SMBE 2018 Symposia

1. Asian population genomics

Organizers:: Hie Lim Kim, Atsushi Tajima
Invited Speakers:: Changhoon Kim

Asia is the largest continent in the world and includes natural environments ranging from the tropics to the Arctic. The continent was the first destination for out-of-Africa migrants, who adapted to the diverse environments and dramatic environmental changes, giving rise to countless Asian ethnic groups. The recently generated, large- and fine-scale whole genome datasets, especially containing data from indigenous populations living in Asia for a long time, uncover the diversity of Asian ethnic groups and their complex demographic histories. The genome dataset-based research provides the understanding of the genetic basis of an individual genome and differences between populations, which is essential for developing precision medicine for Asians. This symposium will present the latest and most advanced studies on Asian population genomics and aim to raise the research activity of the fields related to population genomics and human genetics in Asia.

2. Associate Editors Symposium

Organizers:: TBD
Invited Speakers:: N/A

The journals MBE and GBE combined have over 100 Associate Editors (AEs). These AEs are among the most senior researchers in the areas of interest to SMBE, and in many ways they represent the backbone of the society. Yet only a small number of the AEs tend to present at any SMBE meeting. This symposium will provide an opportunity for the AEs to showcase what they are currently working on.

3. Ecological genomics

Organizers:: Polina Yu. Novikova, Daniele Filiault
Invited Speakers:: Melissa Pespeni, Thomas Mitchell-Olds

Drawing on recent rapid increases in the availability of genomics data, the field of ecological genomics continues to provide exciting new insight into how organisms and populations interact with their environment. From deepening our knowledge of the genetic basis of local adaptation and ecological speciation, to understanding and predicting the effects of rapid climate change, ecological genomics studies address fundamental questions of adaptive evolution. The impact of such work becomes increasingly powerful when it draws on collaborative efforts to integrate genomics with classical physiological, ecological, and conservation biology approaches. Therefore, we would like this ecological genomics symposium to foster broad discussion by presenting current advances that span the diversity in study organisms and approaches that make up this growing and dynamic field.

4. Evolution of adaptive immunity and MHC genes

Organizers:: Sabyasachi Das, Masayuki Hirano, Alicia Sanchez-Mazas
Invited Speakers:: Masanori Kasahara, Jim Kaufman, Tobias Lenz

The evolution of adaptive immunity is complex and controlled at multiple levels. Phylogenetic studies indicate the emergence of two parallel recombinatorial adaptive immune systems in vertebrates. Cardinal recognition elements of the adaptive immune system in jawed vertebrates are immunoglobulins (Ig), T cell receptors (TCRs) and the major histocompatibility complex (MHC), but none of these components are present in jawless vertebrates. Instead, jawless vertebrates use leucine-rich-repeat (LRR) domain-based variable lymphocyte receptors (VLRs) for antigen recognition. Among important components of adaptive immunity, the MHC genes are the most extensively studied because of their biomedical and theoretical importance. Their high level of molecular variability is assumed to be selected for resistance to a wide range of pathogens and cancers. The classical MHC genes in humans represent the most important early examples of selection against which the impact of neutral evolution could be measured.

The objective of this symposium is to highlight the important progress done in our current understanding of the evolution of adaptive immunity and MHC genes in relation to pathogenic threats, and to demonstrate that a very wide range of non-exclusive evolutionary mechanisms can explain their remarkable complexity.

5. Evolution of non-coding RNAs and their regulatory networks

Organizers:: Yehu Moran, Masafumi Nozawa
Invited Speakers:: Celina E. Juliano, Eric A. Miska

Research over the last decade has elucidated the pivotal roles of non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs) and long non-coding RNAs (lncRNAs) in diverse biological processes via transcriptional and post-transcriptional gene regulation. These important regulatory roles make the evolution of ncRNA pathways a fascinating topic, especially as the roots of these systems are still understudied and not fully elucidated. Further, the evolutionary conservation of miRNAs and lncRNAs serves as an important indication for their functionality, whereas species differences in miRNAs may be invaluable predictors of phylogenetic relationships. We propose that holding a symposium about the evolution of ncRNAs as part of the SMBE annual meeting is a unique opportunity to bring representatives of the communities of ncRNA biochemistry and molecular evolution together. Further, we secured the participation of Profs. Eric Miska and Celina Juliano, two excellent researchers that frequently include strong evolutionary aspects in their studies of ncRNAs. We believe that their participation as keynote speakers will serve as a focal point for drawing researchers from both communities to participate in the symposium and the meeting, resulting in stronger interactions that can benefit both communities.

