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2018 Ecological, Evolutionary and Conservation Genomics (EECG)

2018 Ecological, Evolutionary and Conservation Genomics (EECG)
photo by Elise Lauterbur

The AGA grants EECG Research Awards to graduate and post-doctoral researchers who are at a critical point in their research, where additional funds would allow them to conclude their research project and prepare it for publication. 51 students and post-docs applied for funding this year.

The AGA Council is pleased to announce the recipients of this year's EECG Awards:

1.  $9,362 to Nicolas Nesi (Queen Mary University London): Comparative genomics of sugar-eating bats: Implications for the genetics of glucose metabolism and diabetes

2.  $9,927 to Kendall Beals (University of Tennessee): Identifying the drivers of plant functional traits through exploration of the soil microbiome

3.  $10,000 to Sheela Turbek (University of Colorado): Explaining mismatches between genetic and phenotypic divergence in a rapid radiation of finch-like birds

4.  $6,205 to Kathryn Uckele (University of Nevada Reno): Utilizing a recombinant hybrid zone to elucidate links among genotypic environmental and phenotypic variation

5.  $9,673 to Elise Lauterbur (Stony Brook University of California): Genetic complexity of cyanide adaptation in specialist herbivores

6.  $9387 to Zachary Cabin (University of California Santa Barbara): Evidence of positive selection on a homeotic mutant of Aquilegia coerulea

7.  $10,000 to Paivi Leinonen (Duke University): 'Unearthing the genetic basis of adaptation: Detecting loci involved in local adaptation in the wildflower model system Mimulus

EECG Details:

1. Nesi – Bats
Diabetes and impaired glucose tolerance are major threats to human health. These conditions are linked to obesity and poor diet but also have major genetic components. To date, most knowledge of the genetics of sugar metabolism and diabetes comes from epidemiological studies of humans and lab studies of mice. Yet powerful insights may also be obtained by studying non-model species that show evolutionary adaptations for high sugar diets. Among mammals, bats are unique in their dietary specializations with up to eight lineages having independently evolved nectar-feeding. How these bats are able to survive on high sugar diets, and regulate their blood sugar to resist the damaging effects of glucose toxicity, is not known. To discover the genes that confer these abilities in bats, we are using state-of-the-art cross-species targeted sequence capture to obtain thousands of orthologous sequences from all nectar-feeding fruit bats and their non-nectar feeding relatives. We will first identify loci showing molecular adaptation for key branches associated with nectar feeding. Second, we will compare these gene sets, and protein-protein interaction networks, to determine whether unrelated nectarivores have recruited the same genes and pathways. Our findings will improve our understanding of how natural selection has driven dietary specialization in mammals, and will shed light on whether related metabolic diseases arise via mutations occurring at the same sites, or instead arise from the disruption of more evolutionarily conserved sites.

2.  Beals – Soil microbiome
While just below our feet, the soil microbiome contains some of the world’s most unexplored genetic diversity, yet we still know very little of the role of this diversity for plant function. Using three species of the widely occurring and phenotypically-diverse perennial genus Solidago (Asteraeceae), this project investigates the role of a plant’s associating soil microbial community on plant phenotype and function. I conducted a reciprocal transplant greenhouse experiment using field-collected Solidago-conditioned soil to address the following questions: 1) What is the role of an active soil microbial community on plant phenotype and function? and 2) How do changes in genetic and/or functional diversity of the soil microbiome affect plant function? To conduct this project, I am analyzing amplicon and metagenomic sequence data from root-associated soil of Solidago individuals grown in conspecific and heterospecific soil to identify relationships between plant functional traits and soil microbial genetic and functional diversity.

3.  Turbek – Finch-like birds
Recent genomic studies have revealed that several species exhibit striking differences in appearance despite little genomic differentiation. Both pre- and post-mating mechanisms may underlie mismatches between genetic and phenotypic divergence. However, we currently lack an understanding of the reproductive barriers maintaining phenotypic differences in genetically homogenous populations that would improve our ability to interpret these genomic patterns. I propose to examine the importance of pre- and post-mating processes in maintaining phenotypic differences in the capuchino seedeaters, a highly sympatric avian radiation that shows little genetic divergence despite striking differences in plumage coloration and song. I will collect tissue from unhatched eggs and blood samples from breeding pairs and nestlings of co-occurring species to test for patterns of assortative mating and post-mating selection against hybrids. These investigations will provide insight into the mechanisms that maintain barriers to reproduction extremely early in speciation.

