From Arms to Trees: Opportunity Costs and Path Dependence and the Exploration-Exploitation Tradeoff

2021 ◽  
Author(s):  
Daniel A. Levinthal

The literature on the exploration-exploitation tradeoff has anchored on the n-armed bandit problem as its canonical formal representation. This structure, however, omits a fundamental property of evolutionary dynamics. Contrary to a bandit formulation, foregoing an opportunity may negate the possibility of engaging in that opportunity in the future, not just modifying the beliefs about the attractiveness of engaging in that opportunity. Thus, the bandit structure only incorporates path dependence with respect to beliefs and not with regard to capabilities as our usual conceptions of dynamics of learning and capabilities would suggest. Furthermore, the consideration of opportunity cost is rather static and does not address the dynamic unfolding of opportunity structures. The nature of path dependence and opportunity costs are used to frame many of our existing conceptualizations of search processes and firm dynamics, including bandit models, real options, pivoting, the “secretary problem,” and “island” models of firm diversification. The discussion points to the need to develop canonical models of what evolutionary biologists’ term phylogenetic trees and opens up a set of new questions, such as what is the degree of parallelism of trajectories that is possible within an organization, what is the fecundity of different trajectories in terms of likelihood of branching possibilities arising, and how are these latent branching opportunities accessed?

10.37236/8322 ◽  
2019 ◽  
Vol 26 (1) ◽  
Author(s):  
Madeline Crews ◽  
Brant Jones ◽  
Kaitlyn Myers ◽  
Laura Taalman ◽  
Michael Urbanski ◽  
...  

The game of best choice, also known as the secretary problem, is a model for sequential decision making with many variations in the literature. Notably, the classical setup assumes that the sequence of candidate rankings is uniformly distributed over time and that there is no expense associated with the candidate interviews. Here, we weight each ranking permutation according to the position of the best candidate in order to model costs incurred from conducting interviews with candidates that are ultimately not hired. We compare our weighted model with the classical (uniform) model via a limiting process. It turns out that imposing even infinitesimal costs on the interviews results in a probability of success that is about 28%, as opposed to 1/e (about 37%) in the classical case.


2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Concepción Pérez-García ◽  
Ninoska S. Hurtado ◽  
Paloma Morán ◽  
Juan J. Pasantes

The chromosomal changes accompanying bivalve evolution are an area about which few reports have been published. To improve our understanding on chromosome evolution in Veneridae, ribosomal RNA gene clusters were mapped by fluorescentin situhybridization (FISH) to chromosomes of five species of venerid clams (Venerupis corrugata,Ruditapes philippinarum,Ruditapes decussatus,Dosinia exoleta, andVenus verrucosa). The results were anchored to the most comprehensive molecular phylogenetic tree currently available for Veneridae. While a single major rDNA cluster was found in each of the five species, the number of 5S rDNA clusters showed high interspecies variation. Major rDNA was either subterminal to the short arms or intercalary to the long arms of metacentric or submetacentric chromosomes, whereas minor rDNA signals showed higher variability. Major and minor rDNAs map to different chromosome pairs in all species, but inR. decussatusone of the minor rDNA gene clusters and the major rDNA cluster were located in the same position on a single chromosome pair. This interspersion of both sequences was confirmed by fiber FISH. Telomeric signals appeared at both ends of every chromosome in all species. FISH mapping data are discussed in relation to the molecular phylogenetic trees currently available for Veneridae.


2018 ◽  
Vol 92 (15) ◽  
Author(s):  
Divya Venkatesh ◽  
Marjolein J. Poen ◽  
Theo M. Bestebroer ◽  
Rachel D. Scheuer ◽  
Oanh Vuong ◽  
...  

