Early Career Scientist Seminars

Previous speakers:

Meredith Zettlemoyer

University of Georgia

Integrating the effects of phenological shifts on performance across biological scales

Fall 2022

Rising temperatures have dramatically accelerated the phenology of many species, but we still have limited evidence of whether variation in phenological responses really influences population dynamics or macroecological patterns of extinction and spread. Even fewer studies test for individual variability in phenological responsiveness. Since phenology’s potential benefits for species success are common motivations for documenting phenological shifts, we need to consider mechanisms underlying how phenology influences performance across biological scales. Here, I link phenological shifts to performance at three scales: selection on population-level phenology, individual variability in phenology, and phenology’s role in macroecological patterns of invasion and extirpation. First, I leverage a long-term dataset on phenology and demography in an alpine plant to conduct a rare quantitative assessment of the adaptive value of phenological plasticity. I find adaptive phenological plasticity is insufficient to maintain fitness as climates warm. I then quantify individual x environment variation in this same system. Individuals differed in the magnitude of plasticity, driving greater variability in flowering with warming. Finally, I use a combination of herbarium records and experimental warming to examine how phenological plasticity in response to rising temperatures affect patterns of invasion and extirpation in tallgrass prairies. Non-native species advance flowering more in response to warming than native species, potentially providing them an advantage under global change. Extirpated species showed weaker responses to spring temperatures than closely-related extant species, suggesting that differences in phenological responsiveness could influence extinction risk under climate change. Altogether, we need to consider how phenology might affect performance across biological scales for phenology to truly serve as an indicator of species’ success under climate change.

Armita Manafzadeh

Yale University

Reconstructing locomotion: Lessons from the joints of living animals

Fall 2022

Our understanding of major transformations in locomotor evolution hinges on our ability to accurately reconstruct how extinct vertebrates walked, ran, swam, and flew. These analyses typically begin with manipulations of fossil limb bones, which paleontologists use to estimate the range of motion (i.e., mobility) of each limb joint. But how do we decide which joint poses to include, and which ones not to? Once we reconstruct joint mobility, what can it tell us about how a joint was used in life? In this talk, I’ll cover how studies of joint function in living animals like birds and alligators have changed and are actively changing our perspectives on reconstructing locomotion. By merging data from biplanar X-ray videos and computed tomography scans, we are able to create precise and accurate 3-D animations that give us “X-ray vision” into the joints of living animals. These studies have helped us evaluate paleontological assumptions about articular function, teaching us about the risks of reconstructing joint mobility without soft tissues, the importance of considering joint translations in reconstructions of articular function, the value of characterizing the relationship between full joint mobility and the poses used during locomotion, and the power of harnessing data from articular surface interactions in new ways. Undertaking this research is essential not only to illuminating vertebrate locomotor evolution, but also to uncovering fundamental gaps in understanding about articular function that affect evolutionary studies by paleontologists and neontologists alike. Continuing to probe and test our assumptions about joints will ultimately enable us to better disentangle the complex articular form-function relationship that underlies all vertebrate animal motion.

Andrew Swafford

University of Massachusetts Amherst

The molecular evolution underlying vision and photosensory systems

Fall 2022

Complex sensory systems such as vision shape the way organisms perceive, interact, and adapt to the environment. Of these systems, sight is a unique sense that has arisen multiple times from a deceptively small cadre of genes given the complex coordination of molecular machinery it requires. In animals, almost every instance of vision relies on a single gene family, opsin, which is widely regarded as the evolutionary lynchpin that triggered the evolution of complex eyes. However, our understanding of when opsins first originated and how the gene family has diversified throughout time remains largely unexplored. Here I develop new methods to reveal opsins as an ancient gene family that first appeared in early animals. In opposition to the current hypothesis that opsins represent the only photosensitive clade of G-protein coupled receptors (GPCRs), I find evidence of photosensitive non-opsin GPCRs. Additionally, I discover a staggering amount of convergent evolution in GPCRs on specific amino acids at positions known to enable light sensitivity. Lastly, I present the chytrid fungi as a system which can be used to broaden our study of sensory systems, their integration with conserved modes of motility, impact on conservation, and how sensory motor networks remodel after the gain and loss of integral components.