4.  Uckele – Hybrid zone
Traditionally, hybrid zones have been used as ‘windows’ into the process of divergence and speciation; however, hybrid zones are also powerful ‘natural laboratories’ (Hewitt 1988) where recombined genotypes and replicated instances of hybridization provide the raw materials to identify patterns among hierarchical levels of biological organization. The links between genomic introgression and phenotypic variation have remained relatively unexplored despite their ramification for the structuring of ecological communities (Whitham et al. 2006) and their role in plant speciation (Bomblies and Weigel 2007). To explore the relative contributions of interspecific recombination and environmental variation on the expression of chemical traits in hybrids and associated arthropod community composition, I propose utilizing advances in 'short read' DNA sequencing and metabolomic profiling to characterize fine-scale variation in plant genetic structure and phytochemistry over the landscape of a conifer hybrid zone.

5.  Lauterbur – Herbivores
Eating is dangerous – it exposes organisms to natural and anthropogenic toxins. Their ability to tolerate these toxins is fundamentally shaped by their ability to adapt. My dissertation is focused on investigating concerted convergence in genetic adaptations to cyanide across bamboo-specialized mammals. Bamboo-specialized mammals are well- adapted to the extreme physiological demands imposed by the cyanide some bamboos produce as a chemical defense, and I have shown adaptations to a high-cyanide diet across a suite of physiological pathways. I am using gene capture, facilitated by a new program I created to increase the diversity of capture probes, to investigate the complex genetic patterns of this suite of adaptations across 3 suborders, including primates, rodents, and bears. With these data, I will test the hypothesis that cyanide adaptation has required concerted convergence among a suite of genes and genetic pathways, shaped by fundamental physiological requirements, with applications to other metabolic toxins. This is particularly important in light of understanding potential adaptation in species exposed to novel anthropogenic toxins.

6.  Cabin – Aquilegia
Naturally occurring homeotic mutants offer a rare chance to study how a radical morphological shift affects fitness. Aquilegia coerulea var. daileyae is a homeotic mutant where the petals, with long spurs and a nectar reward, have been changed into a second set of sepals. While, this change would appear to be deleterious due to the loss of the nectar reward, I have found that the mutant consistently has a fitness advantage in a polymorphic population and has reached fixation in two other populations. Previous work identified a candidate locus (AP3-3) and I have found that non-functional alleles are perfectly associated with the mutant phenotype. I have found elevated LD at these mutant alleles indicating strong natural selection. I propose to re-sequence individuals from the polymorphic and fixed populations (and nearby wild-type populations) to determine (a) how far the elevated LD extends around AP3-3 and (b) if other regions in the genome also experience similar selection. With this information, I will be able to demonstrate current ecological selective pressure with and molecular signatures of selection favoring a radical homeotic mutant.

7.  Leinonen – Mimulus
My research focuses on how evolution on a local scale results in differentiated, locally adapted populations and understanding the underlying mechanisms by unraveling the genetic basis of adaptation. These studies are vital for estimating effects of climate change on biodiversity, but comprehensive studies are still very few. In my postdoctoral project I have developed a resource using natural populations of a model plant for ecological genomics (Mimulus) originating from different elevations – a Recombinant Inbred Line (RIL) mapping population – for these purposes that has the potential to significantly advance discovery of genes governing adaptive evolution. I have already quantified extensive phenotypic differentiation in flowering responses to photoperiod and started numerous collaborative projects focusing on different aspects of local adaptation, ranging from variation in the circadian clock to transgenerational plasticity responses to temperature.



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Variable Signatures of Selection Despite Conserved Recombination Landscapes Early in Speciation
Sheela P Turbek et al.


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