scholarly journals Gillespie eco‐evolutionary models ( GEM s) reveal the role of heritable trait variation in eco‐evolutionary dynamics

2016 ◽  
Vol 6 (4) ◽  
pp. 935-945 ◽  
Author(s):  
John P. DeLong ◽  
Jean P. Gibert
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Models ◽  
Trait Variation ◽  
Heritable Trait

scholarly journals Predator coevolution and prey trait variability determine species coexistence

2019 ◽  
Vol 286 (1902) ◽  
pp. 20190245 ◽  
Author(s):  
Thomas Scheuerl ◽  
Johannes Cairns ◽  
Lutz Becks ◽  
Teppo Hiltunen
Keyword(s):  
Evolutionary Dynamics ◽  
Biological Diversity ◽  
Species Coexistence ◽  
Ecological Interactions ◽  
Trait Variation ◽  
Ecological Processes ◽  
History Of ◽  
Evolutionary Trajectories ◽  
Ecological Mechanisms

Predation is one of the key ecological mechanisms allowing species coexistence and influencing biological diversity. However, ecological processes are subject to contemporary evolutionary change, and the degree to which predation affects diversity ultimately depends on the interplay between evolution and ecology. Furthermore, ecological interactions that influence species coexistence can be altered by reciprocal coevolution especially in the case of antagonistic interactions such as predation or parasitism. Here we used an experimental evolution approach to test for the role of initial trait variation in the prey population and coevolutionary history of the predator in the ecological dynamics of a two-species bacterial community predated by a ciliate. We found that initial trait variation both at the bacterial and ciliate level enhanced species coexistence, and that subsequent trait evolutionary trajectories depended on the initial genetic diversity present in the population. Our findings provide further support to the notion that the ecology-centric view of diversity maintenance must be reinvestigated in light of recent findings in the field of eco-evolutionary dynamics.

scholarly journals Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guillermo Velo-Antón ◽  
André Lourenço ◽  
Pedro Galán ◽  
Alfredo Nicieza ◽  
Pedro Tarroso
Keyword(s):  
Contact Zone ◽  
Environmental Heterogeneity ◽  
Evolutionary Dynamics ◽  
Morphological Differentiation ◽  
Phenotypic Traits ◽  
Hybrid Zones ◽  
Landscape Resistance ◽  
Phenotypic Differentiation ◽  
Contact Zones

AbstractExplicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.

scholarly journals Loci, genes, and gene networks associated with life history variation in a model ecological organism,Daphnia pulex(complex)

2018 ◽  
Author(s):  
Jacob W. Malcom ◽  
Thomas E. Juenger ◽  
Mathew A. Leibold
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Life History ◽  
Molecular Basis ◽  
Life History Traits ◽  
Evolutionary Dynamics ◽  
Daphnia Pulex ◽  
Life History Trait ◽  
Life History Variation ◽  
Trait Variation

ABSTRACTBackgroundIdentifying the molecular basis of heritable variation provides insight into the underlying mechanisms generating phenotypic variation and the evolutionary history of organismal traits. Life history trait variation is of central importance to ecological and evolutionary dynamics, and contemporary genomic tools permit studies of the basis of this variation in non-genetic model organisms. We used high density genotyping, RNA-Seq gene expression assays, and detailed phenotyping of fourteen ecologically important life history traits in a wild-caught panel of 32Daphnia pulexclones to explore the molecular basis of trait variation in a model ecological species.ResultsWe found extensive phenotypic and a range of heritable genetic variation (~0 < H2< 0.44) in the panel, and accordingly identify 75-261 genes—organized in 3-6 coexpression modules—associated with genetic variation in each trait. The trait-related coexpression modules possess well-supported promoter motifs, and in conjunction with marker variation at trans- loci, suggest a relatively small number of important expression regulators. We further identify a candidate genetic network with SNPs in eight known transcriptional regulators, and dozens of differentially expressed genes, associated with life history variation. The gene-trait associations include numerous un-annotated genes, but also support several a priori hypotheses, including an ecdysone-induced protein and several Gene Ontology pathways.ConclusionThe genetic and gene expression architecture ofDaphnialife history traits is complex, and our results provide numerous candidate loci, genes, and coexpression modules to be tested as the molecular mechanisms that underlieDaphniaeco-evolutionary dynamics.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

scholarly journals Effects of fragmentation on plant adaptation to urban environments

2017 ◽  
Vol 372 (1712) ◽  
pp. 20160038 ◽  
Author(s):  
Jonathan Dubois ◽  
Pierre-Olivier Cheptou
Keyword(s):  
Reproductive Traits ◽  
Urban Ecosystems ◽  
Terrestrial Ecosystems ◽  
Plant Size ◽  
Urban Environments ◽  
Trait Variation ◽  
Fragmented Habitats ◽  
Dispersal Traits ◽  
Neutral Markers

Urban ecosystems are relatively recent and heavily human-altered terrestrial ecosystems with a surprisingly high diversity of animals, plants and other organisms. Urban habitats are also strongly fragmented and subject to higher temperatures, providing a compelling model for studying adaptation to global change. Crepis sancta (Asteraceae), an annual Mediterranean wasteland weed, occupies fragmented urban environments as well as certain unfragmented landscapes in southern France. We tested for shifts in dispersal, reproductive traits and size across a rural–urban gradient to learn whether and how selection may be driving changes in life history in urban and fragmented habitats. We specifically compared the structure of quantitative genetic variation and of neutral markers (microsatellites) between urban and rural and between fragmented and unfragmented habitats. We showed that fragmentation provides a better descriptor of trait variation than urbanization per se for dispersal traits. Fragmentation also affected reproductive traits and plant size though one rural population did conform to this scheme. Our study shows the role of fragmentation for dispersal traits shift in urban environments and a more complex pattern for other traits. We discuss the role of pollinator scarcity and an inhospitable matrix as drivers of adaptation. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’.