Agnese Lanzetti

Natural History Museum of London

Developing a taste: Connecting skull shape ontogeny and evolution of different feeding adaptations in Cetacea using 3D geometric morphometrics

Spring 2022

Ontogeny plays a key role in the evolution of organisms, as changes during this complex process can allow for new traits to arise. Identifying changes in allometry – the relationship between skull shape and size during growth – can reveal important insights into the evolutionary processes at play especially in clades that underwent major transitions. Modern baleen and toothed whales (Mysticeti and Odontoceti, Cetacea), while sharing a deep evolutionary history in their fossils ancestors that made the transition from land to water, present distinct adaptations. Mysticeti are characterized by a long rostrum bordered by keratinous plates (baleen) that they employ in filter feeding. Odontoceti present a variety of feeding adaptations, from the short snouted suction feeders like the beluga to the extremely long rostra of the fish-eating river dolphins. I aim to conduct a completely novel study to investigate the influence of allometric changes in Cetacea evolution.

I expect allometric trajectories are markedly different between Mysticeti and Odontoceti, and among families of toothed whales with different skull morphologies. To test these hypotheses, I assembled a unique 3D dataset of over 120 specimens, spanning the developmental and phylogenetic spectrum: from fetal stages to adults, and representing two-thirds of the living Cetacea genera. Skull shape morphology was acquired using both CT and surface scanning methods. I quantified its variation using 3D geometric morphometrics and conducted statistical analyses in R. Results show that the two groups have distinct allometric trajectories, with Mysticeti displaying a decelerated growth relative to the reconstructed ancestral trajectory. Odontoceti instead present an accelerated growth, with significant differences among families with different skull morphologies. This demonstrates the profound influence of developmental changes in the evolution of the disparate feeding adaptations present in modern Cetacea.

Dina Navon

Rutgers University

Where nature met nurture – Understanding phenotypic plasticity and complex traits in fish

Spring 2022

Phenotypic plasticity allows organisms to respond quickly to changing environmental conditions, and may influence patterns of future evolution by exposing new variants to selection. However, relatively little is known about the genetic basis of plasticity – e.g., What are the specific genetic mechanisms that enable an organism to mount a plastic response? Are coordinated plastic responses across anatomical units mediated by many distinct loci or by a few “global” regulators? To address these outstanding questions, we reared a hybrid cichlid mapping population on alternate benthic/pelagic diet regimes, which mimicked natural variation in foraging preference across cichlid species. We documented plasticity for an array of ecologically relevant traits including craniofacial, whole body, pectoral fin, and pharyngeal jaw shapes. We demonstrated that plasticity was coordinated across these distinct traits, which suggests a similar degree of overlap in the genetic control of plasticity. We next scanned the genome for plasticity loci across these distinct traits, and again observed some overlap in the genetic determination of plasticity. We finally functionally verified the importance of a candidate pathway for plasticity in the maintenance of plasticity using a combination of cichlids and zebrafish. In all, our data provide support for the existence of global regulators of plasticity, serve as an important step toward characterizing the genetic basis of plasticity in cichlids, and provide a list of candidate loci for future functional analyses.

Mariah Donohue

University of Kentucky

Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes

Spring 2022

Mammals harbor diverse gut microbiomes (GM) that perform critical functions for host health and fitness. Identifying factors associated with GM variation in nature can help illuminate the role of microbial symbionts in mediating host ecological interactions and evolutionary processes, including diversification and adaptation. Many mammals demonstrate phylosymbiosis, a pattern in which more closely-related species harbor more similar GMs, while others show overwhelming influences of diet and habitat. Here, we generated 16S rRNA sequence data from fecal samples collected from 15 species of wild lemur distributed across southern Madagascar to (1) test a hypothesis of phylosymbiosis, and (2) test for trait correlations between dietary guild, habitat, and GM beta diversity. Overall, our results provide strong evidence of phylosymbiosis. However, some closely-related sympatric species with substantial ecological niche overlap exhibited greater GM similarity than expected under Brownian motion. We also found a significant correlation between diet and phylogenetic measures of beta diversity (UniFrac), but not taxonomic measures (Bray-Curtis and Jaccard). This discrepancy between beta diversity metrics indicates that older microbial clades have stronger associations with diet than younger clades, as UniFrac weights older clades more heavily. We conclude that lemur GM beta diversity is predominately shaped by host phylogeny, though ecology, particularly diet, also plays a significant role. This study is one of the first to use phylogenetic comparative methods in GM research. It also offers new insight into the ecology and evolution of lemurs, an adaptive radiation comprising some of the most endangered mammals on Earth.

