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Ecological and evolutionary dynamics of interconnectedness and modularity.

ABSTRACT: In this contribution, we develop a theoretical framework for linking microprocesses (i.e., population dynamics and evolution through natural selection) with macrophenomena (such as interconnectedness and modularity within an ecological system). This is achieved by developing a measure of interconnectedness for population distributions defined on a trait space (generalizing the notion of modularity on graphs), in combination with an evolution equation for the population distribution. With this contribution, we provide a platform for understanding under what environmental, ecological, and evolutionary conditions ecosystems evolve toward being more or less modular. A major contribution of this work is that we are able to decompose the overall driver of changes at the macro level (such as interconnectedness) into three components: (i) ecologically driven change, (ii) evolutionarily driven change, and (iii) environmentally driven change.

SUBMITTER: Nordbotten JM

PROVIDER: S-EPMC5789935 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Ecological and evolutionary dynamics of interconnectedness and modularity.

Nordbotten Jan M JM Levin Simon A SA Szathmáry Eörs E Stenseth Nils C NC

Proceedings of the National Academy of Sciences of the United States of America 20180108 4

In this contribution, we develop a theoretical framework for linking microprocesses (i.e., population dynamics and evolution through natural selection) with macrophenomena (such as interconnectedness and modularity within an ecological system). This is achieved by developing a measure of interconnectedness for population distributions defined on a trait space (generalizing the notion of modularity on graphs), in combination with an evolution equation for the population distribution. With this co ...[more]

PMID: 29311333

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Project description:BACKGROUND: The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. RESULTS: We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. CONCLUSIONS: Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.

Project description:Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record-phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth's history have shaped-and been shaped by-evolution in Cyanobacteria. We identify a robust core cyanobacterial phylogeny and a smaller set of taxa that exhibit long-branch attraction artifacts. We estimated the age of nodes and reconstruct the ancestral character states of 43 phenotypic characters. We find high levels of phylogenetic signal for nearly all traits, indicating the phylogeny carries substantial predictive power. The earliest cyanobacterial lineages likely lived in freshwater habitats, had small cell diameters, were benthic or sessile, and possibly epilithic/endolithic with a sheath. We jointly analyzed a subset of 25 binary traits to determine whether rates of trait evolution have shifted over time in conjunction with major geologic events. Phylogenetic comparative analysis reveal an overriding signal of decreasing rates of trait evolution through time. Furthermore, the data suggest two major rate shifts in trait evolution associated with bursts of evolutionary innovation. The first rate shift occurs in the aftermath of the Great Oxidation Event and "Snowball Earth" glaciations and is associated with decrease in the evolutionary rates around 1.8-1.6 Ga. This rate shift seems to indicate the end of a major diversification of cyanobacterial phenotypes-particularly related to traits associated with filamentous morphology, heterocysts and motility in freshwater ecosystems. Another burst appears around the time of the Neoproterozoic Oxidation Event in the Neoproterozoic, and is associated with the acquisition of traits involved in planktonic growth in marine habitats. Our results demonstrate how uniting genomic and phenotypic datasets in extant bacterial species can shed light on billion-year old events in Earth's history.

Dataset Information

Ecological and evolutionary dynamics of interconnectedness and modularity.

Publications

Ecological and evolutionary dynamics of interconnectedness and modularity.

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