6. Evolutionary epigenomics, progress and prospects

Organizers:: Soojin V. Yi, Brandon S. Gaut
Invited Speakers:: Shohei Takuno, Mary Gehring

Geneticists and molecular biologists have unraveled some of the intricacies of epigenetic pathways and the interplay of epigenetics with development. In addition, comparative and population epigenetic studies are uncovering substantial epigenetic variation between species as well as strong genetic components in determining epigenetic patterns. These findings bring optimism that evolutionary epigenetic studies may offer new insights into understanding the molecular basis of evolutionary divergence. However, many critical components of how epigenetic variation arise and transmit, and how they affect phenotypes, are currently missing. It is imperative to put various observations into an evolutionary framework. This symposium is aimed to bring researchers who share interests in epigenetics and evolution to disseminate recent progress in this area and to engage in open discussion on how to fully understand and utilize evolutionary epigenomics.

7. Evolutionary genomics of the human brain

Organizers:: Stefano Berto, Noriyoshi Usui, Kazuya Toriumi
Invited Speakers:: Genevieve Konopka, Philipp Khaitovich

Evolutionary expansion of the neocortex is linked with higher cognitive abilities in humans. When compared with our closest genetic relative the chimpanzee, the human brain strikingly shows morphological changes that have been associated with our cognitive specializations and skills, such as complex communication systems, sociality, decision-making, learning and memory. However, brain size alone hardly explains such exceptional cognitive abilities. In past decades, researchers have focused on the molecular mechanisms that might have facilitated the evolution of human-specific cognitive abilities, using techniques spanning from functional imaging to comparative genomics. The recent advent of next-generation sequencing has provided an unprecedented opportunity to better evaluate the human brain transcriptome and the gene regulatory mechanisms linked with the evolution of human cognition. Intriguingly, such human-specific networks may also make us vulnerable to cognitive disorders, such as autism, schizophrenia and Alzheimer's disease.

Thus, in this symposium, we will focus on open questions related to the evolution of gene regulatory networks that have shaped the human brain and cognition and that are disrupted in cognitive disorders. We welcome experimental and computational work that investigates these topics.

8. 50 years since Ohno's genome duplication: integration across disciplines and time scales

Organizers:: Kentaro K. Shimizu, Takashi Makino, Xinzhu Wei
Invited Speakers:: Clare Henry, Steven Maere, Levi Yant

Half a century ago, Susumu Ohno (1968; 1970) proposed that polyploidy is a motive force for evolutionary novelty. In parallel, Ledyard Stebbins (1971) discussed advantages and disadvantages of polyploidization in a work that remains widely cited. In this symposium, we will cover new analyses and new approaches to study genome duplication, across disciplines and time scales, to showcase current views of its evolutionary and ecological consequences. We will include speakers that focus on how allopolyploid species have expanded ecological niches by combining parental transcriptomes, and studies that seek to understand how evolution can overcome early challenges to genome duplication. Medical relevance is highlighted by the finding that duplicated genes derived from genome duplication (now called "ohnologs") are refractory to small-scale duplication due to their high dosage sensitivity, and frequently associated with human diseases. Understanding genome duplication broadly provides a unique opportunity to study evolution and speciation in action, facilitated by experimentally synthesized polyploids. From this symposium we will gain integrated views on the advantages and disadvantages of genome duplication, the genetic and epigenetic evolution of polyploid lineages, and the broader role of polyploidy in evolution and ecology.

9. Gene flow detection and dating methods (Sponsored by Genes)

Organizers:: Francesc Calafell, Simone Andrea Biagini, Carla Garcia Fernandez
Invited Speakers:: John Novembre, Garrett Hellenthal

In Alice in Wonderland by Lewis Carroll, the King of Hearts says "Begin at the beginning and go on till you come to the end: then stop"; is this possible in Human Population Genetics? Can we truly find a beginning and an end to all the different stories that mark the wide variety of current human populations? The application of analytical methods for the genetic composition of our species has reached a good level of definition, allowing us to identify events in the past well ascribable to specific historical moments. Tools like Admixture, fineStructure, and Chromopainter definitely helped the achievement of a progress in different studies of this field. But where are we today? And where are we going? In this symposium, we would like to give a general overview on what are the methods that we are currently using for the gene flow detection and dating studies. At this point, we think that it is important to be aware of the different possibilities that we have for scanning the huge amount of data that we handle day by day, and become capable of making the right choice when working in population genetics.