Sarah Khalil

Tulane University

What’s in a name? How the Red-Backed Fairywren gets its red: from hormones to genomes

Fall 2021

Carotenoid pigments produce most red, orange, and yellow colors in vertebrates. This coloration can serve as an honest signal of quality, but recent work has cast doubt on the degree to which carotenoids function in physiological defenses. Resolving the underlying proximate mechanisms involved in carotenoid production can help inform this debate by improving our ability to interpret how multiple physiological pathways interact to shape and maintain these signals. The red-backed fairywren (RBFW; Malurus melanocephalus) provides a useful system in which to investigate this: within a population, males express either ornamental plumage with a carotenoid-based red patch, or female-like unornamented brown plumage. Females prefer males with redder plumage, and ornamented males have higher reproductive success. Previous work also indicates that testosterone is important in signal acquisition: ornamented males have higher levels of circulating androgens than unornamented males and unornamented males experimentally implanted with testosterone molt into the ornamental red/black plumage. Here I investigate the role of testosterone in mediating gene expression associated with the red plumage sexual signal. Combining correlational analyses with a field-based testosterone implant experiment and qPCR, I show that testosterone mediates expression of carotenoid-based plumage in part by regulating expression of CYP2J19 in the liver, a ketolase gene linked to ketocarotenoid metabolism and red pigmentation in birds. I additionally examined the genomic underpinning of the variation of plumage hue between two subspecies of RBFW. Using whole-genome sequencing of individuals in their hybrid zone, I identified divergent genomic regions associated with plumage variation and tested for selection and introgression of specific genes between subspecies. Together, these results provide novel insights into the endocrine, transcriptomic, and genomic mechanisms underlying a sexually-selected trait.

Michael Hague

University of Montana

Evolution at the interface of species interactions

Fall 2021

The ecological interactions between species like predator and prey or host and microbe can generate rapid (co)evolutionary dynamics that give rise to biodiversity. My research focuses on trait evolution at the interface of these interactions to understand how antagonistic and mutualistic relationships develop over time. First, I will discuss my dissertation work on the arms race between resistant garter snakes and their toxic prey, Pacific newts. I found that multiple lineages of the common garter snake convergently evolved toxin resistance via a repeated first-step mutation to the Nav1.4 skeletal muscle sodium channel that disrupts toxin binding, implying that subsequent increases in resistance were contingent on an initial permissive mutation. In highly resistant snakes, an accumulation of toxin-resistant mutations generates negative trade-offs with Nav1.4 channel function and muscle performance. These pleiotropic effects seem to explain why the evolutionary trajectory of resistant predators is limited to a predictable set of mutations. Next, I will discuss my postdoctoral research on the global spread of Wolbachia, an intracellular symbiont infecting half of all insect species. Maternal transmission of Wolbachia ensures that infections are maintained within host populations. My new work indicates that cold thermal stresses reduce Wolbachia maternal transmission and abundance in hosts, which seems to predict declining Wolbachia frequencies in temperate populations of Drosophila melanogaster. Surprisingly, Wolbachia infecting D. melanogaster in temperate Australia seem to have rapidly adapted to increase the fidelity of maternal transmission in the cold, relative to tropical Wolbachia. Taken together, my research illustrates how intense pressures arising from species interactions can quickly lead to local adaptation, but constraints, like pleiotropy and environmental stresses, can bias this process towards repeated, predictable outcomes.

Pablo Delclos

University of Houston

A conserved trans regulatory loop involving an odorant binding protein controls male mating behavior in flies

Fall 2021

A major goal in evolutionary biology has been to determine how sex, genotype, and the environment interact to maintain variation in sexually selected and sexually dimorphic traits. The house fly, Musca domestica, is a promising system to understand how genotype-by-environment interactions affect sexually selected traits. Two common Y chromosomes segregate as stable polymorphisms in natural house fly populations, appear to be locally adapted to different thermal habitats, and differentially affect male mating success. Here, we perform a meta-analysis of RNA-seq data which identifies genes encoding odorant binding proteins (in the Obp56h family) as differentially expressed between the heads of males carrying the two different Y chromosomes. Differential expression of Obp56h has been associated with variation in male mating behavior in Drosophila melanogaster. We similarly find differences in male mating behavior between house flies carrying the Y chromosomes that are consistent with the direction of differential expression of Obp56h genes. We also find that male mating behaviors are affected by temperature, and the same temperature differentials further affect the expression of Obp56h genes. Using network analysis, we additionally find evidence for a sex-specific trans regulatory loop between Obp56h and the house fly Y chromosome that is conserved between D. melanogaster and house fly. Our results provide a functional mechanism by which the regulatory architecture controlling temperature-dependent gene expression affects male mating behavior, which could explain how genotype-by-environment interactions maintain variation in a sexually selected trait.

