Evolutionary Population Dynamics Research Articles

Biogeography of Korea\u2019s top predator, the yellow-throated Marten: evolutionary history and population dynamics

BackgroundPeninsulas often harvest high genetic diversity through repeated southward migrations of species during glacial maxima. Studies addressing within-species evolutionary responses to climate fluctuations in northeast Asia are limited compared to other regions of the world, and more so in the Korean Peninsula. In this study, we conducted the first population-level study of the yellow-throated marten, Martes flavigula, from the Korean Peninsula, Russian, Taiwanese and Chinese localities in a biogeographic framework using mitochondrial (cyt-b, nd2, cr) and nuclear gene sequencing (ghr).ResultsBayesian analyses revealed a rather young population, with a split from the most recent common ancestor at around 125 kya. Martes flavigula likely colonized the Korean Peninsula from Mainland China through the Yellow Sea twice, ca. 60 kya and 20 kya. Korean martens diversified during the Late Pleistocene with at least two dispersal events out of Korea, towards the southwest to Taiwan (ca. 80 kya) and towards the North into Russia and eastern China; most likely after the Last Glacial Maxima (ca. 20 kya). We argue that the lack of population structure and mixed populations is possibly a consequence of the high dispersal capability of the species. The Bayesian skyline plot revealed a population decline within the last 5000 years, suggesting potential negative biotic and anthropogenic effects in the area. We find that local populations are not genetically differentiated, therefore no perceptible population structure within Korea was found.ConclusionsThe topography and geography of the Korean Peninsula has played a pivotal role in its colonization. Connections between the Korean Peninsula and the Mainland through sea-level drops of the Yellow Sea at times of glacial maxima and the high dispersal capability of M. flavigula adds to the lack of geographical structure in this species and the paraphyly of Korean lineages.

BIFFOA: A Novel Binary Improved Fruit Fly Algorithm for Feature Selection

Feature selection is an important method to reduce the number of attributes of high-dimensional data and an essential preprocess work in classification. It eliminates irrelevant, redundant, and noisy features improves the performance of the model and reduces the computational burden. Fruit fly optimization algorithm is a new algorithm proposed in recent years, which imitates the foraging behavior of fruit fly. To the best of our knowledge, it has not been systematically applied to feature selection. This paper uses the fruit fly optimization algorithm as a search strategy and designs a wrapper-based feature selection method, named binary improved fruit fly optimization algorithm (BIFFOA). Besides, four different strategies based on evolutionary population dynamics (EPD) and new mutation operators are employed to enhance the BIFFOA. The extensive experiments on 25 datasets (see Table 1) show that the performance of the BIFFOA is better than several state-of-the-art algorithms.

Difference equations as models of evolutionary population dynamics

ABSTRACTWe describe the evolutionary game theoretic methodology for extending a difference equation population dynamic model in a way so as to account for the Darwinian evolution of model coefficients. We give a general theorem that describes the familiar transcritical bifurcation that occurs in non-evolutionary models when theextinction equilibrium destabilizes. This bifurcation results in survival (positive) equilibria whose stability depends on the direction of bifurcation. We give several applications based on evolutionary versions of some classic equations, such as the discrete logistic (Beverton–Holt) and Ricker equations. In addition to illustrating our theorems, these examples also illustrate other biological phenomena, such as strong Allee effects, time-dependent adaptive landscapes, and evolutionary stable strategies.

Native American Genomic Diversity through Ancient DNA

Ancient DNA is a powerful tool to understand the evolutionary dynamics of both current and ancestral populations. Posth etal. use ancient DNA to elucidate important questions surrounding the peopling of Central and South America, giving us greater insights into the ancestry of genetically understudied populations.

Evolution of populations expanding on curved surfaces(a)(a)Contribution to the Focus Issue Evolutionary Modeling and Experimental Evolution edited by José Cuesta, Joachim Krug and Susanna Manrubia.

