Evolving Digital Ecological Networks
Publication Date
March 07, 2013
Journal
PLOS Computational Biology
Authors
Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner & Charles Ofria
Volume
9
Issue
3
Pages
e1002928
DOI
http://doi.org/10.1371/journal.pcbi.1002928
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1002928
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23533370
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605903
Europe PMC
http://europepmc.org/abstract/MED/23533370
Web of Science
000316864200005
Scopus
84875997583
Mendeley
http://www.mendeley.com/research/evolving-digital-ecological-networks
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Mendeley | Further Information

{"title"=>"Evolving Digital Ecological Networks", "type"=>"journal", "authors"=>[{"first_name"=>"Miguel A.", "last_name"=>"Fortuna", "scopus_author_id"=>"12781725000"}, {"first_name"=>"Luis", "last_name"=>"Zaman", "scopus_author_id"=>"55202058800"}, {"first_name"=>"Aaron P.", "last_name"=>"Wagner", "scopus_author_id"=>"13612228000"}, {"first_name"=>"Charles", "last_name"=>"Ofria", "scopus_author_id"=>"8110205600"}], "year"=>2013, "source"=>"PLoS Computational Biology", "identifiers"=>{"isbn"=>"1553-7358", "pui"=>"368694284", "issn"=>"1553734X", "pmid"=>"23533370", "doi"=>"10.1371/journal.pcbi.1002928", "sgr"=>"84875997583", "scopus"=>"2-s2.0-84875997583"}, "id"=>"8333a460-e22d-37f2-8e42-e9d36c6f0f42", "abstract"=>"\"It is hard to realize that the living world as we know it is just one among many possibilities\" [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms) that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks) that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).", "link"=>"http://www.mendeley.com/research/evolving-digital-ecological-networks", "reader_count"=>109, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>8, "Researcher"=>29, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>1, "Student > Master"=>13, "Other"=>3, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>8, "Researcher"=>29, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>1, "Student > Master"=>13, "Other"=>3, "Student > Bachelor"=>7, "Lecturer"=>1, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>13, "Biochemistry, Genetics and Molecular Biology"=>3, "Mathematics"=>3, "Agricultural and Biological Sciences"=>67, "Arts and Humanities"=>2, "Business, Management and Accounting"=>1, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>4, "Computer Science"=>11}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>67}, "Computer Science"=>{"Computer Science"=>11}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>13}, "Arts and Humanities"=>{"Arts and Humanities"=>2}}, "reader_count_by_country"=>{"Colombia"=>1, "United States"=>2, "Japan"=>2, "Tanzania"=>1, "United Kingdom"=>1, "Switzerland"=>2, "Portugal"=>2, "Spain"=>1, "India"=>1, "Netherlands"=>1, "Norway"=>1, "Brazil"=>3, "Mexico"=>1, "Israel"=>1, "France"=>3, "Peru"=>1, "Germany"=>4}, "group_count"=>1}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/980943", "https://ndownloader.figshare.com/files/980944", "https://ndownloader.figshare.com/files/980946", "https://ndownloader.figshare.com/files/980947"], "description"=>"<div><p>“<i>It is hard to realize that the living world as we know it is just one among many possibilities</i>” <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002928#pcbi.1002928-Jacob1\" target=\"_blank\">[1]</a>. <b>Evolving digital ecological networks</b> are webs of interacting, <a href=\"http://en.wikipedia.org/w/index.php?title=self-replication\" target=\"_blank\">self-replicating</a>, and <a href=\"http://en.wikipedia.org/w/index.php?title=evolution\" target=\"_blank\">evolving</a><a href=\"http://en.wikipedia.org/w/index.php?title=computer_program\" target=\"_blank\">computer programs</a> (i.e., <a href=\"http://en.wikipedia.org/w/index.php?title=digital_organism\" target=\"_blank\">digital organisms</a>) that experience the same major <a href=\"http://en.wikipedia.org/w/index.php?title=ecology\" target=\"_blank\">ecological interactions</a> as <a href=\"http://en.wikipedia.org/w/index.php?title=biological_organism\" target=\"_blank\">biological organisms</a> (e.g., <a href=\"http://en.wikipedia.org/w/index.php?title=Competition_(biology)\" target=\"_blank\">competition</a>, <a href=\"http://en.wikipedia.org/w/index.php?title=predation\" target=\"_blank\">predation</a>, <a href=\"http://en.wikipedia.org/w/index.php?title=parasitism\" target=\"_blank\">parasitism</a>, and <a href=\"http://en.wikipedia.org/w/index.php?title=Mutualism_(biology)\" target=\"_blank\">mutualism</a>). Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological <a href=\"http://en.wikipedia.org/w/index.php?title=Biological_network\" target=\"_blank\">networks</a> can be observed in real-time by tracking interactions between the constantly evolving organism <a href=\"http://en.wikipedia.org/w/index.php?title=phenotype\" target=\"_blank\">phenotypes</a>. These phenotypes may be defined by combinations of <a href=\"http://en.wikipedia.org/w/index.php?title=Boolean_logic\" target=\"_blank\">logical computations</a> (hereafter tasks) that digital organisms perform and by expressed <a href=\"http://en.wikipedia.org/w/index.php?title=behavior_(biology)\" target=\"_blank\">behaviors</a> that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within <a href=\"http://en.wikipedia.org/w/index.php?title=Evolutionary_ecology\" target=\"_blank\">evolutionary ecology</a> (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved).</p> </div>", "links"=>[], "tags"=>["evolving", "networks"], "article_id"=>647162, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Miguel A. Fortuna", "Luis Zaman", "Aaron P. Wagner", "Charles Ofria"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002928.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002928.s002", "https://dx.doi.org/10.1371/journal.pcbi.1002928.s003", "https://dx.doi.org/10.1371/journal.pcbi.1002928.s004"], "stats"=>{"downloads"=>1, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evolving_Digital_Ecological_Networks_/647162", "title"=>"Evolving Digital Ecological Networks", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-08 10:57:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/980930"], "description"=>"<p>When <a href=\"http://en.wikipedia.org/w/index.php?title=Charles_Darwin\" target=\"_blank\">Darwin</a> received an orchid (<a href=\"http://en.wikipedia.org/w/index.php?title=Angraecum_sesquipedale\" target=\"_blank\">Angraecum sesquipedale</a>) from <a href=\"http://en.wikipedia.org/w/index.php?title=Madagascar\" target=\"_blank\">Madagascar</a> whose <a href=\"http://en.wikipedia.org/w/index.php?title=nectary\" target=\"_blank\">nectary</a> was one and a half feet long, he surmised that there must be a <a href=\"http://en.wikipedia.org/w/index.php?title=pollinator\" target=\"_blank\">pollinator</a><a href=\"http://en.wikipedia.org/w/index.php?title=moth\" target=\"_blank\">moth</a> with a <a href=\"http://en.wikipedia.org/w/index.php?title=proboscis\" target=\"_blank\">proboscis</a> long enough to reach the nectar at the end of the <a href=\"http://en.wikipedia.org/w/index.php?title=Spur_(botany)\" target=\"_blank\">spur</a><a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002928#pcbi.1002928-Kritsky1\" target=\"_blank\">[32]</a>. In its attempt to get the nectar, the moth would have <a href=\"http://en.wikipedia.org/w/index.php?title=pollen\" target=\"_blank\">pollen</a> rubbed onto its head, and the next orchid visited would then be pollinated. In 1903, such a moth was discovered: <a href=\"http://en.wikipedia.org/w/index.php?title=Xanthopan_morgani\" target=\"_blank\">Xanthopan morgani</a>. This was a remarkable example of an evolutionary <a href=\"http://en.wikipedia.org/w/index.php?title=prediction\" target=\"_blank\">prediction</a>. However, because species coevolve within large networks of multispecies ecological interactions, this example of <a href=\"http://en.wikipedia.org/w/index.php?title=pairwise_coevolution\" target=\"_blank\">pairwise coevolution</a> is more the exception than the rule.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology"], "article_id"=>647155, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Miguel A. Fortuna", "Luis Zaman", "Aaron P. Wagner", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002928.g001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pairwise_coevolution_/647155", "title"=>"Pairwise coevolution.