Simulating phase transitions and control measures for network epidemics caused by infections with presymptomatic, asymptomatic, and symptomatic stages.

We investigate phase transitions associated with three control methods for epidemics on small world networks. Motivated by the behavior of SARS-CoV-2, we construct a theoretical SIR model of a virus that exhibits presymptomatic, asymptomatic, and symptomatic stages in two possible pathways. Using agent-based simulations on small world networks, we observe phase transitions for epidemic spread related to: 1) Global social distancing with a fixed probability of adherence. 2) Individually initiated social isolation when a threshold number of contacts are infected. 3) Viral shedding rate. The primary driver of total number of infections is the viral shedding rate, with probability of social distancing being the next critical factor. Individually initiated social isolation was effective when initiated in response to a single infected contact. For each of these control measures, the total number of infections exhibits a sharp phase transition as the strength of the measure is varied.

Associations between genomic ancestry, genome size and capitula morphology in the invasive meadow knapweed hybrid complex (Centaurea × moncktonii) in eastern North America.

Plant invasions are prime opportunities for studying hybridization and the nature of species boundaries, but hybrids also complicate the taxonomic treatment and management of introduced taxa. In this study, we use population genomics to estimate the extent of genomic admixture and test for its association with morphology and genome size in a hybrid complex of knapweeds invasive to North America: meadow knapweed (Centaurea × moncktonii) and its parental species (C. jacea and C. nigra). We sampled 20 populations from New York and Vermont, USA, and used genotyping by sequencing to identify single nucleotide polymorphisms in order to estimate genome-wide ancestry and classify individuals into hybrid genotype classes. We then tested for association between degree of genomic introgression and variation in a subset of traits diagnostic for the parental taxa, namely capitula morphology and monoploid genome size. Genomic clustering revealed two clearly defined lineages, as well as many admixed individuals forming a continuous gradation of introgression. Individual assignments to hybrid genotype classes revealed many advanced generation intercrosses and backcrosses, suggesting introgression has been extensive and unimpeded by strong reproductive barriers between taxa. Variation in capitula traits between the two unadmixed, presumed parental, lineages exhibited continuous, and in some cases transgressive, segregation among introgressed hybrids. Genome size was also divergent between lineages, although advanced generation hybrids had smaller genomes relative to additive expectations. Our study demonstrates deep introgression between the porous genomes of a hybrid invasive species complex. In addition to strong associations among genomic ancestry, genome size and morphology, hybrids expressed more extreme phenotypic values for capitula traits and genome size, indicating transgressive segregation, as well as a bias towards smaller genomes, possibly due to genomic downsizing. Future studies will apply these results to experimentally test how introgression, transgressive segregation and genome size reduction interact to confer invasiveness.

Similarity of introduced plant species to native ones facilitates naturalization, but differences enhance invasion success.

The search for traits associated with plant invasiveness has yielded contradictory results, in part because most previous studies have failed to recognize that different traits are important at different stages along the introduction-naturalization-invasion continuum. Here we show that across six different habitat types in temperate Central Europe, naturalized non-invasive species are functionally similar to native species occurring in the same habitat type, but invasive species are different as they occupy the edge of the plant functional trait space represented in each habitat. This pattern was driven mainly by the greater average height of invasive species. These results suggest that the primary determinant of successful establishment of alien species in resident plant communities is environmental filtering, which is expressed in similar trait distributions. However, to become invasive, established alien species need to be different enough to occupy novel niche space, i.e. the edge of trait space.

Genomic Admixture Between Locally Adapted Populations of Arabidopsis thaliana (mouse ear cress): Evidence of Optimal Genetic Outcrossing Distance.

Admixture can break up divergent genetic architectures between populations, resulting in phenotypic novelty and generating raw material for environmental selection. The contribution of admixture to progeny trait variation and fitness varies based on the degree of genetic isolation between the parental populations, for which most studies have used geographic distance as a proxy. A novel approach is to estimate optimal crossing distance using the adaptive genetic distance between mates estimated from loci that contribute directly to local adaptation. Here, we aim to understand the effect of admixture on disrupting local adaptation of ecotypes of Arabidopsis thaliana separated along gradients of geographic, background, and locally adaptive genetic distances. We created experimental F1 hybrids between ecotypes that vary in geographic distance and used SNP data to estimate background (putatively neutral) and adaptive genetic distance. Hybrids were grown under controlled conditions, and fitness, growth, and phenology traits were measured. The different traits measured showed a clear effect of adaptive genetic distance, but not geographic distance. The earliest bolting hybrids were intermediate in the adaptive genetic distance between their parents, and also had higher biomass and fitness in terms of fruit and seed production. Our results suggest that disruption of locally adaptive genomic loci decreases the performance of offspring between distantly related parents, but that crosses between very closely related parents also reduce performance, likely through the expression of deleterious recessive alleles. We conclude that during admixture, selection may have to balance the consequences of disrupting local adaption while also avoiding inbreeding depression.