Stephany Virrueta Herrera

University of Illinois at Urbana-Champaign

Using genomics to uncover the evolutionary histories of ectoparasites on birds and mammals

Fall 2021

Parasitism is one of the most common life strategies on Earth. While decreasing the fitness of their hosts, parasites are a major component of ecosystems and can regulate host populations. However, much about parasite biology remains unknown. Parasite livelihood is dependent on a host or several hosts, and this interaction creates complex dynamics between host and parasite. Host parasite systems are ideal for studying coevolutionary mechanisms because of parasite dependence on their hosts and the constant battles to evolve to meet the adaptations of the hosts and vice versa. Ectoparasites of the insect order Phthiraptera, more commonly known as lice, exist on a wide variety of hosts. Genomics allows us to study several aspects of parasite evolution. My research is focused on two types of lice, feather lice on different groups of birds and sucking lice on mammals. Here I focus on two avian groups, tinamous, a group of paleognaths, which hosts some of the greatest diversity of lice and coots, a group of water birds, for which we obtained species level sampling across bird hosts and feather lice. My studies have also focused on the lice from a variety of seals and sea lions, and lice on Saimaa ringed seals, one of the most endangered seals in the world. I use genome sequence data from individual lice to estimate phylogenetic trees using both concatenated (RAxML) and coalescent (ASTRAL) methods of phylogenetic estimation. Both bird and mammal lice show evidence of occasional cospeciation with their hosts, but there is much more going on between hosts and parasites. Genomics, and specifically phylogenomics and population genomics, allow us to begin to tease apart these complex relationships. While we can estimate phylogenic relationships, I have also been able to use these data to begin to explore bacterial endosymbionts found within the feather lice as well as the microbiome compositions of the seal lice.

Pavitra Muralidhar

University of California-Davis

Sex chromosomes and genetic conflict

Spring 2021

As an evolutionary geneticist, I am fascinated by the diversity between males and females across the tree of life. Understanding the forces driving differences in morphology, physiology, and behavior between the sexes forms the core of my research program. Using a combination of theoretical and empirical work, I have investigated the interactions between the key evolutionary phenomena of sexual antagonism and sex determination, and their downstream consequences on processes such as sexual selection, mating systems, and sex ratio evolution. In this talk, I will highlight two recent projects which consider the interplay between sexual antagonism and sex determination. In the first portion of my talk, I will present a theoretical explanation for the prevalence of genetic versus environmental sex determination. Under environmental sex determination, a gene that increases the probability that its bearers develop as one of the sexes couples with a sexually antagonistic gene that is beneficial in that sex but detrimental in the other. The coupled haplotype invades, and recruits more sex biasing and sexually antagonistic alleles, eventuating in a sex chromosome, i.e., genetic sex determination. In the second portion of my talk, I propose a novel explanation for the evolution of female preferences for costly male traits, based on the selfish genetic interests of sex chromosomes within the genome. Female-biased genetic elements, such as the W and X sex chromosomes, evolve mating preferences for males displaying traits that reduce those males’ fitness (or that of their male offspring) but increase the fitness of female offspring. I demonstrate that sex-linked preferences can also drive the evolution of extreme handicap signals and costly sex-specific traits such as male parental care. The evolution of selfish sex-linked mating preferences may thus explain differences in ornamentation and behavior across species with divergent sex-determining mechanisms.

Jan Frederik Gogarten

Robert Koch Institute

A natural and unnatural history of primate phages: tools for studying microbial transmission at the human-wildlife interface

Spring 2021

Humans harbor diverse communities of microorganisms, the majority of which are bacteria in the gastrointestinal tract. These gut bacterial communities in turn host diverse phage communities that have a major impact on their structure, function, and ultimately human health. However, the evolutionary and ecological origins of these human-associated bacteriophage (hereafter phages) communities are poorly understood. To address this question, we examined fecal phageomes of 23 wild non-human primate taxa, including multiple representatives of all the major primate radiations. We find relatives of the majority of human-associated phages. Primate taxa have distinct phageome compositions that exhibit a clear phylosymbiotic signal, and phage-superhost co-divergence is often detected for individual phages. Within species, neighboring social groups harbor compositionally and evolutionarily distinct phageomes, which are structured by superhost social behavior. However, captive non-human primate phageomes are more similar to humans than their wild counterparts, revealing replacement of wild-associated phages with human-associated ones. Together, our results suggest that potentially labile primate-phage associations persisted across millions of years of evolution. Across primates, these phylosymbiotic and sometimes co-diverging phage communities are shaped by transmission between groupmates through grooming and are substantially modified when primates are moved into captivity. These phages represent an exciting tool for the study of the rates of microbial transmission at the human-wildlife interface; I briefly discuss other tools in development including the use of carrion flies as tools for biomonitoring and museomics.