10. Genetic conflict and speciation

Organizers:: Chau-Ti Ting, Aya Takahashi
Invited Speakers:: Leonie Moyle, Nitin Phadnis

Accumulating information on the characteristics of genetic factors responsible for reproductive isolation has elucidated some intriguing features of the underlying mechanisms of genetic incompatibility between species. Drosophila studies have identified a number of cases, in which incompatibility is caused by rapid evolution of genes due to conflict between various genetic elements. In other organisms such as in plants, different features (e.g. self-incompatibility, disease resistance) have been highlighted. In this symposium, we discuss genetic conflict as well as other featured mechanisms shown to be involved in speciation process in animal and plant species.

11. Genomic underpinnings of primate phenotypic evolution and diversity

Organizers:: Amanda Dawn Melin, Shoji Kawamura
Invited Speakers:: Wesley Warren, Mariam Okhovat

Diet, activity pattern, and sensory systems have long been central to debates concerning primate origins and adaptive evolution. This symposium will bring together a diversity researchers using comparative genomics to understand how primates have evolved and have adapted to different environments, diets, social systems and timing of activity (e.g. nocturnal, diurnal habits) throughout the course of their evolution. The invited speakers are established expert and an emerging leader who will discuss new discoveries in this area; we will additionally attract other symposium participants to discuss how evolution has shaped the genes and regulatory mechanisms underlying digestion, metabolism, sensory systems, morphology and other systems relevant to primate adaptive radiation. We will additionally attract interdisciplinary scholars who combine state-of-the-art technology with traditional approaches in both field primatology and genomics to approach these topics from multiple angles and achieve a holistic understanding of ecological and evolutionary processes. By bringing together international scholars with a united interest in primate adaptation, we will foster discussion and propel forward our understanding of the genomic contributions to phenotypic adaptations of past and living species, including humans.

12. Genomics and evolution of symbiotic interactions

Organizers:: Cheong Xin Chan, Rebecca A. Chong, Hao Zheng
Invited Speakers:: Debashish Bhattacharya, Takema Fukatsu

Symbiosis is a close and long-term association between two or more organisms, and critical to the vast biodiversity we observe today. Through mutualism, commensalism or parasitism, symbiotic interactions may span any combination of the three kingdoms of life, from bacteria/archaea-eukaryote and eukaryote-eukaryote associations, to those involving multiple of these biotic components. These intimate interactions occur at molecular, cellular, and organismal levels. With the advancement of sequencing technologies, (meta)genomic approaches are increasingly used to investigate symbiosis, particularly to delineate how the corresponding biological components adapt and contribute to sustaining the symbiosis in changing environments. Recent research increasingly illustrates novel and diverse relationships that are fundamentally challenging our understanding of basic biology, ecology, and evolution. Several well-studied systems (e.g. insects, plants, and marine invertebrates) exist, but much of the research is presented to distinctly different audiences. This symposium brings together leading experts in biotic interactions of various organismal systems to engage in a research forum for genomics and evolution of symbiosis, and direct future research in this important area.

13. Human evolution after out-of-Africa

Organizers:: Naruya Saitou, Partha P. Majumder
Invited Speakers:: Partha P. Majumder, Brenna Henn

Study of modern human evolution is quickly moving to comparison of whole genome sequence data, and various previously unknown facts such as introgression of acharic humans and detailed pattern of natural selections were already elucidated. We thus would like to have symposium focusing on human evolution after out-of-Africa.

14. Improving inference frameworks by accounting for population structure

Organizers:: Marcy K. Uyenoyama, Emilia Huerta Sanchez
Invited Speakers:: Sohini Ramachandran, Amy Goldberg

Population structure encompasses a broad range of departures from panmixis, including sex, mating system, geographical subdivision, and admixture. A growing number of empirical studies support the view that population structure constitutes a significant and pervasive feature across the tree of life. Population structure can bias or invalidate a host of inferences, including patterns of gene flow, dates of admixture events, or signatures of selection. Such findings constitute a challenge to develop methods that directly confront population structure and exploit rather than avoid the higher-level associations it generates. For example, some studies for the mapping of disease genes in humans attempt to minimize the effects of population structure by restricting consideration to samples from groups believed to have low admixture. The development of methods that can accommodate population structure not only promotes better inference in all groups but also facilitates research with direct implications for human health in groups that are under-studied because of a history of admixture. This symposium also seeks to encourage the study of the extent to which population structure can mimic signatures of selection or changes in effective number.