ABSTRACTWild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter, or stage. The Republic of Georgia is located at the intersection of three migratory flyways: the Central Asian flyway, the East Africa/West Asia flyway, and the Black Sea/Mediterranean flyway. For six complete study years (2010 to 2016), we collected AIV samples from various duck and gull species that breed, migrate, and overwinter in Georgia. We found a substantial subtype diversity of viruses that varied in prevalence from year to year. Low-pathogenic AIV (LPAIV) subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, and H16N3, and two highly pathogenic AIVs (HPAIVs) belonging to clade 2.3.4.4, H5N5 and H5N8, were found. Whole-genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide sequence diversity for LPAIVs among different host species. Hemagglutinin clade 2.3.4.4 H5N8 viruses, which circulated in Eurasia during 2014 and 2015, did not reassort, but analysis after their subsequent dissemination during 2016 and 2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions, with maintenance of local AIVs in Georgia, whereas other lineages showed considerable genetic interrelationships with viruses circulating in other parts of Eurasia and Africa, despite relative undersampling in the area.IMPORTANCEWaterbirds (e.g., gulls and ducks) are natural reservoirs of avian influenza viruses (AIVs) and have been shown to mediate the dispersal of AIVs at intercontinental scales during seasonal migration. The segmented genome of influenza viruses enables viral RNA from different lineages to mix or reassort when two viruses infect the same host. Such reassortant viruses have been identified in most major human influenza pandemics and several poultry outbreaks. Despite their importance, we have only recently begun to understand AIV evolution and reassortment in their natural host reservoirs. This comprehensive study illustrates AIV evolutionary dynamics within a multihost ecosystem at a stopover site where three major migratory flyways intersect. Our analysis of this ecosystem over a 6-year period provides a snapshot of how these viruses are linked to global AIV populations. Understanding the evolution of AIVs in the natural host is imperative to mitigating both the risk of incursion into domestic poultry and the potential risk to mammalian hosts, including humans.


2014 ◽  
Vol 5 (7) ◽  
pp. 701-707 ◽  
Author(s):  
Daniel L. Rabosky ◽  
Michael Grundler ◽  
Carlos Anderson ◽  
Pascal Title ◽  
Jeff J. Shi ◽  
...  

2014 ◽  
Vol 95 (11) ◽  
pp. 2390-2401 ◽  
Author(s):  
Laure Bellec ◽  
Joelle Cabon ◽  
Sven Bergmann ◽  
Claire de Boisséson ◽  
Marc Engelsma ◽  
...  

Wild freshwater eel populations have dramatically declined in recent past decades in Europe and America, partially through the impact of several factors including the wide spread of infectious diseases. The anguillid rhabdoviruses eel virus European X (EVEX) and eel virus American (EVA) potentially play a role in this decline, even if their real contribution is still unclear. In this study, we investigate the evolutionary dynamics and genetic diversity of anguiillid rhabdoviruses by analysing sequences from the glycoprotein, nucleoprotein and phosphoprotein (P) genes of 57 viral strains collected from seven countries over 40 years using maximum-likelihood and Bayesian approaches. Phylogenetic trees from the three genes are congruent and allow two monophyletic groups, European and American, to be clearly distinguished. Results of nucleotide substitution rates per site per year indicate that the P gene is expected to evolve most rapidly. The nucleotide diversity observed is low (2–3 %) for the three genes, with a significantly higher variability within the P gene, which encodes multiple proteins from a single genomic RNA sequence, particularly a small C protein. This putative C protein is a potential molecular marker suitable for characterization of distinct genotypes within anguillid rhabdoviruses. This study provides, to our knowledge, the first molecular characterization of EVA, brings new insights to the evolutionary dynamics of two genotypes of Anguillid rhabdovirus, and is a baseline for further investigations on the tracking of its spread.