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-08 10:55:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/980931"], "description"=>"<p>The circular genome of a digital organism, on the left, consists of a set of instructions (represented here as letters). Some of these instructions are involved in the copy process and others in completing computational tasks. The experimenter determines the probability of mutations. Copy mutations occur when an instruction is copied incorrectly, and is instead replaced by a random instruction in the forming offspring's genome (as can be seen in the offspring, on the right). Other types of mutations, such as <a href=\"http://en.wikipedia.org/w/index.php?title=insertion_(genetics)\" target=\"_blank\">insertions</a> and <a href=\"http://en.wikipedia.org/w/index.php?title=deletion_(genetics)\" target=\"_blank\">deletions</a> are also implemented. All three of the parent's hardware <a href=\"http://en.wikipedia.org/w/index.php?title=pointer_(computer_programming)\" target=\"_blank\">pointers</a> are represented: the instruction pointer (indicated by an <i>i</i>), the write-head pointer (indicated by a <i>w</i>), and the flow pointer (indicated by an <i>f</i>). Arcs inside the circular genome represent the <a href=\"http://en.wikipedia.org/w/index.php?title=control_flow\" target=\"_blank\">execution flow</a>, showing most of the <a href=\"http://en.wikipedia.org/w/index.php?title=instruction_cycle\" target=\"_blank\">CPU cycles</a> being used during the copying process. After genome replication is complete, the parent organism divides off its offspring, which must now fend for itself within the Avida world. The last snapshot of an animation representing the self-replication process of a digital organism, Video S1, is shown. It was generated using <a href=\"http://en.wikipedia.org/w/index.php?title=Avida\" target=\"_blank\">Avida-ED</a>, which is available under the terms of the <a href=\"http://en.wikipedia.org/w/index.php?title=GNU_Lesser_General_Public_License\" target=\"_blank\">GNU Lesser General Public License</a> at <a href=\"http://avida-ed.msu.edu/\" target=\"_blank\">http://avida-ed.msu.edu/</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology"], "article_id"=>647156, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Miguel A. Fortuna", "Luis Zaman", "Aaron P. Wagner", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002928.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Self_replication_of_a_digital_organism_/647156", "title"=>"Self-replication of a digital organism.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-08 10:55:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/980932"], "description"=>"<p>Digital organisms process <a href=\"http://en.wikipedia.org/w/index.php?title=Binary_numeral_system\" target=\"_blank\">binary numbers</a> taken from the environment using the instructions that constitute their <a href=\"http://en.wikipedia.org/w/index.php?title=Genome\" target=\"_blank\">genomes</a>. When the output of processing those numbers equals the result of applying a <a href=\"http://en.wikipedia.org/w/index.php?title=Boolean_algebra\" target=\"_blank\">logic function</a>, the digital organism is said to have performed that task. The combination of tasks performed by a digital organism partially defines its phenotype. The center of the figure depicts the output of applying eight <a href=\"http://en.wikipedia.org/w/index.php?title=Truth_table\" target=\"_blank\">logical operators</a> (tasks) on the two input numbers above. On the left and right, five hypothetical <a href=\"http://en.wikipedia.org/w/index.php?title=Host_(biology)\" target=\"_blank\">host</a> (green) and <a href=\"http://en.wikipedia.org/w/index.php?title=Parasitism\" target=\"_blank\">parasite</a> (red) phenotypes are represented as columns (on the top) and as circles (below). On the top, each column depicts a phenotype and each row represents a task. Tasks performed by each phenotype are filled. In the lower part, the interaction networks between hosts and parasites are illustrated, which result from phenotypic matching: a parasite infects a host (indicated by a line) if it performs at least one task that is also performed by the host. Inset numbers indicate the identity of phenotypes represented on the top. Arrows represent the temporal direction of the <a href=\"http://en.wikipedia.org/w/index.php?title=coevolution\" target=\"_blank\">coevolutionary process</a>: from the earliest phenotype to the most recent one. The order of tasks (from top to bottom) indicates the time needed for a digital organism to perform that task over the course of the evolutionary trajectory. Depending on the pattern of tasks performed by the digital organisms, a <a href=\"http://en.wikipedia.org/w/index.php?title=modularity\" target=\"_blank\">modular</a> (left) or <a href=\"http://en.wikipedia.org/w/index.php?title=nestedness\" target=\"_blank\">nested</a> (right) interaction network can emerge.