15. Integrating ancient and modern DNA for evolutionary genomics

Organizers:: Michael Dannemann, Hernán A. Burbano, Kay Prüfer
Invited Speakers:: Kelley Harris, Sriram Sankararaman

Advances in sequencing technologies no longer limit population studies to single genomes. Simultaneous improvements in the recovery of ancient DNA made it possible to add to these datasets ancient genomes, including those from humans, non-human vertebrates, plants, and plant and animal pathogens. Complementary datasets are often crucial for studying population history, admixture and selection, since ancient genomes allow for the direct observation of genetic changes over time. Recently, catalogs of ancient and present-day genetic variation have been further complemented with large-scale phenotyping efforts. These measurements help uncover the evolution of phenotype over time in contexts such as population dispersal, plant and animal domestication, and the consequences of admixture. This symposium provides a forum for the discussion of these integrated datasets and the broad insights and specific challenges associated with them.

16. Intra-host evolutionary dynamics

Organizers:: Alison F. Feder, Katherine S. Xue
Invited Speakers:: Christina Curtis, Richard Neher

Many clinically relevant processes ranging from cancer to infectious diseases experience rapid intra-host evolutionary dynamics. Recent advances in high-throughput sequencing have made it possible to examine these intra-host population dynamics in space and time to uncover the evolutionary forces that drive them. Intra-patient processes also enable us to watch evolution in parallel across many hosts, revealing generalizable and predictable features of evolution. This symposium will highlight progress in understanding rapid intra-host evolutionary dynamics across diverse settings including infectious diseases, immune dynamics, cancer evolution, and microbial ecosystems. These subject areas represent unique opportunities to watch evolution unfold in complex natural settings, and we invite studies that examine how spatial structure, host heterogeneity, and variable selective pressures shape intra-host evolution. We also invite theoretical work describing the evolutionary dynamics emergent in intra-patient populations with characteristically large population sizes, high mutation rates and strong selective pressures. Finally, we encourage studies that compare evolutionary trajectories across hosts to examine the genetic landscapes underlying phenotypes like drug resistance and tumorigenesis. For infectious diseases, these inter-host comparisons can also shed light on the origins of population-level genetic diversity. Altogether, we hope that this symposium can shed light on clinically relevant but poorly understood evolutionary processes.

17. Linking the mitochondrial genotype to phenotype: a complex endeavour

Organizers:: Liliana Milani, Fabrizio Ghiselli
Invited Speakers:: Kateryna Makova, John F. Allen

Finding causal links between genotype and phenotype is a major issue in biology, particularly in mitochondrial biology.

Mitochondria are dynamic organelles. They undergo fission and fusion and we do not know how these dynamics influence the distribution of mtDNA variants across the mitochondrial network and how they affect the phenotype.
The mechanism of mitochondrial inheritance is still poorly understood, and it is not clear how selection/drift act on mtDNA genetic variation each generation.
We still do not know how mtDNA expression is regulated. There is growing evidence for a convoluted mechanism which includes RNA editing, mRNA stability/turnover, post-transcriptional and post-translational modifications.
It is difficult to predict the effects of nucleotide substitutions on protein structure and function. Nonsynonymous mutations can have mild or no effects, whereas synonymous substitutions might not be neutral (e.g. codon bias).
Mitochondrial functions and activity change in a tissue specific way within a species, and it can differ across species.

The goal of this symposium is to bring together evolutionary biologists studying mitochondria from different points of view along the path from genotype to phenotype; this will generate discussions that hopefully will help to elucidate such a complex problem.

18. Looking beyond the genome: cultural and behavioral drivers of biological evolution

Organizers:: Maanasa Raghavan, Nicole Creanza
Invited Speakers:: Susanne Shultz, Evelyne Heyer

It is becoming increasingly apparent that biological evolution and cultural evolution are interlinked. Behavioral and cultural changes have been shown to impose strong and novel selection pressures that can manifest as inheritable changes in the (epi)genome of organisms. Such changes and differences have the potential to introduce unique phenotypes and adaptations in populations and, eventually, even drive genetic isolation and population differentiation. Examples include changing diets of human populations to match lifestyle and subsistence changes, cultural barriers to gene flow such as languages and castes, kinship systems and marriage customs that lead to demographic structuring, and assortative mating on cultural traits such as religion and educational attainment. Cultural evolution can also affect genetic evolution in non-human species; for example, learned vocalizations can influence mate choice in whales, birds, and other animals. Intersecting cultural and genetic markers can reveal how these two systems act in tandem to influence evolutionary trajectories. Through this symposium, we aim to create a platform for cross-disciplinary discussions on the combined evolutionary impact of genes and culture.