The ubiquity of phenotypic plasticity in plants: a synthesis.

Adaptation to heterogeneous environments can occur via phenotypic plasticity, but how often this occurs is unknown. Reciprocal transplant studies provide a rich dataset to address this issue in plant populations because they allow for a determination of the prevalence of plastic versus canalized responses. From 31 reciprocal transplant studies, we quantified the frequency of five possible evolutionary patterns: (1) canalized response-no differentiation: no plasticity, the mean phenotypes of the populations are not different; (2) canalized response-population differentiation: no plasticity, the mean phenotypes of the populations are different; (3) perfect adaptive plasticity: plastic responses with similar reaction norms between populations; (4) adaptive plasticity: plastic responses with parallel, but not congruent reaction norms between populations; and (5) nonadaptive plasticity: plastic responses with differences in the slope of the reaction norms. The analysis included 362 records: 50.8% life-history traits, 43.6% morphological traits, and 5.5% physiological traits. Across all traits, 52% of the trait records were not plastic, and either showed no difference in means across sites (17%) or differed among sites (83%). Among the 48% of trait records that showed some sort of plasticity, 49.4% showed perfect adaptive plasticity, 19.5% adaptive plasticity, and 31% nonadaptive plasticity. These results suggest that canalized responses are more common than adaptive plasticity as an evolutionary response to environmental heterogeneity.

Ecological niche differentiation of polyploidization is not supported by environmental differences among species in a cosmopolitan grass genus.

UNLABELLED: • PREMISE OF THE STUDY: Polyploidization frequently results in the creation of new plant species, the establishment of which is thought to often be facilitated by ecological niche differentiation from the diploid species. We tested this hypothesis using the cosmopolitan grass genus Phalaris (Poaceae), consisting of 19 species that range from diploid to tetraploid to hexaploid. Specifically, we tested whether (1) polyploids occupy more extreme environments and/or (2) have broader niche breadths and/or (3) whether the polyploid species' distributions indicate a niche shift from diploid species.• METHODS: We employed a bootstrapping approach using distribution data for each species and eight environmental variables to investigate differences between species in the means, extremes, and breadths of each environmental variable. We used a kernel smoothing technique to quantify niche overlap between species.• KEY RESULTS: Although we found some support for the three hypotheses for a few diploid-polyploid pairs and for specific environmental variables, none of these hypotheses were generally supported.• CONCLUSIONS: Our results suggest that these commonly held hypotheses about the effects of polyploidization on ecological distributions are not universally applicable. Correlative biogeographic studies like ours provide a necessary first step for suggesting specific hypotheses that require experimental verification. A combination of genetic, physiological, and ecological studies will be required to achieve a better understanding of the role of polyploidization in niche evolution.

Human-aided admixture may fuel ecosystem transformation during biological invasions: theoretical and experimental evidence.

Biological invasions can transform our understanding of how the interplay of historical isolation and contemporary (human-aided) dispersal affects the structure of intraspecific diversity in functional traits, and in turn, how changes in functional traits affect other scales of biological organization such as communities and ecosystems. Because biological invasions frequently involve the admixture of previously isolated lineages as a result of human-aided dispersal, studies of invasive populations can reveal how admixture results in novel genotypes and shifts in functional trait variation within populations. Further, because invasive species can be ecosystem engineers within invaded ecosystems, admixture-induced shifts in the functional traits of invaders can affect the composition of native biodiversity and alter the flow of resources through the system. Thus, invasions represent promising yet under-investigated examples of how the effects of short-term evolutionary changes can cascade across biological scales of diversity. Here, we propose a conceptual framework that admixture between divergent source populations during biological invasions can reorganize the genetic variation underlying key functional traits, leading to shifts in the mean and variance of functional traits within invasive populations. Changes in the mean or variance of key traits can initiate new ecological feedback mechanisms that result in a critical transition from a native ecosystem to a novel invasive ecosystem. We illustrate the application of this framework with reference to a well-studied plant model system in invasion biology and show how a combination of quantitative genetic experiments, functional trait studies, whole ecosystem field studies and modeling can be used to explore the dynamics predicted to trigger these critical transitions.