Games ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 93
Author(s):  
Atin Basuchoudhary

Empirical investigation suggests that conflict is path-dependent, i.e., current conflict leads to more conflict in the future. However, there is very little formal theory for why conflict path dependence exists. We propose a mathematical model to explore one possible pathway to explain the persistence of conflict once it starts. In this model, there are three types of cultures in two boundedly rational populations. The two populations are State Actors and Insurgents. The three cultures are Peaceable, Warring, or Bargainers. The distribution of these types is different in each population. Evolutionary dynamics determine which of these three cultures might predominate. Our simulations suggest that it is rational for people to learn to be warlike even in environments where State Actors are willing to give large side payments to “buy” peace to avoid bargaining failure. War can also be learned when State Actors and Insurgents are extremely patient and, therefore, potentially committed to Pareto improving peace deals. The outcomes of these simulations suggest that cultural learning can be a hitherto ignored explanation for why conflict is path dependent. If culture is indeed a possible cause for conflict, the best intentions of technocratic peacemakers trying to build frameworks for resource sharing and/or institutional building may fail, simply because such structures are not suited to local conditions. On the flip side, our model also provides theoretical reasoning for the observation that conflict is not a deterministic outcome of bargaining and commitment failures.


2020 ◽  
Vol 26 (1) ◽  
pp. 58-79 ◽  
Author(s):  
Emily Dolson ◽  
Alexander Lalejini ◽  
Steven Jorgensen ◽  
Charles Ofria

Fine-scale evolutionary dynamics can be challenging to tease out when focused on the broad brush strokes of whole populations over long time spans. We propose a suite of diagnostic analysis techniques that operate on lineages and phylogenies in digital evolution experiments, with the aim of improving our capacity to quantitatively explore the nuances of evolutionary histories in digital evolution experiments. We present three types of lineage measurements: lineage length, mutation accumulation, and phenotypic volatility. Additionally, we suggest the adoption of four phylogeny measurements from biology: phylogenetic richness, phylogenetic divergence, phylogenetic regularity, and depth of the most-recent common ancestor. In addition to quantitative metrics, we also discuss several existing data visualizations that are useful for understanding lineages and phylogenies: state sequence visualizations, fitness landscape overlays, phylogenetic trees, and Muller plots. We examine the behavior of these metrics (with the aid of data visualizations) in two well-studied computational contexts: (1) a set of two-dimensional, real-valued optimization problems under a range of mutation rates and selection strengths, and (2) a set of qualitatively different environments in the Avida digital evolution platform. These results confirm our intuition about how these metrics respond to various evolutionary conditions and indicate their broad value.


2019 ◽  
Author(s):  
Tymofii H. Sokolskyi

AbstractVaults are large cone-shaped and highly conservative ribonucleoprotein complexes present in the cells of most major eukaryote clades. However, despite their wide distribution, their functions and evolutionary dynamics still remain enigmatic. Several minor functions in modulating signaling cascades and multidrug resistance phenotypes were previously discovered for eukaryotic vaults, yet nothing is known about bacterial homologs of the major vault protein (MVP), a protein that comprises the entirety of vault external surface. Using gene and protein BLAST searches in NCBI and UniProt databases we identified a number of bacterial species in prokaryotic orders Myxococcales, Cytophagales and Oscillatoriales with >50% identity to eukaryotic MVP sequences. Interestingly, all of these species are characterized by one common feature – gliding type of motility. Secondary structures of the identified proteins were predicted using RAPTORX web service and aligned via jFATCAT-flexible algorithm in the RCSB PDB Java Structure Alignment tool to elucidate structural identity. Coiled coil domain at the MVP C-terminus of all studied bacterial species resembled TolA protein of Escherichia coli by both structure and sequence. We also showed that MVP sequences from chemotrophic bacteria Myxococcales and Cytophagales contain a domain homologous to eukaryotic band-7 domain, unlike cyanobacterial and eukaryotic major vault proteins. As expected, maximum-likelihood phylogenetic trees for MVP sequences separate studied taxa into two clades – first clade contains Oscillatoriales (Cyanobacteria) and Eukaryotes and the second one contains chemotrophic bacteria. In addition, binding prediction via RAPTORX showed great multiplicity GMP and CMP nucleoside monophosphate binding pockets in Myxococcales and Cytophagales MVP, unlike eukaryotic and cyanobacterial proteins which had much lower affinity to these substrates.Due to high similarity of eukaryotic and cyanobacterial MVP sequences and a pattern of its phylogenetic distribution, we can speculate that the most likely scenario for vault appearance in eukaryotes is horizontal gene transfer from cyanobacteria. Presence of GMP and CMP binding pockets in MVP could also point to a function in depleting cytosolic nucleotide concentration which would be beneficial, for instance, during a viral infection. Further research is necessary to uncover potential functions of this enigmatic protein in bacteria and to determine its evolutionary patterns. In addition, a correlation between MVP presence and gliding motility in bacteria could also lead to elucidating selective pressures on the early evolution of this protein.