19. Machine learning approaches in evolutionary genetics

Organizers:: Andrew D. Kern, Daniel R. Schrider
Invited Speakers:: Adam C. Siepel, Haipeng Li

As genomic datasets grow in size empiricists are faced with the daunting task of making sense of a flood of information. To keep pace with this explosion in data, computational methodologies are being rapidly developed to best utilize genomic sequence data from hundreds to tens of thousands of individuals for the purposes of evolutionary genetic inference. This symposium centers upon a new paradigm that has emerged in computational genomics: that of machine learning. Machine learning approaches such as random forests, support vector machines, and deep artificial neural networks have been shown to outperform traditional model based alternatives in many settings. Recently, evolutionary geneticists have begun to exploit the potential of machine learning, with exciting and often transformative results suggesting that these approaches have the potential to revolutionize the landscape of evolutionary genetic inquiry. This symposium will highlight recent methodological advances in evolutionary and population genomics enabled by machine learning as well as important findings produced by applying these techniques to empirical data.

20. Mapping genotype and phenotype to fitness

Organizers:: Sandeep Venkataram, Georg Rieckh
Invited Speakers:: Claudia Bank, Rowan Barrett

The evolutionary fate of a mutation depends on the relationship between genotype, phenotype and fitness. These relationships are never constant, as the phenotypic and fitness effects of a mutation may be influenced by other mutations present in the organism (epistasis) and also by the abiotic and biotic environment in which the organism exists. After extensive theoretical work, notably developing the concept of a fitness landscape, it was only recently that we were able to empirically quantify the phenotypic and fitness effects of large numbers of single mutations. Increasing attention is being paid to the genetic and environmental context in which these relationships between genotype, phenotype, and fitness is measured. Here we showcase a variety of approaches to studying these relationships, emphasizing the contributions from lab, field, and theory based efforts utilizing empirical genotype-phenotype-fitness maps to model evolutionary outcomes. While studies concerning only one of the relationships (i.e. the genetic or the phenotypic basis of fitness) will be presented, special consideration will be given to those that combine all three levels. In addition, we will highlight studies testing the genetic and environmental dependency of the genotype-phenotype-fitness relationship.

21. Microbial evolution: human-microbe interactions and the role of deep sequencing in time series analysis

Organizers:: Ana Duggan, Ashleigh Porter, Yuan Zhu
Invited Speakers:: Weiwei Zhai

The complex interaction of microbes on human health and wellbeing is indisputable. The burden of infectious disease remains ubiquitous, with 25% of global mortality attributed to emerging pathogens. Where natural defense fails, humans have responded by aggressively targeting disease-causing species with antimicrobials and vaccination, and in doing so shaped the evolution of many human-associated microbes. In the past few thousand years, we have also begun exploiting beneficial microbes for our own use, first through processes such as fermentation, and more recently, through bioengineering strains for specific industrial purposes. With the help of NGS deep sequencing, ancient DNA, time series data and contextualised phylodynamics, we are able to study historical as well as contemporary evolution of microbes in reaction to human intervention, and thus improve our understanding of host-microbe interaction. With this symposium we will discuss microbial evolution, focusing on the response of microbes to human defenses through the development of resistance, zoonotic shifts and adaptive evolution.

22. Molecular bases of the different forms of flowers on plants of the same species

Organizers:: Tatsuya Ota, Yasuo Yasui
Invited Speakers:: Philip M. Gilmartin, Takashi Akagi

Since the publication of "The different forms of flowers on plants of the same species" by Charles Robert Darwin, heterostyly of flower has attracted many evolutionary biologists. For example, primrose, which is described in the first and second chapters of the historical book, has been studied intensively from various evolutionary perspectives, including examination on the nature of supergene complex controlling multiple phenotypic characters. Independent and frequent emergence and parallel evolution are also another notable feature of heteromorphic self-incompatibility in plants. Recent advances on genomic and trascriptomic analyses by new generation sequencers have paved the way to investigate non-model organisms as well as organisms of little commercial importance with exhibiting biologically intriguing phenomena and a few unprecedented findings are emerging. In the symposium, recent progresses on researches on the molecular bases of S locus which regulates both heteromorphy and self-incompatibility as a supergene complex in primrose Primula vulgaris and other species will be presented. We also welcome, if any contributed speakers, to present molecular basis of different forms of flowers such as of polygamous, dioecious, or gyno-dioecious plants in addition to heterostyled plants.

