scholarly journals Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly

2016 ◽  
Vol 113 (10) ◽  
pp. 2678-2683 ◽  
Author(s):  
Toby Fountain ◽  
Marko Nieminen ◽  
Jukka Sirén ◽  
Swee Chong Wong ◽  
Rainer Lehtonen ◽  
...  
Keyword(s):  
Habitat Fragmentation ◽  
Evolutionary Dynamics ◽  
Allele Frequencies ◽  
Candidate Snps ◽  
Fragmented Landscape ◽  
Outlier Loci ◽  
Evolutionary Response ◽  
Museum Samples ◽  
Glanville Fritillary Butterfly ◽  
Frequency Changes

Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

scholarly journals Evolution of a predator-induced, nonlinear reaction norm

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170859 ◽  
Author(s):  
Mauricio J. Carter ◽  
Martin I. Lind ◽  
Stuart R. Dennis ◽  
William Hentley ◽  
Andrew P. Beckerman
Keyword(s):  
Evolutionary Dynamics ◽  
Daphnia Pulex ◽  
Reaction Norm ◽  
Maximum Response ◽  
Selective Predation ◽  
Evolutionary Trajectory ◽  
Defensive Reaction ◽  
Selection Gradients ◽  
Hunting Strategies ◽  
Evolutionary Response

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the micro-evolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex .

scholarly journals Understanding the Evolutionary Games in NSCLC Microenvironment

2020 ◽  
Author(s):  
Ranjini Bhattacharya ◽  
Robert Vander Velde ◽  
Viktoriya Marusyk ◽  
Bina Desai ◽  
Artem Kaznatcheev ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Targeted Therapies ◽  
Evolutionary Dynamics ◽  
Fusion Gene ◽  
Evolutionary Game ◽  
Therapy Resistance ◽  
Resistance Mechanisms ◽  
Intrinsic Resistance ◽  
Frequency Changes

AbstractWhile initially highly successful, targeted therapies eventually fail as populations of tumor cells evolve mechanisms of resistance, leading to resumption of tumor growth. Historically, cell-intrinsic mutational changes have been the major focus of experimental and clinical studies to decipher origins of therapy resistance. While the importance of these mutational changes is undeniable, a growing body of evidence suggests that non-cell autonomous interactions between sub-populations of tumor cells, as well as with non-tumor cells within tumor microenvironment, might have a profound impact on both short term sensitivity of cancer cells to therapies, as well as on the evolutionary dynamics of emergent resistance. In contrast to well established tools to interrogate the functional impact of cell-intrinsic mutational changes, methodologies to understand non-cell autonomous interactions are largely lacking.Evolutionary Game Theory (EGT) is one of the main frameworks to understand the dynamics that drive frequency changes in interacting competing populations with different phenotypic strategies. However, despite a few notable exceptions, the use of EGT to understand evolutionary dynamics in the context of evolving tumors has been largely confined to theoretical studies. In order to apply EGT towards advancing our understanding of evolving tumor populations, we decided to focus on the context of the emergence of resistance to targeted therapies, directed against EML4-ALK fusion gene in lung cancers, as clinical responses to ALK inhibitors represent a poster child of limitations, posed by evolving resistance. To this end, we have examined competitive dynamics between differentially labelled therapy-naïve tumor cells, cells with cell-intrinsic resistance mechanisms, and cells with cell-extrinsic resistance, mediated by paracrine action of hepatocyte growth factor (HGF), within in vitro game assays in the presence or absence of front-line ALK inhibitor alectinib. We found that producers of HGF were the fittest in every pairwise game, while also supporting the proliferation of therapy-naïve cells. Both selective advantage of these producer cells and their impact on total population growth was a linearly increasing function of the initial frequency of producers until eventually reaching a plateau. Resistant cells did not significantly interact with the other two phenotypes. These results provide insights on reconciling selection driven emergence of subpopulations with cell non-cell autonomous resistance mechanisms, with lack of evidence of clonal dominance of these subpopulations. Further, our studies elucidate mechanisms for co-existence of multiple resistance strategies within evolving tumors. This manuscript serves as a technical report and will be followed up with a research paper in a different journal.

scholarly journals Fragmentation mediates thermal habitat choice in ciliate microcosms

2020 ◽  
Vol 287 (1919) ◽  
pp. 20192818
Author(s):  
Estelle Laurent ◽  
Nicolas Schtickzelle ◽  
Staffan Jacob
Keyword(s):  
Habitat Fragmentation ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Tetrahymena Thermophila ◽  
Habitat Choice ◽  
Emigration And Immigration ◽  
Dispersal Rate ◽  
Thermal Habitat ◽  
Twofold Increase ◽  
Dynamics Of Populations

