This research will apply new expertise and a novel approach to fundamental questions in Biological Oceanography: how is population structure affected by connectivity and transport and what traits drive spatial patterns in survival of larvae or adults. Many key species in the marine environment inhabit and need to deal with spatially and temporally variable environments. Yet, in Biological Oceanography and for the study of ecology in non-model species (those lacking genomes, or strong genetic analyses), investigators have largely relied on one or a few loci to investigate spatial and temporal patterns. This shortcoming provides little resolution of population structure and how oceanographic parameters affect populations.
In this EAGER project, the PIs will use high throughput genomic approaches to identify and analyze genetic markers in hundreds of individuals without a need for prior genome information. The approach will use a modification of methods used with model species to sequence a reduced representation cDNA library made from many individuals in the species of choice in order to identify, at minimum, 300-500 single nucleotide polymorphisms (SNPs). SNP identification will be followed by MassARRAY genotyping of 100s of individuals within and among populations and, depending on genetic distance, species. Analyses will reveal population structure and importantly, SNPs associated with particular traits in the genotyped individuals. Because these SNPs are from coding sequences (expressed genes), the associations will be between specific genes and traits of interest (e.g., survivorship, fitness, growth).
This approach is novel and innovative and contains some risk, making it highly suitable as an EAGER project. It does not rely on existing genome sequences, yet provides many SNPs per chromosome. This depth of information provides two important results: very high resolution of population structure and association between SNP and biologically important traits. The interdisciplinary aspects of the work combine bioinformatics, statistics, biological oceanography, molecular biology, marine conservation, and population genetics.
By applying the most recent high-throughput technology with methods to identify SNPs in outbred natural populations, the PIs will resolve species distributions and the effects of global warming and habitat change on populations and better assess conservation practices. Additionally, because so many (300-500) markers are used for coding regions, it will be possible to ascertain selective differences among genes that affect biologically important traits. Thus, by identifying and utilizing 100s of SNPs from the coding sequences of any organism, the PIs will both measure population structure and connectivity and identify genes important for particular life-history traits. Notably, a sequenced genome is not necessary for this work, making it broadly applicable across species.
The Broader Impacts consist of introducing new technologies to important, basic problems in population structure of marine organisms, with broad applicability in biological oceanography.
For many (most) marine species there is a lack of rich molecular markers to discern subtle but important differences among populations or to associate genetic changes with adaptive divergences that are necessary for species to adapt to global change. That is, particularly for organisms with planktonic life stages, there is too little resolution to quantify important population genetic parameters that allow us to predict the effects of global change. Using high throughput sequencing approaches, we have developed thousands of molecular markers for a widely studied reef fish, the bluehead wrasse (Thalassoma bifasciatum). A subset of these molecular markers was used to genotype hundreds of individuals in order to determine population structure if it exists. Previous research using fewer molecular markers failed to find population structure in this species. However, with the depth of coverage provided by hundreds of markers across the genome for hundreds of individuals, there is sufficient power to identify population subdivision. Larvae and juveniles collected off the east coast of Florida belong to two distinct genetic groups. This information on population subdivision and connectivity provides a the means to estimate how global change will affect species and more importantly, provides a foundation to empirically measure the changes through time. Furthermore, some of the markers can be associated with phenotypes and thus be used to identify genes important for growth and survival in a changing environment.
