore be correlated with fitness; Reed & Frankham 2003, Cons. Biol. 17, 230-237). At the same time, a primary objective (and almost a mantra) of conservation genetics has been the conservation of adaptive potential. This is necessarily associated with phenotype and local adaptation, each of which will be determined by functional genetic loci, and gene-environment interactions. The objective is to conserve the ability of wildlife species to respond to changing environments, essential in the context of anthropogenic global climate change. However, this has been difficult to assess and support. Although there is weak correlation between quantitative trait diversity (QST, reflecting phenotypic diversity) and Wright’s inbreeding coefficient measure of population structure (FST, based on neutral markers; McKay & Latta 2002, TREE 17, 285-291), a clear relationship has remained elusive (Whitlock 2014, J. Ecol. 102, 857–872).
In the marine environment there are few obvious barriers to gene flow, and in fact marine species of management concern (such as pelagic fish species) often show little evidence of structure at neutral genetic markers. This was the case for several deep sea fish species studied in our lab, where 15-20 polymorphic microsatellite DNA markers showed no evidence of structure across a broad geographic range (e.g. White et al. 2009, Mol. Ecol. 18: 2563-2573). However, for each of these species, genome sampling (by restriction-associated DNA analysis: RADseq), showed evidence of weak structure at neutral loci, consistent with isolation by distance in most cases. However, RADseq also permits an analysis of structure at putative functional loci, detected as outliers from predicted divergence metrics under neutral theory. At those loci, a different pattern of structure emerged, highlighting especially stand out differentiation for populations south of the sub-polar front (in warmer waters, influenced by a different current system). The differential pattern of structure suggests local adaptation, but the more specific mechanisms associated with particular loci or genetic pathways could not easily be determined from the RADseq data (where 1000’s of single nucleotide polymorphic (SNP) sites are revealed, but millions may be required).

Aims & novelty: To test hypotheses about the more specific mechanisms that generate distinct patterns of diversity at functional loci across environmental gradients using high resolution next generation sequencing data and working with reference genomes. The key objectives will be to identify loci or gene systems that reflect diversity requiring conservation management that are not detectable using conventional methods based on neutral loci. At the same time, these data will enhance our understanding of the process of adaptive evolution, providing novel inference about the evolution of diversity in the marine ecosystem.

Funding Notes

This is a competitive studentship through the NERC IAPETUS program (View Website), providing full funding for tuition, living expenses and research expenses. For further details please contact Rus Hoelzel () or Per Berggen(). Application materials should include a c.v., academic records and at least two letters of reference sent to .

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