Julia M Kreiner

University of Toronto

The repeatability and genomic architecture of herbicide resistance evolution

Spring 2021

The evolution of resistance in response to herbicides is a striking example of convergent, human-induced evolution. While much is known about the effects of particular point mutations that confer resistance, the extent to which they arise repeatedly de novo, draw from standing variation, or spread across populations through gene flow is unclear. Beyond these simple mutations, complex genetic bases such as gene amplification and polygenic architectures also contribute to resistance in weed populations but have yet to be described at a genomic level. My work aims to quantify the repeatability of resistance evolution across these genomic architectures by characterizing adaptive origins and processes that generate heterogeneity in the spread of resistance across the landscape. To do so, we have developed genomic resources for one of the most problematic agricultural weeds in North America, Amaranthus tuberculatus. I first characterize demographic history and the distribution of ancestry across the range and environments to disentangle the spread of a complex resistance-conferring gene amplification across the range from repeated origins. Simpler genetic bases allow for more precise inference of evolutionary histories; for 3 common resistance-conferring SNPs, I infer heterogeneity in the age, consistency of selection over time, and spread of repeated mutational origins across populations—in part driven by allelic interactions. Lastly, I characterize the polygenic architecture of herbicide resistance, finding that alleles across ~100 genes, shaped by strong balancing selection despite possible pleiotropic costs, explain a comparable amount of variation in resistance as monogenic mechanisms. This work contributes to our understanding of the genetic nature of adaptation, the impact of human pressures on genomic variation, and the management of resistance in agricultural environments.

Arjuna Rajakumar

McGill University

Origin and elaboration of a major evolutionary transition in individuality

Spring 2021

Obligate endosymbiosis, in which distantly related species integrate to form a single replicating individual, represents a major evolutionary transition in individuality. Although such transitions are thought to increase biological complexity the evolutionary and developmental steps that lead to integration remain poorly understood. Here we show that obligate endosymbiosis between the bacteria Blochmannia and the hyperdiverse ant tribe Camponotini originated and also elaborated through radical alterations in embryonic development, as compared to other insects. The Hox genes Abdominal A (abdA) and Ultrabithorax (Ubx)—which, in arthropods, normally function to differentiate abdominal and thoracic segments after they form—were rewired to also regulate germline genes early in development. Consequently, the mRNAs and proteins of these Hox genes are expressed maternally and colocalize at a subcellular level with those of germline genes in the germplasm and three novel locations in the freshly laid egg. Blochmannia bacteria then selectively regulate these mRNAs and proteins to make each of these four locations functionally distinct, creating a system of coordinates in the embryo in which each location performs a different function to integrate Blochmannia into the Camponotini. Finally, we show that the capacity to localize mRNAs and proteins to new locations in the embryo evolved before obligate endosymbiosis and was subsequently co-opted by Blochmannia and Camponotini. This pre-existing molecular capacity converged with a pre-existing ecological mutualism to facilitate both the horizontal transfer and developmental integration of Blochmannia into Camponotini. Therefore, the convergence of pre-existing molecular capacities and ecological interactions—as well as the rewiring of highly conserved gene networks—may be a general feature that facilitates the origin and elaboration of major transitions in individuality.