The expansion of a population into new habitat is a transient process that leaves its footprints in the genetic composition of the expanding population. How the structure of the environment shapes the population front and the evolutionary dynamics during such a range expansion is little understood. Here, we investigate the evolutionary dynamics of populations consisting of many selectively neutral genotypes expanding on curved surfaces. Using a combination of individual-based off-lattice simulations, geometrical arguments, and lattice-based stepping-stone simulations, we characterise the effect of individual bumps on an otherwise flat surface. Compared to the case of a range expansion on a flat surface, we observe a transient relative increase, followed by a decrease, in neutral genetic diversity at the population front. In addition, we find that individuals at the sides of the bump have a dramatically increased expected number of descendants, while their neighbours closer to the bump's centre are far less lucky. Both observations can be explained using an analytical description of straight paths (geodesics) on the curved surface. Complementing previous studies of heterogeneous flat environments, the findings here build our understanding of how complex environments shape the evolutionary dynamics of expanding populations.

Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution.

RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.

Statistical theory of phenotype abundance distributions: A test through exact enumeration of genotype spaces(a)(a)Contribution to the Focus Issue Evolutionary Modeling and Experimental Evolution edited by José Cuesta, Joachim Krug and Susanna Manrubia.

The evolutionary dynamics of molecular populations are strongly dependent on the structure of genotype spaces. The map between genotype and phenotype determines how easily genotype spaces can be navigated and the accessibility of evolutionary innovations. In particular, the size of neutral networks corresponding to specific phenotypes and its statistical counterpart, the distribution of phenotype abundance, have been studied through multiple computationally tractable genotype-phenotype maps. In this work, we test a theory that predicts the abundance of a phenotype and the corresponding asymptotic distribution (given the compositional variability of its genotypes) through the exact enumeration of several GP maps. Our theory predicts with high accuracy phenotype abundance, and our results show that, in navigable genotype spaces —characterised by the presence of large neutral networks— phenotype abundance converges to a log-normal distribution.

On the networked architecture of genotype spaces and its critical effects on molecular evolution.

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at the macroevolutionary, ecological and molecular level. Actually, when the complex architecture of genotype spaces is taken into account, the evolutionary dynamics of molecular populations becomes intrinsically non-uniform, sharing deep qualitative and quantitative similarities with slowly driven physical systems: nonlinear responses analogous to critical transitions, sudden state changes or hysteresis, among others. Furthermore, the phenotypic plasticity inherent to genotypes transforms classical fitness landscapes into multiscapes where adaptation in response to an environmental change may be very fast. The quantitative nature of adaptive molecular processes is deeply dependent on a network-of-networks multilayered structure of the map from genotype to function that we begin to unveil.

Enhanced multi-objective particle swarm optimisation for estimating hand postures

Multi-objective problems with conflicting objectives cannot be effectively solved by aggregation-based methods. The answer to such problems is a Pareto optimal solution set. Due to the difficulty of solving multi-objective problems using multi-objective algorithms and the lack of enough expertise, researchers in different fields tend to aggregative objectives and use single-objective algorithms. This work is a seminal attempt to propose the use of multi-objective algorithms in the field of hand posture estimation. Hand posture estimation is a key step in hand gesture recognition, which is a part of an overall attempt to make human-computer interaction more like human face-to-face communication. Hand posture estimation is first formulated as a bi-objective problem. A modified version of Multi-Objective Particle Swarm Optimisation (MOPSO) is then proposed to approximate the Pareto optimal font of 50 different postures. The main motivation of integrating a new operator (called Evolutionary Population Dynamics — EPD) in MOPSO is due to the nature of hand posture estimation problems in which parameters should not be tuned in a same manner since they show varied impacts on the objectives. EPD allows randomising different parameters in a solution and provides different exploratory behaviours for the parameters of an optimisation algorithm rather than each individual solution. The MOPSO algorithm is equipped with a mechanism to randomly re-initialise poor particles around the optimal solutions in the archive. The improved MOPSO is tested on ZDT and CEC2009 test functions and compared with the standard MOPSO, NSGA-II, and MOEA/D. The results show that the proposed MOPSO (MOPSO+EPD) significantly outperforms MOPSO on the majority of test functions in terms of both convergence and coverage. MOPSO+EPD also approximates well-distributed Pareto optimal fronts for most of the postures considered in this work. The post analysis of the results is conducted to understand the relationship between the parameters and objectives of this problem (design principals) for the first time in the literature as well.

Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region

BackgroundThe ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa.MethodsSequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution.ResultsPopulation genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa.ConclusionsTwo sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes.

New versions of evolutionary models with lethal mutations

In this paper, the impact of lethal mutations on evolutionary dynamics of asexual populations is analyzed. We suggest distinguishing different definitions of lethality, which lead to different mathematical formalizations of the microscopic model. Most of the studies focus on polyphasic lethality, meaning that individuals carrying lethal mutations have no offspring but consume common resources. In an alternative problem setting, monophasic lethal mutants die without giving offspring on the first stage of development. In the third case, semi-lethal mutations are considered when the lethal mutants survive with some probability. We suggest and investigate mathematical models for these cases, deriving the evolutionary characteristics of the steady state. We found that the peak sequence probability drastically depends on the version of lethality. The results obtained here can be used to solve the error threshold paradox at the origin of life.

Neutral Theory in Cancer Cell Population Genetics.

Kimura's neutral theory provides the whole theoretical basis of the behavior of mutations in a Wright-Fisher population. We here discuss how it can be applied to a cancer cell population, in which there is an increasing interest in genetic variation within a tumor. We explain a couple of fundamental differences between cancer cell populations and asexual organismal populations. Once these differences are taken into account, a number of powerful theoretical tools developed for a Wright-Fisher population could be readily contribute to our deeper understanding of the evolutionary dynamics of cancer cell population.

Evolutionary Dynamics of Plant Populations Studied by Population Genomics: Genomics of Adaptation

Evolutionary Dynamics of Plant Populations Studied by Population Genomics: Genomics of Adaptation

Effects of spatial aggregation of nests on population recruitment: the case of a small population of Atlantic salmon

AbstractSpatial aggregation within a population is a widespread phenomenon which may both exacerbate local competition and the stochastic effect of local environmental perturbations. In particular, the spatial aggregation of nests may strongly affect recruitment and hence population dynamics. Although the negative effect of local density on local recruitment has often been theoretically extended to population dynamics, very few studies have demonstrated the effect of local aggregation on the whole population recruitment. Using a long‐term survey of a small Atlantic salmon population, we tested the effect of spatial aggregation on the whole population recruitment and whether accounting for population stock is important or not when explaining the population recruitment. We found that accounting for population stock is necessary and that spatial aggregation of nests improved estimates of population recruitment. The spatial aggregation of nests did not impact the average population recruitment; however, a stronger aggregation diminished the variability of population recruitment. Our findings suggest that the aggregation of nests among some breeding areas does not necessarily impair the whole population recruitment and significantly reduces the stochasticity of the recruitment. In addition, the aggregation of nests seems to be the result of an ideal distribution of females, selecting the best‐breeding sites. Our results also indicate that females select breeding sites on environmental risk to spawn within the safest sites. This study warns against the extrapolation of local density dependence observations to the population level, and advocates for investigating the effect of aggregation on the demographic and evolutionary population dynamics, a clear contribution of aggregation on population dynamic processes being found in the Nivelle population.

Role of colonization history and species‐specific traits on contemporary genetic variation of two salamander species in a Holocene island‐mainland system

AbstractAimInvestigate the role of colonization history and life history traits on contemporary patterns of genetic variation in two salamander species in a Holocene island‐mainland system.LocationRías Baixas, north‐western Spain.MethodsWe analysed mitochondrial and species‐specific nuclear markers (eight microsatellite markers) in 16 populations of Salamandra salamandra and Lissotriton boscai. Contemporary gene flow patterns between mainland and island populations were evaluated by migration analyses, whereas approximate Bayesian computation (ABC) was used to assess colonization history of insular populations of both species.ResultsLand bridge populations of both species exhibited reduced genetic diversity and increased genetic structure compared to mainland populations. ABC analysis showed that insular populations of both species were established by vicariance rather than by colonization via dispersal. We did not find evidence for contemporary gene flow, though the L. boscai insular population of Sálvora showed genetic admixture with mainland populations.Main conclusionsThis study supports the role of genetic drift in driving contemporary genetic variation of small and isolated populations. Other interplaying factors (e.g. island size, bathymetry) seemed to influence genetic variation, highlighting the importance of integrative studies to better understand the evolutionary dynamics of land bridge populations of amphibians.