23. Open Symposium

Organizers:: TBD
Invited Speakers:: N/A

This symposium will accept submissions on any topic.

24. Phylogenomics - genome-scale data and the methods and analyses for phylogeny construction and time estimation

Organizers:: Naoko Takezaki, Koichiro Tamura
Invited Speakers:: Jeffrey Townsend, Carolina Granados Mendoza

Due to the decline of sequencing costs, a large number of loci from genomic data are widely used for phylogenetic analyses. However, for efficient and accurate phylogenetic inference the problems exist in various levels. In the basic experimental design, the choice of markers for aiming cost-effective acquisition of informative loci for resolving particular relationships, and taxon-sampling vs. the number of loci to increase accuracy and confidence should be considered. In the compilation of data there is a need of the selection of loci to reduce systematic error and increase phylogenetic information in the presence of paralogs and missing data. In the analyses of large data sets, because different lineages and genes are subjected to heterogeneous evolutionary processes, models and methods to be used, and arrangement of data such as concatenated, partitioned, or gene-by-gene can affect the results.

In this symposium studies that address the problems on both methodologies and actual data analyses in phylogenomics will be presented.

25. Post-transcriptional modifications: functions, diversity, pathogenesis and evolution

Organizers:: Helen Piontkivska, Sabyasachi Das, Marta L. Wayne
Invited Speakers:: Jianzhi George Zhang, Reuben S. Harris

Advances in deep sequencing underlie the expansion of our knowledge of a variety of post-transcriptional modifications, ranging from mRNA processing to different nucleotide modifications, including A-to-I editing, and their roles in genome function. Post-transcriptional modifications occupy a prominent place in transcriptome diversification and regulation, and have been shown to be involved in cancer, developmental processes and immune responses. However, our current understanding of these multiple roles and consequences of modifications, including short-term and long-term evolutionary outcomes, is still limited, such as how tissue-specific expression and regulation occurs, whether (and how) they play a role in host-pathogen interactions, whether they can contribute to infectious disease pathogenesis,etc. This symposium will highlight the diversity of known post-transcriptional modifications, their use as biomarkers, and their roles in various aspects of genome function and evolution, including host-pathogen interactions and diseases.

26. Predictability of rapid evolutionary processes

Organizers:: Marta Luksza, Armita Nourmohammad
Invited Speakers:: Michael Lassig, Thierry Mora

In recent years, insights from molecular sequence data have pushed theoretical work in population genetics to account for the complexity of the evolutionary processes. Rapidly evolving populations show non-trivial dynamics: many beneficial mutations arise within a population leading to a highly non-linear stochastic evolution with competing clones. On the other hand the large amounts of evolutionary data are creating new perspectives for the field: from reconstructing the past to understanding the mechanism that drive the evolution today and predicting the dynamics into the future. In particular, there has been much progress in inference of adaptation and immune interactions in populations of viruses, bacteria and cancer, with significant translational impact. The goal of this symposium is to explore fundamental limits of predictability and, ultimately, control of evolution of such rapidly evolving biological systems.

27. Quantitative genetics of developmental evolution

Organizers:: Christina Zakas, Luke Noble
Invited Speakers:: Katrina McGuigan

There is no theory of development, only details. An improved synthesis of developmental evolution calls for quantitative study across traits, through ontogeny, interpreted in the light of population genetics. This symposium will feature evolutionary research applying quantitative genetic methods (in both classical and broad senses) to the study of development at multiple levels of organization, from life-history traits to the structure of gene expression networks underlying phenotypic microevolution. Central topics will be trait variance (pleiotropy, mutational variance, multivariate analysis), genetic architecture, and population genetic effects on developmental evolution.