Comparing the genetic architecture and potential response to selection of invasive and native populations of reed canary grass.

Evolutionary processes such as migration, genetic drift, and natural selection are thought to play a prominent role in species invasions into novel environments. However, few empirical studies have explored the mechanistic basis of invasion in an evolutionary framework. One promising tool for inferring evolutionarily important changes in introduced populations is the genetic variance-covariance matrix (G matrix). G matrix comparisons allow for the inference of changes in the genetic architecture of introduced populations relative to their native counterparts that may facilitate invasion. Here, we compare the G matrices of reed canary grass (Phalaris arundinacea L.) populations across native and invasive ranges, and between populations along a latitudinal gradient within each range. We find that the major differences in genetic architecture occur between populations at the Northern and Southern margins within each range, not between native and invasive populations. Previous studies have found that multiple introductions in introduced populations caused an increase in genetic variance on which selection could act. In addition, we find that differences in the evolutionary potential of Phalaris populations are driven by differences in latitude, suggesting that selection also shapes the evolutionary trajectory of invasive populations.

Genome size reduction can trigger rapid phenotypic evolution in invasive plants.

BACKGROUND AND AIMS: The study of rapid evolution in invasive species has highlighted the fundamental role played by founder events, emergence of genetic novelties through recombination and rapid response to new selective pressures. However, whether rapid adaptation of introduced species can be driven by punctual changes in genome organization has received little attention. In plants, variation in genome size, i.e. variation in the amount of DNA per monoploid set of chromosomes through loss or gain of repeated DNA sequences, is known to influence a number of physiological, phenological and life-history features. The present study investigated whether change in genome size has contributed to the evolution of greater potential of vegetative growth in invasive populations of an introduced grass. METHODS: The study was based on the recent demonstration that invasive genotypes of reed canarygrass (Phalaris arundinacea) occurring in North America have emerged from recombination between introduced European strains. The genome sizes of more than 200 invasive and native genotypes were measured and their genome size was related to their phenotypic traits measured in a common glasshouse environment. Population genetics data were used to infer phylogeographical relationships between study populations, and the evolutionary history of genome size within the study species was inferred. KEY RESULTS: Invasive genotypes had a smaller genome than European native genotypes from which they are derived. This smaller genome size had phenotypic effects that increased the species' invasive potential, including a higher early growth rate, due to a negative relationship between genome size and rate of stem elongation. Based on inferred phylogeographical relationships of invasive and native populations, evolutionary models were consistent with a scenario of genome reduction by natural selection during the invasion process, rather than a scenario of stochastic change. CONCLUSIONS: Punctual reduction in genome size could cause rapid changes in key phenotypic traits that enhance invasive ability. Although the generality of genome size variation leading to phenotypic evolution and the specific genomic mechanisms involved are not known, change in genome size may constitute an important but previously under-appreciated mechanism of rapid evolutionary change that may promote evolutionary novelties over short time scales.

Invasiveness in plant communities with feedbacks.

The detrimental effects of invasive plant species on ecosystems are well documented. While much research has focused on discovering ecological influences associated with invasiveness, it remains unclear how these influences interact, causing some introduced exotic species to become invasive threats. Here we develop a framework that incorporates the influences of propagule pressure, frequency independent growth rates, feedback relationships, resource competition and spatial scale of interactions. Our results show that these ecological influences interact in complex ways, resulting in expected outcomes ranging from inability to establish, to naturalization, to conditional invasion dependent on quantity and spatial distribution of propagules, to unconditional takeover. We propose a way to predict the likelihood of these four possible outcomes, for a species recently introduced into a given target community. Such information could enable conservation biologists to craft strategies and target remediation efforts more efficiently and effectively in order to help maintain biodiversity in ecological communities.

Increased genetic variation and evolutionary potential drive the success of an invasive grass.

