Geographic variation in evolutionary rescue under climate change in a crop pest-predator system.

Species distribution models (SDMs) are often built upon the "niche conservatism" assumption, such that they ignore the possibility of "evolutionary rescue" and may underestimate species' future range limits under climate change. We select aphids and ladybirds as model species and develop an eco-evolutionary model to explore evolutionary rescue in a predator-prey system under climate change. We model the adaptive change of species' thermal performances, accounting for biotic interactions.

Deleterious mutation/epimutation-selection balance with and without inbreeding: a population (epi)genetics model.

Epigenetics in the form of DNA methylation and other processes is an established property of genotypes and a focus of empirical research. Yet, there remain fundamental gaps in the evolutionary theory of epigenetics. To support a comprehensive understanding of epigenetics, this paper investigates theoretically the combined effects of deleterious mutation and epimutation with and without inbreeding.

A Measure of the DNA Barcode Gap for Applied and Basic Research.

DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives.

Spatial structure and benefits to hosts allow plasmids with and without post-segregational killing systems to coexist.

To persist, a plasmid relies on being passed on to a daughter cell, but this does not always occur. Plasmids with post-segregational killing (PSK) systems kill a daughter cell if the plasmid has not been passed on. By killing the host, it also kills competing plasmids in the same host, something competing plasmids without a similar system cannot do.

Meiosis at three loci in autotetraploids: Probabilities of gamete modes and genotypes without and with preferential cross-over formation.

A long-standing goal in the field of polyploid biology has been the derivation of mathematical models of gamete mode formation. These models form the basis of statistical inference and evolutionary theory. Here, we present 3-locus models of gamete mode formation in autotetraploids without and with preferential cross-over formation.

A dynamic ancestral graph model and GPU-based simulation of a community based on metagenomic sampling.

In this paper, we present an ancestral graph model of the evolution of a guild in an ecological community. The model is based on a metagenomic sampling design in that a random sample is taken at the community, as opposed the taxon, level and species are discovered by genetic sequencing. The specific implementation of the model envisions an ecological guild that was founded by colonization at some point in the past that then potentially undergoes diversification by natural selection.

Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias.

Background: Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated.

The effects of migration load, selfing, inbreeding depression, and the genetics of adaptation on autotetraploid versus diploid establishment in peripheral habitats.

The distribution and abundance of polyploids has intrigued biologists since their discovery in the early 20th century. A pattern in nature that may give insight to processes that shape the distribution and abundance of polyploids is that polyploid populations are sometimes associated with peripheral habitats within the range of a species of mixed ploidy. Here, adaptation and competition of a diploid versus an autotetraploid population in a peripheral habitat are examined theoretically.

Two-Locus Local Adaptation by Additive or Epistatic Gene Combinations in Autotetraploids Versus Diploids.

In this article, we present a theoretical comparison of local adaptation between diploid and autotetraploid populations when fitness is determined by either additive or epistatic interactions between alleles at 2 loci. A continent-island model of local adaptation is derived, with 1-way migration from the continent to the island and distinct genotypes adaptive on the continent versus the island. The meiotic component of the model accounts for multivalent formation and the processes of chromosomal gametic disequilibrium and double reduction, which are unique to autotetraploids.

Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species.

In polymerase chain reaction (PCR)-based DNA sequencing studies, there is the possibility that mutations at the binding sites of primers result in no primer binding and therefore no amplification. In this article, we call such mutations PCR dropouts and present a coalescent-based theory of the distribution of segregating PCR dropout mutations within a species. We show that dropout mutations typically occur along branch sections that are at or near the base of a coalescent tree, if at all.

An ancestral process with selection in an ecological community.

An ecological community is a geographical area composed of two or more species. The ancestral histories of individuals from the same and different species in an ecological community may be interconnected due to direct and indirect interactions. Here, we present a model of the ancestral history of an ecological community that is built upon the framework of coalescent and ancestral graph theory.

A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size.

Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles.

Additive genetic variation and evolvability of a multivariate trait can be increased by epistatic gene action.

Epistatic gene action occurs when mutations or alleles interact to produce a phenotype. Theoretically and empirically it is of interest to know whether gene interactions can facilitate the evolution of diversity. In this paper, we explore how epistatic gene action affects the additive genetic component or heritable component of multivariate trait variation, as well as how epistatic gene action affects the evolvability of multivariate traits.

Epistasis can accelerate adaptive diversification in haploid asexual populations.