Habitat fragmentation is expected to reduce dispersal movements among patches as a result of increased inter-patch distances. Furthermore, since habitat fragmentation is expected to raise the costs of moving among patches in the landscape, it should hamper the ability or tendency of organisms to perform informed dispersal decisions. Here, we used microcosms of the ciliate Tetrahymena thermophila to test experimentally whether habitat fragmentation, manipulated through the length of corridors connecting patches differing in temperature, affects habitat choice. We showed that a twofold increase of inter-patch distance can as expected hamper the ability of organisms to choose their habitat at immigration. Interestingly, it also increased their habitat choice at emigration, suggesting that organisms become choosier in their decision to either stay or leave their patch when obtaining information about neighbouring patches gets harder. This study points out that habitat fragmentation might affect not only dispersal rate but also the level of non-randomness of dispersal, with emigration and immigration decisions differently affected. These consequences of fragmentation might considerably modify ecological and evolutionary dynamics of populations facing environmental changes.

scholarly journals Mutation Rate Model Used in the DNA VIEW Program

2020 ◽  
Vol 10 (10) ◽  
pp. 3585 ◽  
Author(s):  
Tomasz Krajka
Keyword(s):  
Computer Simulation ◽  
Allele Frequency ◽  
Mutation Rate ◽  
Allele Frequencies ◽  
Rate Model ◽  
Dna Database ◽  
Mutation Model ◽  
Population Allele Frequency ◽  
Frequency Changes

The first problem considered in this paper is the problem of correctness of a mutation model used in the DNA VIEW program. To this end, we theoretically predict population allele frequency changes in time according to this and similar models (we determine the limit frequencies of alleles—they are uniformly distributed). Furthermore, we evaluate the speed of the above changes using computer simulation applied to our DNA database. Comparing uniformly distributed allele frequencies with these existing in the population (for example, using entropy), we conclude that this mutation model is not correct. The evolution does not follow this direction (direction of uniformly distributed frequencies). The second problem relates to the determination of the extent to which an incorrect mutation model can disturb DNA VIEW program results. We show that in typical computations (simple paternity testing without maternal mutation) this influence is negligible, but in the case of maternal mutation, this should be taken into account. Furthermore, we show that this model is inconsistent from a theoretical viewpoint. Equivalent methods result in different error levels.

Effects of habitat fragmentation on the genetic diversity and differentiation of Dendrolimus punctatus (Lepidoptera: Lasiocampidae) in Thousand Island Lake, China, based on mitochondrial COI gene sequences

2018 ◽  
Vol 109 (1) ◽  
pp. 62-71 ◽  
Author(s):  
K. Lv ◽  
J.-R. Wang ◽  
T.-Q. Li ◽  
J. Zhou ◽  
J.-Q. Gu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Geographic Distance ◽  
Haplotype Diversity ◽  
Shape Index ◽  
Coi Gene ◽  
Fragmented Landscape ◽  
Dispersal Capacity ◽  
Island Populations ◽  
High Dispersal

AbstractThousand Island Lake (TIL) is a typical fragmented landscape and an ideal model to study ecological effects of fragmentation. Partial fragments of the mitochondrial cytochrome oxidase subunit I gene of 23 island populations of Dendrolimus punctatus in TIL were sequenced, 141 haplotypes being identified. The number of haplotypes increased significantly with the increase in island area and shape index, whereas no significant correlation was detected between three island attributes (area, shape and isolation) and haplotype diversity. However, the correlation with number of haplotypes was no longer significant when the ‘outlier’ island JSD (the largest island) was not included. Additionally, we found no significant relationship between geographic distance and genetic distance. Geographic isolation did not obstruct the gene flow among D. punctatus populations, which might be because of the high dispersal capacity of this pine moth. Fragmentation resulted in the conversion of large and continuous habitats into isolated, small and insular patches, which was the primary effect on the genetic diversity of D. punctatus in TIL. The conclusion to emphasize from our research is that habitat fragmentation reduced the biological genetic diversity to some extent, further demonstrating the importance of habitat continuity in biodiversity protection.

scholarly journals Eco-evolutionary dynamics: disentangling phenotypic, environmental and population fluctuations

2009 ◽  
Vol 364 (1523) ◽  
pp. 1491-1498 ◽  
Author(s):  
Thomas H.G. Ezard ◽  
Steeve D. Côté ◽  
Fanie Pelletier
Keyword(s):  
Population Growth ◽  
Evolutionary Dynamics ◽  
Environmental Variability ◽  
Phenotypic Variability ◽  
Ecological Change ◽  
Population Fluctuations ◽  
Rapid Responses ◽  
Evolutionary Response ◽  
Anthropogenic Threats ◽  
The Impact