Andrew W. Thompson

Evolution of Annualism in Killifishes: An Eco-Evo-Devo Approach

Michigan State University

Seminar Date: May 2, 2019

Annual killifishes inhabit seasonal pools that desiccate, resulting in the death of the adult population. Unique adaptations including specialized egg structures, desiccation resistance, and up to three diapause stages slowing developmental and metabolic rates enable the embryonic population to survive annual dry seasons. When the habitat floods, annual killifish terminate their third and final diapause (DIII), hatch, and begin a new lifecycle. Here we explore the genomics of embryonic DIII in annual killifishes. We use scanning electron microscopy, comparative transcriptomics, phylogenetic methods, and model rates of gene evolution to investigate the genetics of killifish annualism, diapause, and environmentally-cued hatching. We discover hundreds of candidate genes involved in diapause and delayed hatching in three killifish species. Specifically, we find 10 differentially expressed killifish transcripts with homologs also differentially expressed in the same direction during dormancy in other animals. These 10 transcripts illustrate the conserved roles of these homologs during delayed development in metazoans. Additionally, tight linkage of diapause and hatching with the expression of a complex family of hatching enzymes leads us to analyze regulatory mechanisms associated with environmentally-cued hatching. Lastly, we show that diapause has up to 7 origins in killifishes and detect over 160 genes with increased rates of molecular evolution in annual compared to non-annual killifishes. Our integrative framework combining development, genomics, evolution, and ecology provides important insights into the mechanisms of diapause and the diversity of vertebrate hatching strategies as well as candidate genes associated with stress tolerance in the face of changing environments.

Jeffrey P. Spence

University of California, Berkeley

Inference and analysis of population-specific recombination maps

Seminar Date: ­­­April 11, 2019

Meiotic recombination—the shuffling of genetic material in sexually reproducing populations—plays an important role in evolution by decoupling the evolutionary fate of physically linked alleles. Recombination is also crucial for proper segregation of chromosomes during meiosis, and changes in the recombination machinery have been suggested as a possible mechanism for speciation.  Meanwhile, the rate of recombination along the genome is highly non-homogeneous: in many species recombination tends to occur in small regions called “hotspots” that correspond to locations in the genome where a protein, PRDM9, binds. PRDM9 is one of the fastest evolving proteins and as such there is rapid turnover in the location of these hotspots.  While the evolutionary dynamics of recombination hotspots have been studied from a theoretical perspective, attempts to link the theory to data have been stymied by the confounding effect of differences in the demographic histories of different populations.  I will present a new method capable of disentangling these demographic effects that I have applied to the 26 diverse human populations in the 1000 Genomes Project.  The resulting population-specific fine-scale recombination maps allow us to directly test theoretical predictions about the rate at which hotspots become cold and explore modulators of fine-scale recombination rate beyond PRDM9 binding.

John Gerhardt Phillips

University of Idaho 

Macroevolution, biogeography, and conservation in subterranean ecosystems: A tail of two salamanders

Seminar Date: March 28, 2019

Recent studies have begun to shed light on genetic patterns in cave species, which frequently display high levels of endemism, small range sizes, and habitat specialization. The combination of these factors limit dispersal and predispose subterranean organisms to higher rates of extinction. I investigate these ideas by testing how habitat specialization can constrain patterns of dispersal, as some species vary in mobility across ontogeny. Understanding such patterns provides insight into the influence of ontogenetic shifts on patterns of biogeography. Therefore, I use two plethodontid salamanders with different life histories using genome-scale data and a method newly applied to salamanders. I test for molecular variance among populations and associations between genetic distance and geographic features. In one species, divergence time estimates suggest rapid formation of the three major lineages in the Middle Miocene (relatively old for cave-adapted lineages). Gene flow among these populations appears negligible, indicating that most populations across the distribution are effectively isolated from one another. Paleodrainages, contemporary drainages, and geologic division all explain a proportion of genetic variation within one species, but none of these factors appear important in phylogeographic structure in the other (Georgia Blind Salamanders) where most sampled localities are non-monophyletic with a high frequency of haplotype sharing, even among localities in separate drainages. These results may reflect historical fragmentation and secondary admixture within the UFA. These results are important in understanding genetic structure and evolutionary patterns, and also are needed for conservation and management.

Liming Cai

Harvard University

Thrive with additional sets of genome: widespread paleopolyploidization buffers plants through Eocene global climatic upheaval

Seminar Date: February 28, 2019

Ancient whole genome duplications (WGDs) are important in eukaryotic genome evolution, and are especially prominent in plants. Recent genomic studies from large vascular plant clades, including ferns, gymnosperms, and angiosperms suggest that WGDs may represent a crucial mode of speciation. Moreover, numerous WGDs have been dated to events coinciding with major episodes of global and climatic upheaval, including the mass extinction at the KT boundary (~65 Ma) and during more recent intervals of global aridification in the Miocene (~10-5 Ma). These findings have led to the hypothesis that polyploidization may buffer lineages against the negative consequences of such disruptions. My recent work explores WGDs in the largely tropical flowering plant clade Malpighiales using a combination of newly sequenced transcriptomes and complete genomes from 42 species. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene Transition (~54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climate Optimum represents another, previously unrecognized, period of prolific WGDs in plants, and lends support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during major episodes of global change. Malpighiales, in particular, may have been particularly influenced by these events given their predominance in the tropics where Eocene warming likely had profound impacts owing to the relatively tight thermal tolerances of tropical organisms.