2017 ◽  
Vol 114 (9) ◽  
pp. 2289-2294 ◽  
Author(s):  
Shashi Thutupalli ◽  
Sravanti Uppaluri ◽  
George W. A. Constable ◽  
Simon A. Levin ◽  
Howard A. Stone ◽  
...  

The ecological and evolutionary dynamics of populations are shaped by the strategies they use to produce and use resources. However, our understanding of the interplay between the genetic, behavioral, and environmental factors driving these strategies is limited. Here, we report on a Caenorhabditis elegans–Escherichia coli (worm–bacteria) experimental system in which the worm-foraging behavior leads to a redistribution of the bacterial food source, resulting in a growth advantage for both organisms, similar to that achieved via farming. We show experimentally and theoretically that the increased resource growth represents a public good that can benefit all other consumers, regardless of whether or not they are producers. Mutant worms that cannot farm bacteria benefit from farming by other worms in direct proportion to the fraction of farmers in the worm population. The farming behavior can therefore be exploited if it is associated with either energetic or survival costs. However, when the individuals compete for resources with their own type, these costs can result in an increased population density. Altogether, our findings reveal a previously unrecognized mechanism of public good production resulting from the foraging behavior of C. elegans, which has important population-level consequences. This powerful system may provide broad insight into exploration–exploitation tradeoffs, the resultant ecoevolutionary dynamics, and the underlying genetic and neurobehavioral driving forces of multispecies interactions.


2018 ◽  
Author(s):  
Divya Venkatesh ◽  
Marjolein J. Poen ◽  
Theo M. Bestebroer ◽  
Rachel D. Scheuer ◽  
Oanh Vuong ◽  
...  

AbstractWild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter or stage. The Republic of Georgia is located at the intersection of three migratory flyways: Central Asian Flyway, East Asian/East African Flyway and Black Sea/Mediterranean Flyway. For six consecutive years (2010-2016), we collected AIV samples from various duck and gull species that breed, migrate and overwinter in Georgia. We found substantial subtype diversity of viruses that varied in prevalence from year to year. Low pathogenic (LP)AIV subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, H16N3, plus two H5N5 and H5N8 highly pathogenic (HP)AIVs belonging to clade 2.3.4.4. Whole genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences for LPAIVs among different host species in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide diversity. Hemagglutinin clade 2.3.4.4 H5N8 viruses, circulated in Eurasia during 2014-2015 did not reassort, but analysis after its subsequent dissemination during 2016-2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions with maintenance of local AIV viruses in Georgia, whereas other lineages showed considerable genetic inter-relationship with viruses circulating in other parts of Eurasia and Africa, despite relative under-sampling in the area.ImportanceWaterbirds (e.g., gulls/ducks) are natural reservoirs of avian influenza viruses (AIVs) and have been shown to mediate dispersal of AIV at inter-continental scales during seasonal migration. The segmented genome of influenza viruses enables viral RNA from different lineages to mix or re-assort when two viruses infect the same host. Such reassortant viruses have been identified in most major human influenza pandemics and several poultry outbreaks. Despite their importance, we have only recently begun to understand AIV evolution and reassortment in their natural host reservoirs. This comprehensive study illustrates of AIV evolutionary dynamics within a multi-host ecosystem at a stop-over site where three major migratory flyways intersect. Our analysis of this ecosystem over a six-year period provides a snapshot of how these viruses are linked to global AIV populations. Understanding the evolution of AIVs in the natural host is imperative to both mitigating the risk of incursion into domestic poultry and potential risk to mammalian hosts including humans.


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