</p>", "links"=>[], "tags"=>["phenotypic", "matching", "leads"], "article_id"=>647157, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Miguel A. Fortuna", "Luis Zaman", "Aaron P. Wagner", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002928.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Logical_computations_i_e_tasks_partially_define_phenotypes_and_phenotypic_matching_leads_to_ecological_interactions_/647157", "title"=>"Logical computations, i.e., tasks, partially define phenotypes, and phenotypic matching leads to ecological interactions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-08 10:55:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/980934"], "description"=>"<p>Starting from a host phenotype (green node) and a parasite phenotype (red node), a complex network of interactions (arrows) between hosts and parasites emerges out of the coevolutionary process. Nodes representing new host and parasite phenotypes appear and disappear over evolutionary time. The abundance of individuals expressing each phenotype changes continuously (indicated by node size) altering interaction patterns, and thus influencing subsequent coevolutionary dynamics. Interactions between a host phenotype and a parasite phenotype are depicted as arrows pointing in opposite directions: the thickness of red arrows indicates the fraction of <a href=\"http://en.wikipedia.org/w/index.php?title=infectious_disease\" target=\"_blank\">infections</a> that a particular parasite is responsible for inflicting on the indicated host phenotype, while the thickness of the green arrows indicates the fraction of all of the hosts a particular parasite phenotype infects that is accounted for by the indicated host phenotype. Often asymmetry between the thicknesses of arrow-pairs leads to red arrows dominating the picture. At these times, most parasite phenotypes are infecting only a small fraction of hosts expressing a given phenotype. Instead, the majority of those hosts are being infected by parasites with other phenotypes. This is a single snapshot of Video S2, which depicts the evolutionary dynamics of a host–parasite community. It was generated using Pajek, which is available under the <a href=\"http://en.wikipedia.org/w/index.php?title=GNU_General_Public_License\" target=\"_blank\">GNU General Public License</a> at <a href=\"http://pajek.imfm.si/doku.php\" target=\"_blank\">http://pajek.imfm.si/doku.php</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Evolutionary biology"], "article_id"=>647159, "categories"=>["Biological Sciences", "Evolutionary Biology"], "users"=>["Miguel A. Fortuna", "Luis Zaman", "Aaron P. Wagner", "Charles Ofria"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002928.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolving_host_8211_parasite_webs_/647159", "title"=>"Evolving host–parasite webs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-08 10:55:38"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Ecology", "average_usage"=>[290, 478, 601, 716, 816, 914, 1016, 1112, 1203, 1285, 1373, 1451, 1516]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Parasitology", "average_usage"=>[354, 586, 723, 820, 941, 1045, 1176, 1283, 1391, 1469, 1526, 1639, 1730]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[284, 475, 603, 722, 826, 928, 1026, 1129, 1225, 1310, 1390, 1468, 1549]}, {"subject_area"=>"/Ecology and environmental sciences/Community ecology", "average_usage"=>[285, 478]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[298, 487, 610, 722, 827, 929, 1029, 1125, 1217, 1306, 1388, 1464, 1535]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}]}
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