A fundamental goal of the biological sciences is to determine processes that facilitate the evolution of diversity. These processes can be separated into ecological, physiological, developmental and genetic. An ecological process that facilitates diversification is frequency-dependent selection caused by competition.

Body size, carry-over effects and survival in a seasonal environment: consequences for population dynamics.

In seasonal populations, vital rates are not only determined by the direct effects of density at the beginning of each season, but also by density at the beginning of past seasons. Such delayed density dependence can arise via non-lethal effects on individuals that carry over to influence per capita rates. In this study, we examine (i) whether parental breeding density influences offspring size, (ii) how this could carry over to affect offspring survival during the subsequent non-breeding period and (iii) the population consequences of this relationship.

A comparative study indicates both positive and purifying selection within ryanodine receptor (RyR) genes, as well as correlated evolution.

Ryanodine receptors are Ca(2+) ion channels that allow Ca(2+) to flow into the cytosol, from an internal store, in the form of transients. RyRs form a small gene family and vertebrates have three major isoforms, RyR1, RyR2, and RyR3, which are mixed and matched in different combinations in different tissues resulting in different Ca(2+) transients for each tissue. In this study, we characterized the interspecies evolution of RyRs within vertebrates.

Density-mediated carry-over effects explain variation in breeding output across time in a seasonal population.

In seasonal environments, where density dependence can operate throughout the annual cycle, vital rates are typically considered to be a function of the number of individuals at the beginning of each season. However, variation in density in the previous season could also cause surviving individuals to be in poor physiological condition, which could carry over to influence individual success in the following season. We examine this hypothesis using replicated populations of Drosophila melanogaster, the common fruitfly, over 23 non-overlapping generations with distinct breeding and non-breeding seasons.

Carry-over effects, sequential density dependence and the dynamics of populations in a seasonal environment.

Most animal populations have distinct breeding and non-breeding periods, yet the implications of seasonality on population dynamics are not well understood. Here, we introduce an experimental model system to study the population dynamics of two important consequences of seasonality: sequential density dependence and carry-over effects (COEs). Using a replicated seasonal population of Drosophila, we placed individuals at four densities in the non-breeding season and then, among those that survived, placed them to breed at three different densities.

Epistasis can increase multivariate trait diversity in haploid non-recombining populations.

We evaluate the effect of epistasis on genetically-based multivariate trait variation in haploid non-recombining populations. In a univariate setting, past work has shown that epistasis reduces genetic variance (additive plus epistatic) in a population experiencing stabilizing selection. Here we show that in a multivariate setting, epistasis also reduces total genetic variation across the entire multivariate trait in a population experiencing stabilizing selection.

The mapping of epistatic effects onto a genealogical tree in haploid populations.

In this paper we present a model that maps epistatic effects onto a genealogical tree for a haploid population. Prior work has demonstrated that genealogical structure causes the genotypic values of individuals to covary. Our results indicate that epistasis can reduce genotypic covariance that is caused by genealogical structure.

A model of the physiological basis of a multivariate phenotype that is mediated by Ca(2+) signaling and controlled by ryanodine receptor composition.

Calcium-signals occur in a wide variety of tissue types - from skeletal, smooth and cardiac muscle to pancreatic and brain tissues. Ca(2+) signals regulate diverse processes including muscle contraction, hormone secretion, neural communication and gene expression. Together these different tissues and processes form the basis of a multivariate trait.

The evolution of migration in a seasonal environment.

Despite the fact that migration occurs in a wide variety of taxa worldwide, little is known about the conditions under which migration is expected to evolve from an ancestral resident population. We develop a model that focuses on ecological factors affecting the evolution of migration in a seasonal environment within a genetically explicit framework. We model the evolution of migration for two common types of migration: 'shared breeding' where migrants share a breeding ground with residents and migrate to a separate non-breeding area, versus 'shared non-breeding', where migrants share a non-breeding ground with residents and migrate to a separate breeding area.

Complex adaptations can drive the evolution of the capacitor [PSI], even with realistic rates of yeast sex.

The [PSI(+)] prion may enhance evolvability by revealing previously cryptic genetic variation, but it is unclear whether such evolvability properties could be favored by natural selection. Sex inhibits the evolution of other putative evolvability mechanisms, such as mutator alleles. This paper explores whether sex also prevents natural selection from favoring modifier alleles that facilitate [PSI(+)] formation.