Katherine Xue

University of Washington

Evolutionary dynamics of influenza across spatiotemporal scales

Seminar Date: January 31, 2019

Influenza viruses evolve rapidly from year to year around the globe, with important consequences for human health. Recent advances in genome sequencing make it possible to track this evolution at higher resolution and to uncover evolutionary dynamics that operate at small scales of space and time. I present two case studies of unusual evolutionary dynamics in influenza. First, I will discuss an example of viral cooperation. RNA viruses like influenza mutate rapidly, generating a cloud of genetically diverse variants that have long been known to facilitate adaptation. Recent studies have suggested that cooperation between variants might also increase population fitness. We characterize two viral variants that differ by a single nonsynonymous mutation and show that mixed populations grow better than either variant alone in cell culture. Next, I will discuss the evolutionary dynamics of influenza within individual patient infections. Viral evolution on a global scale begins with de novo mutations within single infected hosts, but it has only recently become possible to systematically capture within-host genetic diversity. We deep-sequence longitudinal samples of influenza from long-term infections in immunocompromised patients and observe complex evolutionary patterns marked by extensive clonal interference. We find remarkable parallelism in evolution within and between hosts, suggesting concordance in evolutionary dynamics across multiple spatiotemporal scales. I end by discussing how the within-host dynamics of influenza contribute to the virus’s global evolution.

Justa Heinen-Kay

University of Minnesota

Ecology, sexual selection, and phenotypic diversification

Seminar Date: April 26, 2018 

Sexual traits are often the most flamboyant aspects of biodiversity and are critically important in generating and maintaining species boundaries. The classic paradigm is that natural and sexual selection act in opposite directions, with sexual selection favoring trait elaboration while natural selection provides a braking force. However, this often fails to reflect what is observed in nature because the evolutionary dynamics of sexual traits are rarely that simple. My research takes a novel, integrative approach to understanding the evolution of sexual traits that involves ecology, social dynamics, trait interactions, physiology, and plasticity. First, I will discuss some of my dissertation work with Bahamian mosquitofish that demonstrates divergence in conspicuous signals, behaviors, and male genitalia driven by population-level differences in predation due to natural variation over 1000’s of years and human impacts on the environment over 10’s of years. Next, I will discuss my postdoctoral research that takes the question of how natural and sexual selection interact a step further to investigate what happens when one evolutionary force overpowers the other. This work centers on Pacific field crickets in Hawaii that rapidly experienced the evolutionary loss of male song due to selection from a deadly parasitoid fly. My work has shown both plastic and pleiotropic influences on female reproductive investment and exploratory behaviors following rapid spread of the silencing mutation. Together, my research sheds light on how the interplay between natural and sexual selection influences diversification, and the causes and consequences of sexual trait evolution in the wild.

Elizabeth Mandeville 

University of Wyoming

Variable hybridization outcomes reflect variable reproductive isolation

Seminar Date: April 12, 2018

Interspecific hybridization can reveal mechanisms of reproductive isolation between related species, and also has long term implications for the evolution of hybridizing taxa. Although hybridizing species are often distributed across heterogeneous environments in the context of variable communities, variation in outcomes of hybridization is still incompletely understood. My recent work quantifies variation in hybridization across replicate instances of hybridization in fish taxa in the mountain west, specifically suckers and trout. Comparison of these two empirical instances of hybridization is informative about how hybridization varies across a large geographic area. My collaborators and I analyzed hybridization among six Catostomus species across the Upper Colorado River basin and found extreme variation in hybridization across locations. Different hybrid crosses were present in different locations, despite similar species assemblages. Within hybrid crosses, hybridization varied from only first generation hybrids to extensive hybridization with backcrossing. Similarly, our study of hybridization between introduced rainbow trout and native Yellowstone cutthroat trout revealed variation in extent of hybridization across 27 replicate tributaries, but patterns of variation were slightly different. Species always hybridized when sympatric, but the degree and direction of backcrossing varied. The next challenge in our work will be identifying precisely why hybridization outcomes vary. Variation might result from uneven fitness of hybrids across locations, polymorphism in genetic incompatibilities, chance, unidentified historical contingencies, or some combination thereof. We are currently investigating these possible mechanisms in both study systems. Our results suggest that one or a few instances of hybridization represent all interactions between the focal species.