28. Selection on complex traits: reuniting quantitative and population genetics

Organizers:: Fernando Racimo, Jeremy Jackson Berg
Invited Speakers:: Guy Sella, Anna Kukekova

Population and quantitative genetics were viewed as two fundamentally interconnected disciplines through much of the first half of the twentieth century. For the last 50 years, however, they have largely evolved in separation. Quantitative geneticists focused on understanding complex trait dynamics without disentangling their underlying genetic architecture. Meanwhile, population geneticists strayed away from the complexities of quantitative traits, and largely focused on positive selection operating via alleles of large effect. Now, the advent of high-throughput genomics and large multi-dimensional phenomic databases (like the UK Biobank, the International Plant Phenotyping Network and the International Mouse Phenotyping Consortium) is providing an opportunity for these two old fields to build new bridges: we are beginning to understand how adaptive processes operate on hundreds of alleles of small effect. For example, recent studies have found substantial evidence for both positive and negative selection on alleles associated with height and BMI during recent human evolution. This symposium will showcase efforts to understand adaptive polygenic processes based on multivariate genomic and phenomic data. It will feature a special emphasis on cross-disciplinary approaches in both human and non-human systems, incorporating insights from population and quantitative genetics, and using present-day and/or ancient genomes.

29. Somatic mutation and the evolution of multicellularity

Organizers:: Reed Cartwright, Rob Lanfear
Invited Speakers:: Inigo Martincorena, Maria Orive

Somatic mutations are mutations which affect somatic cells in multicellular organisms. Understanding somatic mutation is important to understanding the evolution and maintenance of multicellularity, including the pathology of cancer. Most of the research in somatic mutations has been focused on animal systems, while plants, algae, fungi, and protists have received less attention. However, with modern advances in whole-genome sequencing and bioinformatics, biologists are beginning to understand somatic mutation across the tree of life. This in turn will allow molecular evolutionists to answer questions about selection and diversity in soma, and how this impacts on long-term patterns of molecular evolution in the germline.

This symposium will bring together scientists working on diverse systems to share biological and methodological insights into measuring and understanding somatic mutations, and their impact on the evolution of genes and genomes. The symposium will forge new links between fields that do not often interact (e.g. plant genomics, cancer biology, social protists, bioinformatics of accurate variant calling), helping to set the direction for the field in the years to come.

30. Timing methodologies and applications

Organizers:: Fabia Ursula Battistuzzi, Beatriz Mello
Invited Speakers:: Blair Hedges, Lindell Bromham

Timing of species and gene divergences is a primary outcome of many evolutionary analyses. The widespread application of molecular clocks to a variety of datasets and evolutionary histories has driven the diversification of these methods into many different approaches that often produce discordant timelines. Despite many efforts, generally applicable rules to reconcile these disagreements are still elusive leaving researchers with the difficult task of selecting most appropriate methods based on limited information or requiring complex comparative evaluations of multiple methods. Unfortunately, many of the current approaches that require multiple hypotheses testing are difficult to apply to large phylogenomic datasets, thus exacerbating the uncertainty in produced timelines. Participants in this symposium will explore the diversity of molecular clock methods and discuss their applications to simulated and empirical sequences from methodological and applied perspectives. The goal is to have an open discussion on the strengths and weaknesses of each method and identify best practices to reconcile different timelines. The research studies showcased in this symposium will explore the application of molecular clocks to species and gene divergences in an effort to shed light on the evolution of life through time.

31. Tracing back bacterial pathogen evolution from ancient and modern genomics

Organizers:: Verena J. Schuenemann
Invited Speakers:: Johannes Krause, Caitlin Pepperell

In recent years, our understanding of the evolution of bacterial pathogens has been revolutionized by integrating the research in population genomics, phylogenomics, and ancient DNA. These contributions allow us to trace back the evolutionary and demographic processes of bacterial pathogens, revealing the history of ancient pathogens presumed to be out of reach by prior methods. Notably the integration of ancient genomics to the study of host-pathogen interactions and pathogen evolution affords us the opportunity for a deeper exploration of the evolution of virulence and host interactions. These recent key developments in genetic methods, novel and ancient, provide wide applications to infectious disease research with great relevance to antibiotic resistance and disease prevention.

In this respect, we propose a symposium that brings together key researchers from different scientific backgrounds to showcase recent cutting-edge research on pathogen genomics ranging from phylogenomics to evolutionary and demographic history. The symposium aims to: 1) bridge the gap between ancient DNA research, microbiology, and epidemiology; 2) consolidate the distributed knowledge about bacterial evolution and distribution patterns; 3) devise new interdisciplinary directions of research in this area.