Despite the increasing biological and economic impacts of invasive species, little is known about the evolutionary mechanisms that favor geographic range expansion and evolution of invasiveness in introduced species. Here, we focus on the invasive wetland grass Phalaris arundinacea L. and document the evolutionary consequences that resulted from multiple and uncontrolled introductions into North America of genetic material native to different European regions. Continental-scale genetic variation occurring in reed canarygrass' European range has been reshuffled and recombined within North American introduced populations, giving rise to a number of novel genotypes. This process alleviated genetic bottlenecks throughout reed canarygrass' introduced range, including in peripheral populations, where depletion of genetic diversity is expected and is observed in the native range. Moreover, reed canarygrass had higher genetic diversity and heritable phenotypic variation in its invasive range relative to its native range. The resulting high evolutionary potential of invasive populations allowed for rapid selection of genotypes with higher vegetative colonization ability and phenotypic plasticity. Our results show that repeated introductions of a single species may inadvertently create harmful invaders with high adaptive potential. Such invasive species may be able to evolve in response to changing climate, allowing them to have increasing impact on native communities and ecosystems in the future. More generally, multiple immigration events may thus trigger future adaptation and geographic spread of a species population by preventing genetic bottlenecks and generating genetic novelties through recombination.

Extinction dynamics in experimental metapopulations.

Metapopulation theory provides a framework for understanding population persistence in fragmented landscapes and as such has been widely used in conservation biology to inform management of fragmented populations. However, classical metapopulation theory [Levins, R. (1970) Lect. Notes Math. 2, 75-107] ignores metapopulation structure and local population dynamics, both of which may affect extinction dynamics. Here, we investigate metapopulation dynamics in populations that are subject to different migration rates by using experimental metapopulations of the annual plant Cardamine pensylvanica. As predicted by classical metapopulation theory, connected populations persisted longer than did isolated populations, but the relationship between migration and persistence time was nonlinear. Extinction risk sharply increased as the distance between local populations increased above a threshold value that was consistent with stochastic simulations and calculation of metapopulation capacity [Hanski, I. & Ovaskainen, O. (2000) Nature 404, 755-758]. In addition, the most connected metapopulations did not have the highest persistence levels. Stochastic simulations indicated an increase in extinction risk with the highest migration rates. Moreover, calculation of population coherence [Earn, D. J. D., Levin, S. A. & Rohani, P. (2000) Science 290, 1360-1364], a metric that predicts synchronous cycles, indicated that continuous populations should cycle in phase, resulting in an increased extinction risk. Determining empirically the optimal migration level to improve survival chances will be challenging for any natural population. Migration rates that would not increase migration above the threshold value would be ineffectual, but migration rates that would homogenize local densities could increase the risk of coherent oscillations and enhance extinction risk.

A novel theory to explain species diversity in landscapes: positive frequency dependence and habitat suitability.

Theories to explain the diversity of species have required that individual species occupy unique niches and/or vary in their response to environmental factors. Positive interactions within a species, although common in communities, have not been thought to maintain species diversity because in non-spatial models the more abundant species always outcompetes the rarer species. Here, we show, using a stochastic spatial model, that positive intraspecific interactions such as those caused by positive frequency dependence and/or priority effects, can maintain species diversity if interactions between individuals are primarily local and the habitat contains areas that cannot be colonized by any species, such as boulders or other physical obstructions. When intraspecific interactions are primarily neutral, species diversity will eventually erode to a single species. When the landscape is homogeneous (i.e. does not contain areas that cannot be colonized by any species), the presence of strong intraspecific interactions will not maintain diversity.

Allee effect, spatial structure and species coexistence.

Both positive and negative interactions among species are common in communities. Until recently, attention has focused on negative interactions such as competition. However, the importance of positive interactions such as the Allee effect has recently been recognized. We construct a single-patch model that incorporates both an Allee effect and competition between two species. A species that experiences an Allee effect cannot establish in a patch which is already occupied by a competitor unless its density is over a critical value. This effect, when translated into a metapopulation, makes migrants of a species unable to colonize patches where another species has established. This interaction between the Allee effect and inter-specific competition creates and stabilizes spatial segregation of species. Therefore, under circumstances in which competition would preclude local coexistence, the presence of an Allee effect can allow coexistence at a metapopulation scale. Furthermore, we found that a species can resist displacement if stronger competitors experience an Allee effect.