Liana Burghardt

University of Minnesota

Revealing rhizobial fitness across symbiotic and free-living environments: identifying fitness tradeoffs and genomic variants

Seminar Date: March 22, 2018

When living in symbiosis with legume hosts, rhizobial bacteria convert atmospheric nitrogen into a plant-available form. In exchange, rhizobia receive carbon in the form of dicarboxylates and a favorable environment for reproduction. Rhizobia do not always live in symbiosis and the majority of the population at any given time is free-living in the soil. Little is known about how adaptation to the free-living environment affects the stability of the mutualism or the extent to which host genotype mediates competitive outcomes between closely related microbial strains. Here we present a variant of the ‘evolve and re-sequence’ approach that provides a robust method to estimate bacterial fitness and identify genetic variants responsible for fitness. We show that plant hosts impose strong selection on rhizobial populations, symbiotic fitness and free-living fitness are not correlated, and there is a trade-off between success in soil and in resource-rich liquid media. Selection in hosts caused strong shifts in allele frequency across the genome and these shifts were particularly strong for variants in genes associated with motility, transcriptional master regulators of nitrogen fixation, and genes involved in host/rhizobia signaling. Our work demonstrates the potential power of select and re-sequencing approaches to characterize fitness in microbial species as well as the naturally occurring allelic variants responsible for that variation. In the case of rhizobia, characterizing soil- and host-specific selection and identifying the causative rhizobial genes may allow for manipulation of this symbiosis to increase agricultural yields and provide insight into the biological processes that govern ecosystem productivity.

Brian Metzger

Disentangling the effects of mutation and selection on the evolution of gene expression and regulation

University of Chicago

Seminar Date: March 15, 2018

New mutations are the ultimate source of heritable variation. Unfortunately, the action of natural selection alters the types and frequencies of phenotypes observed in natural populations. As a consequence, the relative roles mutation and selection play in shaping patterns of phenotypic variation in natural populations are often difficult to disentangle. This is particularly true for changes in gene expression as the effects of mutations altering gene regulation are difficult to predict. To address this problem, I measured the effects of hundreds of new cis- and trans-regulatory mutations in the absence of natural selection on the expression of the Saccharomyces cerevisiae TDH3 gene. These measurements revealed differences in the effects of cis- and trans-regulatory mutations, indicating that the molecular mechanism by which a mutation alters gene expression plays an important role in the likely phenotypic consequences of that mutation. To determine how natural selection acts on these differences, I compared the effects of these new mutations to the effects of cis- and trans-regulatory polymorphisms segregating amongst over 60 S. cerevisiae strains isolated from a variety of natural environments. This comparison revealed differences in the action of natural selection between cis- and trans-regulatory changes due to differences in the effects of new mutations, including differences in the action of natural selection on the variability in gene expression amongst genetically identical cells, i.e. gene expression noise. These results show how the mutational process helps shape patterns of natural variation by producing biases in the types and frequencies of phenotypic variation.

Christopher Weiss-Lehman

University of Minnesota

Riding the wave: testing how rapid evolution shapes the dynamics of range expansions

Seminar Date: February 22, 2018

Although range expansions have long been modeled as purely ecological phenomena, recent evidence shows that evolutionary changes can shape the expansion process. Multiple possible selection pressures can cause evolution during range expansion, some of them direct outcomes of expansion dynamics. However, neutral processes also can play a significant role in driving evolutionary change during expansion, particularly in the form of gene surfing. The patterns in allele frequency changes produced by adaptive and neutral mechanisms in a single realization of the expansion process and the resulting impacts on expansion dynamics from different mechanisms can be difficult to distinguish. I present results from a highly replicated microcosm experiment with the red flour beetle (Tribolium castaneum) assessing the impact of neutral and adaptive evolutionary changes on range expansion dynamics. Using data from pooled, whole genome sequencing of beetles from the experiment with demographic data on spread rates and trait values, my collaborators and I quantified the relative contributions of adaptive and neutral mechanisms in driving evolutionary changes during expansion. In particular, we demonstrated an important role for gene surfing, as a neutral evolutionary process, in driving increased variance in expansion speeds among replicate populations. I explore this result further by pairing data from the red flour beetle system with a theoretical model exploring the interaction of habitat heterogeneity and rapid evolution in driving variance in expansion patterns. The results I present in this talk demonstrate a clear need to incorporate evolutionary mechanisms when making predictions for range expansions, even over relatively short timescales.