32. Transposable elements in gene regulation and genome evolution

Organizers:: Luz Mayela Soto-Jimenez, Robin Burns
Invited Speakers:: Cedric Feschotte, Doris Bachtrog

It is becoming increasingly clear that in order to understand genome evolution and function we need to better understand transposable elements (TEs), their regulation and host genome interaction. TEs were named by Barbara McClintock as "controlling elements" because of their capacity to regulate genes. As we continue to uncover the secrets behind these elusive mobile DNA sequences, this name becomes more fitting. Advances in sequencing technologies, the development of TE-detecting software and thorough analyses, which can range from a genetic cross up to a species-wide and global population level, have placed TEs as central players in adaptation, gene regulation and genome evolution. Several sequencing data types have helped towards this discovery, such as methylomes, transcriptomes, smallRNA sequencing, chromatin profiling and genome sequencing. We are just beginning to piece together this exciting jigsaw. This symposium will attract scientists from different backgrounds with different perspectives, furthering our understanding of how TEs shape gene regulation and genome evolution by discussing the current knowledge, methods being used and setting the stage for new questions to be asked. It will appeal to a broad audience outside the TE field because the dynamic TE-genome arms race continues to intrigue and connects many fields in biology.

33. Trash to treasure and treasure to trash: invasion, persistence, neofunctionalization, and gene decay in evolution

Organizers:: Peter Gogarten, Dan Graur, Anthony Poole
Invited Speakers:: Lilach Hadany, Dan Graur

Goal of the proposed session is to present data on selfish DNA evolving to make contributions to cellular physiology, genetics and regulation, including a critical assessment of how frequently these transitions occur, and how long they persist. The session will discuss bacterial, archaeal and eukaryotic systems.

Initial relationships between selfish or parasitic genetic and their host often can be described as commensalism or parasitism; however, in a few instances the selfish elements acquired a function that may be targeted by purifying selection acting on the host organism. Proposed examples include the self-splicing domain of inteins acting as an emergency shut-off switch, homing endonucleases evolving into mating type switching endonucleases, restriction modification addiction system protecting against additive gene transfer, the nonsense-mediated mRNA decay pathway in eukaryotes, and the use of formylmethionine in the initiation of bacterial protein synthesis. In some of these instances purifying selection acting on these elements may reflect an assumed benefit to the host organism; however, in other instances constructive neutral evolution made the continued function of the selfish DNA a necessity for host survival.

34. Virus genome evolution

Organizers:: Anne Kupczok, Marina Escalera Zamudio, Richard Goldstein
Invited Speakers:: Adi Stern, Marcia F. Marston

Viruses exhibit a unique parasitic situation that shapes the evolution of their genomes. They evolved an extensive amount of genomic diversity with a wide range of complex life, reproduction, and inheritance strategies, including the use of different genetic materials, genome sizes, and a wide range of mutation rates. Virus evolution has had a strong influence on the evolution of other life forms, acting as source of novel genes, facilitating horizontal transfer, eliciting genomic alterations caused by virus integration, and creating potent co-evolutionary selective pressure. The evolutionary process is also explicitly involved in many processes with medical implications, such as host switching, immune avoidance, and the development of drug resistance. The study of virus evolution has proven critical for the study of disease emergence and spread, exemplified by the recent Ebola and Zika outbreaks. The use of genomic approaches has transformed the field of virology, enabling these and other issues to be answered with ever more depth and precision. This symposium will highlight recent advances on virus genome evolution and will bring together different approaches on prokaryotic and eukaryotic virus evolution; how these viruses originated, diversified, and spread, how they change and adapt, and how they co-evolve with their hosts.

35. Weak forces in genome evolution

Organizers:: Hiroshi Akashi, Tomoko Ohta
Invited Speakers:: Laurent Duret, Rebekah Rogers

This symposium will focus on recent advances in our understanding of "weak" evolutionary forces that can have strong cumulative effects over long time-scales. The session will include genome analysis and experimental studies with a focus on two major mechanisms of genome evolution: weak natural selection and biased gene conversion. Comparative and experimental studies demonstrate the importance of mild effect mutations in both the evolution of novel traits and in lineage-specific evolution potentially leading to species decline. In addition, mounting evidence supports biased gene conversion as a major factor in genome evolution that shapes global nucleotide landscapes and local rates of evolution. Importantly, weak selection and biased gene conversion can result in similar signals in polymorphism/divergence data and both factors can underlie spurious signals of adaptive evolution. Establishing the importance of weak forces, distinguishing among such forces, and determining how they should be considered in tests of adaptive evolution will be key topics for the session.