Population genetics strategies to characterize long-distance dispersal of insects

Population genetics strategies offer an alternative and powerful approach for obtaining information about long-distance movement, and have been widely used for examining patterns and magnitude of insect dispersal over geographic and temporal scales. Such strategies are based on the principle that genetic divergence between local populations reflects the interplay between genetic drift and gene flow, and thus can function as an indicator of dispersal capacity. Relatively new approaches for inferring population history are widely applicable for documenting introduction routes of invasive or quarantine species. These approaches are based on genetic variability calculated from changes in gene frequency of subpopulations, measured using molecular genetic markers. Inferences from population genetics can supplement and corroborate conventional observational approaches for characterizing insect dispersal and have provided important clues to many questions raised in the field of behavior and ecology of insects. Here, we summarize our work on the boll weevil as a case study to illustrate the kinds of information on dispersal capacity and dispersal patterns that can be obtained from population genetics techniques that would be difficult or impossible to acquire in other ways. Then we provide examples of how the molecular markers and population genetics tools have been applied to answer immediate questions of relevance to eradication program managers. Though the latter are idiosyncratic to this particular pest, they demonstrate the kinds and range of problems that can be addressed in other systems through application of population genetics strategies.     

Future prospects for human genetics and genomics in drug discovery

Evidence from human genetics supporting the therapeutic hypothesis increases the likelihood that a drug will succeed in clinical trials. Rare and common disease genetics yield a wide array of alleles with a range of effect sizes that can proxy for the effect of a drug in disease. Recent advances in large scale population collections and whole genome sequencing approaches have provided a rich resource of human genetic evidence to support drug target selection. As the range of phenotypes profiled increases and ever more alleles are discovered across world-wide populations, these approaches will increasingly influence multiple stages across the lifespan of a drug discovery programme.     

Molecular population genetics.

Molecular population genetics is entering a new era dominated by studies of genomic polymorphism. Some of the theory that will be needed to analyze data generated by such studies is already available, but much more work is needed. Furthermore, population genetics is becoming increasingly relevant to other fields of biology, for example to genetic epidemiology, because of disease gene mapping in general populations.     

Predatory prokaryotes: an emerging research opportunity

Predatory prokaryotes have evolved a unique strategy of obtaining energy and biosynthetic materials from their surroundings: acquiring them from other living bacterial cells. These types of microbes have been found in a diverse variety of environments, and may play an important role in modulating microbial population structure and dynamics, as has been hypothesized for marine viruses and possibly protists. Only one genus of predatory bacterium, Bdellovibrio, has been extensively described and studied, though several other examples have been reported in the literature. In this review, the four basic strategies used by currently described predatory prokaryotes will be discussed: "wolfpack" group predation, epibiotic attachment, direct cytoplasmic invasion, and periplasmic invasion. Special adaptations to each approach will be considered, and compared overall to the genetic and biochemical characteristics of symbiotic or pathogenic prokaryotes living within eukaryotic cells. Two specific examples of predatory microbes, Bdellovibrio and Ensifer, will be described in terms of predation strategy, association with host cells, and host range. The prospects for bringing to bear the tools of molecular microbial genetics to the study of predatory prokaryotes will be explored, using current research with Bdellovibrio and Ensifer as examples.     

One way traffic of pulses in a neuron

In this paper we investigate the effect of a change in geometry of a nerve axon on the propagation of potential waves along the axon. In particular we show that potential waves are stopped at a sudden large increase of cross-section area such as increase of diameter or branching. Some special examples are treated. The results do also apply to problems in population genetics and chemical reaction theory.     

Next‐generation QTL mapping: crowdsourcing SNPs,without pedigrees

For many molecular ecologists, the mantra and mission of the field of ecological genomics could be encapsulated by the phrase ‘to find the genes that matter’ (Mitchell‐Olds 2001 ; Rockman 2012 ). This phrase of course refers to the early hope and current increasing success in the search for genes whose variation underlies phenotypic variation and fitness in natural populations. In the years since the modern incarnation of the field of ecological genomics, many would agree that the low‐hanging fruit has, at least in principle, been plucked: we now have several elegant examples of genes whose variation influences key adaptive traits in natural populations, and these examples have revealed important insights into the architecture of adaptive variation (Hoekstra et al. 2006 ; Shapiro et al. 2009 ; Chan et al. 2010 ). But how well will these early examples, often involving single genes of large effect on discrete or near‐discrete phenotypes, represent the dynamics of adaptive change for the totality of phenotypes in nature? Will traits exhibiting continuous rather than discrete variation in natural populations have as simple a genetic basis as these early examples suggest (Prasad et al. 2012 ; Rockman 2012 )? Two papers in this issue (Robinson et al. 2013 ; Santure et al. 2013 ) not only suggest answers to these questions but also provide useful extensions of statistical approaches for ecological geneticists to study the genetics of continuous variation in nature. Together these papers, by the same research groups studying evolution in a natural population of Great Tits (Parus major), provide a glimpse of what we should expect as the field begins to dissect the genetic basis of what is arguably the most common type of variation in nature, and how genome‐wide surveys of variation can be applied to natural populations without pedigrees.     