Demographic variability and heterogeneity among individuals within and among clonal bacteria strains

Identifying what drives individual heterogeneity has been of long interest to ecologists, evolutionary biologists and biodemographers, because only such identification provides deeper understanding of ecological and evolutionary population dynamics. In natural populations one is challenged to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting‐edge microfluidic techniques, provides high control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction is dominating at about 90–92%, over the 8–10% genetically (adaptive fixed) driven differences. The genetic differences among the clonal strains still lead to substantial variability in population growth rates (fitness), but, as well understood based on foundational work in population genetics, the within strain neutral variability slows adaptive change, by enhancing genetic drift, and lowering overall population growth. We also revealed a surprising diversity in senescence patterns among the clonal strains, which indicates diverse underlying cell‐intrinsic processes that shape these demographic patterns. Such diversity is surprising since all cells belong to the same bacteria species, E. coli, and still exhibit patterns such as classical senescence, non‐senescence, or negative senescence. We end by discussing whether similar levels of non‐genetic variability might be detected in other systems and close by stating the open questions how such heterogeneity is maintained, how it has evolved, and whether it is adaptive.

Limited pollen dispersal, small genetic neighborhoods, and biparental inbreeding in Vallisneria americana.

Pollen dispersal is a key process that influences ecological and evolutionary dynamics of plant populations by facilitating sexual reproduction and gene flow. Habitat loss and fragmentation have the potential to reduce pollen dispersal within and among habitat patches. We assessed aquatic pollen dispersal and mating system characteristics in Vallisneria americana-a water-pollinated plant with a distribution that has been reduced from historic levels. We examined pollen neighborhood size, biparental inbreeding, and pollen dispersal, based on seed paternity using the indirect paternity method KinDist, from samples of 18-39 mothers and 14-20 progeny per mother from three sites across 2 years. On average, fruits contained seeds sired by seven fathers. We found significant biparental inbreeding and limited pollen dispersal distances (0.8-4.34 m). However, in a number of cases, correlated paternity did not decline with distance, and dispersal could not be reliably estimated. Frequent pollen dispersal is not expected among patches, and even within patches, gene flow via pollen will be limited. Limited pollen dispersal establishes genetic neighborhoods, which, unless overcome by seed and propagule dispersal, will lead to genetic differentiation even in a continuous population. Unless loss and fragmentation drive populations to extreme sex bias, local pollen dispersal is likely to be unaffected by habitat loss and fragmentation per se because the spatial scale of patch isolation already exceeds pollen dispersal distances. Therefore, managing specifically for pollen connectivity is only relevant over very short distances.

Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts.

Foot-and-mouth disease (FMD) is a severe infection caused by a picornavirus that affects livestock and wildlife. Persistence in ruminants is a well-documented feature of Foot-and-mouth disease virus (FMDV) pathogenesis and a major concern for disease control. Persistently infected animals harbor virus for extended periods, providing a unique opportunity to study within-host virus evolution. This study investigated the genetic dynamics of FMDV during persistent infections of naturally infected Asian buffalo. Using next-generation sequencing (NGS) we obtained 21 near complete FMDV genome sequences from 12 sub-clinically infected buffalo over a period of one year. Four animals yielded only one virus isolate and one yielded two isolates of different serotype suggesting a serial infection. Seven persistently infected animals yielded more than one virus of the same serotype showing a long-term intra-host viral genetic divergence at the consensus level of less than 2.5%. Quasi-species analysis showed few nucleotide variants and non-synonymous substitutions of progeny virus despite intra-host persistence of up to 152 days. Phylogenetic analyses of serotype Asia-1 VP1 sequences clustered all viruses from persistent animals with Group VII viruses circulating in Pakistan in 2011, but distinct from those circulating on 2008–2009. Furthermore, signature amino acid (aa) substitutions were found in the antigenically relevant VP1 of persistent viruses compared with viruses from 2008–2009. Intra-host purifying selective pressure was observed, with few codons in structural proteins undergoing positive selection. However, FMD persistent viruses did not show a clear pattern of antigenic selection. Our findings provide insight into the evolutionary dynamics of FMDV populations within naturally occurring subclinical and persistent infections that may have implications to vaccination strategies in the region.