Decomposing variation in population growth into contributions from both ecological and evolutionary processes is of fundamental concern, particularly in a world characterized by rapid responses to anthropogenic threats. Although the impact of ecological change on evolutionary response has long been acknowledged, the converse has predominantly been neglected, especially empirically. By applying a recently published conceptual framework, we assess and contrast the relative importance of phenotypic and environmental variability on annual population growth in five ungulate populations. In four of the five populations, the contribution of phenotypic variability was greater than the contribution of environmental variability, although not significantly so. The similarity in the contributions of environment and phenotype suggests that neither is worthy of neglect. Population growth is a consequence of multiple processes, which strengthens arguments advocating integrated approaches to assess how populations respond to their environments.

scholarly journals Fitness estimation for viral variants in the context of cellular coinfection

2021 ◽  
Author(s):  
Huisheng Zhu ◽  
Brent E Allman ◽  
Katia Koelle
Keyword(s):  
Evolutionary Dynamics ◽  
Sequence Data ◽  
Population Level ◽  
Viral Fitness ◽  
Fitness Effects ◽  
Fitness Advantage ◽  
Viral Adaptation ◽  
Zoonotic Viruses ◽  
Frequency Changes

AbstractAnimal models are frequently used to characterize the within-host dynamics of emerging zoonotic viruses. More recent studies have also deep-sequenced longitudinal viral samples originating from experimental challenges to gain a better understanding of how these viruses may evolve in vivo and between transmission events. These studies have often identified nucleotide variants that can replicate more efficiently within hosts and also transmit more effectively between hosts. Quantifying the degree to which a mutation impacts viral fitness within a host can improve identification of variants that are of particular epidemiological concern and our ability to anticipate viral adaptation at the population level. While methods have been developed to quantify the fitness effects of mutations using observed changes in allele frequencies over the course of a host’s infection, none of the existing methods account for the possibility of cellular coinfection. Here, we develop mathematical models to project variant allele frequency changes in the context of cellular coinfection and, further, integrate these models with statistical inference approaches to demonstrate how variant fitness can be estimated alongside cellular multiplicity of infection. We apply our approaches to empirical longitudinally-sampled H5N1 sequence data from ferrets. Our results indicate that previous studies may have significantly underestimated the within-host fitness advantage of viral variants. These findings underscore the importance of considering the process of cellular coinfection when studying within-host viral evolutionary dynamics.

scholarly journals Modelling single nucleotide effects in phosphoglucose isomerase on dispersal in the Glanville fritillary butterfly: coupling of ecological and evolutionary dynamics

2009 ◽  
Vol 364 (1523) ◽  
pp. 1519-1532 ◽  
Author(s):  
Chaozhi Zheng ◽  
Otso Ovaskainen ◽  
Ilkka Hanski
Keyword(s):  
Evolutionary Dynamics ◽  
Extinction Risk ◽  
Network Size ◽  
Phosphoglucose Isomerase ◽  
Landscape Matrix ◽  
Isolated Populations ◽  
Single Nucleotide ◽  
Spatially Correlated ◽  
Demographic Dynamics ◽  
Glanville Fritillary Butterfly

Dispersal comprises a complex life-history syndrome that influences the demographic dynamics of especially those species that live in fragmented landscapes, the structure of which may in turn be expected to impose selection on dispersal. We have constructed an individual-based evolutionary sexual model of dispersal for species occurring as metapopulations in habitat patch networks. The model assumes correlated random walk dispersal with edge-mediated behaviour (habitat selection) and spatially correlated stochastic local dynamics. The model is parametrized with extensive data for the Glanville fritillary butterfly. Based on empirical results for a single nucleotide polymorphism (SNP) in the phosphoglucose isomerase ( Pgi ) gene, we assume that dispersal rate in the landscape matrix, fecundity and survival are affected by a locus with two alleles, A and C, individuals with the C allele being more mobile. The model was successfully tested with two independent empirical datasets on spatial variation in Pgi allele frequency. First, at the level of local populations, the frequency of the C allele is the highest in newly established isolated populations and the lowest in old isolated populations. Second, at the level of sub-networks with dissimilar numbers and connectivities of patches, the frequency of C increases with decreasing network size and hence with decreasing average metapopulation size. The frequency of C is the highest in landscapes where local extinction risk is high and where there are abundant opportunities to establish new populations. Our results indicate that the strength of the coupling of the ecological and evolutionary dynamics depends on the spatial scale and is asymmetric, demographic dynamics having a greater immediate impact on genetic dynamics than vice versa.

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