Statistical analyses of population genetic data: new tools, old concepts

Several methods or tests and various software are currently being developed for analyzing data in population genetics and ecology, which often rely on computer-intensive algorithms. The potential user is thus confronted with the painful experience of freedom and, in particular, has to makea priori choices between different methods. Using examples drawn from population genetics, we explain some of these recently developed tools.     

National Institute on Drug Abuse genomics consortium white paper: Coordinating efforts between human and animal addiction studies

The National Institute on Drug Abuse Genetics and Epigenetics Cross‐Cutting Research Team convened a diverse group of researchers, clinicians, and healthcare providers on the campus of the University of California, San Diego, in June 2018. The goal was to develop strategies to integrate genetics and phenotypes across species to achieve a better understanding of substance use disorders through associations between genotypes and addictive behaviors. This conference (a) discussed progress in harmonizing large opioid genetics cohorts, (b) discussed phenotypes that are used for genetics studies in humans, (c) examined phenotypes that are used for genetics studies in animal models, (d) identified synergies and gaps in phenotypic analyses of human and animal models and (e) identified strategies to integrate genetics and genomics data with phenotypes across species. The meeting consisted of panels that focused on phenotype harmonization (Dr. Laura Bierut, Dr. Olivier George, Dr. Dan Larach and Dr. Sesh Mudumbai), translating genetic findings between species (Dr. Elissa Chesler, Dr. Gary Peltz and Dr. Abraham Palmer), interpreting and understanding allelic variations (Dr. Vanessa Troiani and Dr. Tamara Richards) and pathway conservation in animal models and human studies (Dr. Robert Hitzemann, Dr. Huda Akil and Dr. Laura Saba). There were also updates that were provided by large consortia (Dr. Susan Tapert, Dr. Danielle Dick, Dr. Howard Edenberg and Dr. Eric Johnson). Collectively, the conference was convened to discuss progress and changes in genome‐wide association studies.     

Method of path coefficients: a trademark of Sewall Wright

This address is a tribute to a pioneer of population genetics, including human population genetics. The unique methodology employed by Sewall Wright in many genetic problems is the method of path coefficients. This essay traces the historical landmarks in the development of the path method and then shows how some of the conventional statistical results can be converted into expressions involving path coefficients. The construction of a path diagram to represent such statistical results is explained in terms of examples. In the last section an example of applying the path method to the problem of genetic linkage in a random mating population is given. I hope that, despite the ending of the Sewall Wright era, the path method will continue to serve the scientific world.     

The phenotypic gambit: selective pressures and ESS methodology in evolutionary game theory

The ‘phenotypic gambit,’ the assumption that we can ignore genetics and look at the fitness of phenotypes to determine the expected evolutionary dynamics of a population, is often used in evolutionary game theory. However, as this paper will show, an overlooked genotype to phenotype map can qualitatively affect evolution in ways the phenotypic approach cannot predict or explain. This gives us reason to believe that, even in the long-term, correspondences between phenotypic predictions and dynamical outcomes are not robust for all plausible assumptions regarding the underlying genetics of traits. This paper shows important ways in which the phenotypic gambit can fail and how to proceed with evolutionary game theoretic modeling when it does.     

Bias in Behaviour Genetics: An Ecological Perspective

Research in behaviour genetics uncovers causes of behaviour at the population level. For inferences about individuals we also need to know how genes and the environment affect phenotypes. Behaviour genetics fosters a biased view of individual behaviour since it identifies the environment with psychosocial factors and disregards ecology.     

生态遗传学在生物多样性保护中的作用

本文就生态遗传学在生物多样性保护中的作用问题谈了几点看法。首先陈述了生态遗传学的性质,它是种群生态学和种群遗传学的结合,研究种群层次上正在进行着的进化;其次列举了生态遗传学的基本内容,说明生态遗传学是生物多样性研究和保护不可缺少的基本知识。最后举两个实例阐明生态遗传学在生物多样性保护中的具体应用。     

Toward a new synthesis: population genetics and evolutionary developmental biology

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.     

I3:A Self-organising Learning Workflow for Intuitive Integrative Interpretation of Complex Genetic Data

We propose a computational workflow(I3) for intuitive integrative interpretation of complex genetic data mainly building on the self-organising principle.We illustrate the use in interpreting genetics of gene expression and understanding genetic regulators of protein phenotypes,particularly in conjunction with information from human population genetics and/or evolutionary history of human genes.We reveal that loss-of-function intolerant genes tend to be depleted of tissue-sharing genetics of gene expression in brains,and if highly expressed,have broad effects on the protein phenotypes studied.We suggest that this workflow presents a general solution to the challenge of complex genetic data interpretation.I3 is available at http://suprahex.r-forge.r-project.org/I3.html.     