The role of biotic interactions in invasion ecology: theories and hypotheses.

2020 ◽  
pp. 26-44
Author(s):  
Cang Hui ◽  
◽  
Pietro Landi ◽  
Guillaume Latombe ◽  
◽  
...  
Keyword(s):  
Native Species ◽  
Evolutionary Dynamics ◽  
Biotic Interactions ◽  
Evolutionary Games ◽  
Invasion Ecology ◽  
Ecological Communities ◽  
Dynamic Interactions ◽  
Ecological Fitting ◽  
And Function

Changes in biotic interactions in the native and invaded range can enable a non-native species to establish and spread in novel environments. Invasive non-native species can in turn generate impacts in recipient systems partly through the changes they impose on biotic interactions; these interactions can lead to altered ecosystem processes in the recipient systems. This chapter reviews models, theories and hypotheses on how invasion performance and impact of introduced species in recipient ecosystems can be conjectured according to biotic interactions between native and non-native species. It starts by exploring the nature of biotic interactions as ensembles of ecological and evolutionary games between individuals of both the same and different groups. This allows us to categorize biotic interactions as direct and indirect (i.e. those involving more than two species) that emerge from both coevolution and ecological fitting during community assembly and invasion. We then introduce conceptual models that can reveal the ecological and evolutionary dynamics between interacting non-native and resident species in ecological networks and communities. Moving from such theoretical grounding, we review 20 hypotheses that have been proposed in invasion ecology to explain the invasion performance of a single non-native species, and seven hypotheses relating to the creation and function of assemblages of non-native species within recipient ecosystems. We argue that, although biotic interactions are ubiquitous and quintessential to the assessment of invasion performance, they are nonetheless difficult to detect and measure due to strength dependency on sampling scales and population densities, as well as the non-equilibrium transient dynamics of ecological communities and networks. We therefore call for coordinated efforts in invasion science and beyond, to devise and review approaches that can rapidly map out the entire web of dynamic interactions in a recipient ecosystem.

scholarly journals The role of multilevel selection in host microbiome evolution

2019 ◽  
Vol 116 (41) ◽  
pp. 20591-20597 ◽  
Author(s):  
Simon van Vliet ◽  
Michael Doebeli
Keyword(s):  
Generation Time ◽  
Evolutionary Dynamics ◽  
Horizontal Transmission ◽  
Multilevel Selection ◽  
Microbiome Composition ◽  
Active Debate ◽  
Multilevel Selection Theory ◽  
Verbal Arguments ◽  
Host Generation

Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.

scholarly journals Transcriptional Mutagenesis Prevents Ribosomal DNA Deterioration: The Role of Duplications and Deletions

2019 ◽  
Vol 11 (11) ◽  
pp. 3207-3217
Author(s):  
Enrico Sandro Colizzi ◽  
Paulien Hogeweg
Keyword(s):  
Genome Stability ◽  
Evolutionary Dynamics ◽  
Point Mutations ◽  
Gene Duplications ◽  
Genetic Operators ◽  
Theory Of Evolution ◽  
Long Term Stability ◽  
Number Variation

Abstract Clashes between transcription and replication complexes can cause point mutations and chromosome rearrangements on heavily transcribed genes. In eukaryotic ribosomal RNA genes, the system that prevents transcription–replication conflicts also causes frequent copy number variation. Such fast mutational dynamics do not alter growth rates in yeast and are thus selectively near neutral. It was recently found that yeast regulates these mutations by means of a signaling cascade that depends on the availability of nutrients. Here, we investigate the long-term evolutionary effect of the mutational dynamics observed in yeast. We developed an in silico model of single-cell organisms whose genomes mutate more frequently when transcriptional load is larger. We show that mutations induced by high transcriptional load are beneficial when biased toward gene duplications and deletions: they decrease mutational load even though they increase the overall mutation rates. In contrast, genome stability is compromised when mutations are not biased toward gene duplications and deletions, even when mutations occur much less frequently. Taken together, our results show that the mutational dynamics observed in yeast are beneficial for the long-term stability of the genome and pave the way for a theory of evolution where genetic operators are themselves cause and outcome of the evolutionary dynamics.

scholarly journals EVOLUTIONARY DYNAMICS OF A SEXUAL ORNAMENT IN THE HOUSE SPARROW (PASSER DOMESTICUS): THE ROLE OF INDIRECT SELECTION WITHIN AND BETWEEN SEXES

Evolution ◽  
2008 ◽  
Vol 62 (6) ◽  
pp. 1275-1293 ◽  
Author(s):  
Henrik Jensen ◽  
Ingelin Steinsland ◽  
Thor Harald Ringsby ◽  
Bernt-Erik Sæther
Keyword(s):  
Evolutionary Dynamics ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Indirect Selection ◽  
Sexual Ornament
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