Predator arrival elicits differential dispersal, change in age structure and reproductive performance in a prey population

Predators are an important ecological and evolutionary force shaping prey population dynamics. Ecologists have extensively assessed the lethal effects of invasive predators on prey populations. However, the role of non-lethal effects, such as physiological stress or behavioural responses like dispersal, has been comparatively overlooked and their potential population effects remain obscure. Over the last 23 years, we developed a mark-recapture program for the Audouin’s gull and an intensive carnivore monitoring program to assess how the appearance and invasion of the study site by carnivores affects population dynamics. We evaluate changes in turnover of discrete breeding patches within the colony, age structure and breeding performance. Once carnivores entered the colony, the number of occupied patches increased, indicating a higher patch turnover. Breeders responded by moving to areas less accessible to carnivores. More importantly, the presence of carnivores caused differential (and density-independent) breeding dispersal: experienced, better-performing breeders were more likely to leave the colony than younger breeders. This differential dispersal modified the age structure and reduced the reproductive performance of the population. Our results confirm the importance experience in the study of populations. The role of differential dispersal for animal population dynamics might be more important than previously thought, especially under scenarios of global change.

Disentangling biological variables affecting population structure and genetic connectivity

Event Abstract Back to Event Disentangling biological variables affecting population structure and genetic connectivity Sara M. Francisco1*, Ana M. Pereira1 and Joana I. Robalo1 1 Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, MARE—Marine and Environmental Sciences Centre, Portugal Evaluating and understanding the evolutionary dynamics of divergent populations is of paramount importance for both fisheries management and conservation strategies. Nevertheless, direct measurement of marine organisms’ dispersal capabilities can be highly challenging at broad spatial scales. Despite the traditional use of genetic approaches to quantify demographic connectivity, the difficulty to distinguish contemporary from historical connectivity remains. In this study, we aim to disentangle the various biological factors affecting population structure in marine fishes from the Northeastern Atlantic. This work included most of the phylogeography studies available in scientific search engines, encompassing a wide geographical area and using both genetic and genomic data. We did a meta-analysis using exploratory factorial followed by several regression analyses to reveal potential emerging patterns. The fixation index (FST) obtained in the literature was compared against several independent biogeographical, ecological and life-history variables. Despite the lack of available data for several parameters, our results refute general expectations, conventional wisdom and several papers, that PLD and early life-history traits are good predictors of population structure in marine organisms. In fact, the Type of Genetic Marker (mitochondrial, nuclear, microsatellite) and Adult Ability to Dispersal (weak, good or strong) were found to be determinant for significant FST and population structure. These results point to the need of future intercomparable studies with larger species numbers and including marine organisms with distinct life-history traits, which would significantly enrich the present approach and have a huge potential for marine protected areas design and management. Keywords: population structure, Genetic connectivity, fish, Northeastern Atlantic, Meta-analysis Conference: IMMR'18 | International Meeting on Marine Research 2018, Peniche, Portugal, 5 Jul - 6 Jul, 2018. Presentation Type: Poster Presentation Topic: Biodiversity, Conservation and Coastal Management Citation: Francisco SM, Pereira AM and Robalo JI (2019). Disentangling biological variables affecting population structure and genetic connectivity. Front. Mar. Sci. Conference Abstract: IMMR'18 | International Meeting on Marine Research 2018. doi: 10.3389/conf.FMARS.2018.06.00139 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 19 Apr 2018; Published Online: 07 Jan 2019. * Correspondence: Dr. Sara M Francisco, Instituto Universitário de Ciências Psicológicas, Sociais e da Vida, MARE—Marine and Environmental Sciences Centre, Lisbon, , 1149-041, Portugal, sara_francisco@ispa.pt Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Sara M Francisco Ana M Pereira Joana I Robalo Google Sara M Francisco Ana M Pereira Joana I Robalo Google Scholar Sara M Francisco Ana M Pereira Joana I Robalo PubMed Sara M Francisco Ana M Pereira Joana I Robalo Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.