The fate of balanced,phenotypic polymorphisms in fragmented metapopulations

In large populations, genetically distinct phenotypic morphs can be maintained in equilibrium (at a 1 : 1 ratio in the simplest case) by frequency‐dependent selection, as shown by Sewall Wright. The consequences of population fragmentation on this equilibrium are not widely appreciated. Here, I use a simple computational model to emphasize that severe fragmentation biases the morph ratio towards the homozygous recessive genotype through drift in very small populations favouring the more common recessive allele. This model generalizes those developed elsewhere for heterostylous plants and major histocompatibility complex alleles, emphasizes one particular outcome and avoids the restricting assumptions of more analytical models. There are important implications for both fundamental evolutionary biology and conservation genetics. I illustrate this with a range of examples but refer particularly to shell polymorphism in snails. These examples show how habitat fragmentation could have a direct and often unappreciated effect on species at the level of their population genetics.     

一个具选择、突变、迁移的群体的遗传差分模型

假设一个群体是由“单位点—双基因”的个体所组成的,在该群体内存在选择、突变、迁移、生死等效应的作用。本文给出了在上述假设下并满足:(1)世代重叠,选择、突变、迁移、生死等效应的作用均在世代遗传之间完成;(2)群体适当大,个体间交配随机,符合孟德尔式遗传;(3)没有任何意外的灾祸等约定的群体遗传的数学模型。通过模型分析,我们能够进一步用数学语言来解释一些生命现象。模型分析指出:虽然某些群体不满足Hardy-Weinberg定律所叙述的条件,但可能具有和Hardy-Weinberg定律的结论相似的结果。该文中还就几个主要参数的变化讨论了群体遗传和进化的某些性质,如平衡等。最后,我们给出了该模型的一个数值例子。     

Transgressive Hybrids as Hopeful Monsters

The origin of novelty is a critical subject for evolutionary biologists. Early geneticists speculated about the sudden appearance of new species via special macromutations, epitomized by Goldschmidt’s infamous “hopeful monster”. Although these ideas were easily dismissed by the insights of the Modern Synthesis, a lingering fascination with the possibility of sudden, dramatic change has persisted. Recent work on hybridization and gene exchange suggests an underappreciated mechanism for the sudden appearance of evolutionary novelty that is entirely consistent with the principles of modern population genetics. Genetic recombination in hybrids can produce transgressive phenotypes, “monstrous” phenotypes beyond the range of parental populations. Transgressive phenotypes can be products of epistatic interactions or additive effects of multiple recombined loci. We compare several epistatic and additive models of transgressive segregation in hybrids and find that they are special cases of a general, classic quantitative genetic model. The Dobzhansky-Muller model predicts “hopeless” monsters, sterile and inviable transgressive phenotypes. The Bateson model predicts “hopeful” monsters with fitness greater than either parental population. The complementation model predicts both. Transgressive segregation after hybridization can rapidly produce novel phenotypes by recombining multiple loci simultaneously. Admixed populations will also produce many similar recombinant phenotypes at the same time, increasing the probability that recombinant “hopeful monsters” will establish true-breeding evolutionary lineages. Recombination is not the only (or even most common) process generating evolutionary novelty, but might be the most credible mechanism for sudden appearance of new forms.     

Integrating floral scent, pollination ecology and population genetics

1 . Floral scent is a key factor in the attraction of pollinators. Despite this, the role of floral scent in angiosperm speciation and evolution remains poorly understood. Modern population genetic approaches when combined with pollination ecology can open new opportunities for studying the evolutionary role of floral scent.
2 . A framework of six hypotheses for the application of population genetic tools to questions about the evolutionary role of floral scent is presented. When floral volatile chemistry is linked to pollinator attraction we can analyse questions such as: Does floral volatile composition reflect plant species boundaries? Can floral scent facilitate or suppress hybridization between taxa? Can the attraction of different pollinators influence plant mating systems and pollen-mediated gene flow? How is population genetic structure indirectly influenced by floral scent variation?
3 . The application of molecular tools in sexually deceptive orchids has confirmed that volatile composition reflects species boundaries, revealed the role of shared floral odour in enabling hybridization, confirmed that the sexual attraction mediated by floral odour has implications for pollen flow and population genetic structure and provided examples of pollinator-mediated selection on floral scent variation. Interdisciplinary studies to explore links between floral volatile variation, ecology and population genetics are rare in other plant groups.
4 . Ideal study systems for future floral scent research that incorporate population genetics will include closely related taxa that are morphologically similar, sympatric and co-flowering as well as groups that display wide variation in pollination mechanisms and floral volatiles.