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Reconstruction of phylogenetic trees using the ant colony optimization paradigm

Mauricio Perretto, Heitor Silvério Lopes
2005 Genetics and Molecular Research  
We developed a new approach for the reconstruction of phylogenetic trees using ant colony optimization metaheuristics.  ...  This methodology was used to develop an algorithm for constructing a phylogenetic tree using a pheromone matrix.  ...  ACKNOWLEDGMENTS The authors thank CNPq for financial support (grant numbers: 350053/03-0, 475049/ 03-9 and 402018/03-6).  ... 
pmid:16342043 fatcat:mnrwwblkzvh43f7diesrcuhasi

Swarm Intelligence Algorithms in Bioinformatics [chapter]

Swagatam Das, Ajith Abraham, Amit Konar
2008 Studies in Computational Intelligence  
In this way, following an algorithm very close in spirit to the ant colony algorithm for solving the TSP, the phylogenetic trees may be reconstructed efficiently.  ...  [76] proposed a slightly modified artificial ant colony based algorithm for the construction of phylogenetic trees.  ... 
doi:10.1007/978-3-540-76803-6_4 fatcat:aqxo2q2pzzbjpehpm4nh3fuxoa

Deep-time convergence in rove beetle symbionts of army ants [article]

Munetoshi Maruyama, Joseph Parker
2016 bioRxiv   pre-print
Army ants are ecologically dominant arthropod predators of the world's tropics, with large nomadic colonies housing diverse communities of socially parasitic myrmecophiles [7].  ...  with colonies and inhabiting temporary nest bivouacs, grooming and feeding with workers, but also consuming the brood [8-11].  ...  We estimated the number of times this has arisen across the tree using parsimony optimization and Bayesian ancestral state reconstruction.  ... 
doi:10.1101/076315 fatcat:3d2s7xe5lfga5aq2zjzt5hfxey

Ant-like Traits in Wingless Parasitoids Repel Attack from Wolf Spiders

Jeffrey A. Harvey, Bertanne Visser, Marl Lammers, Janine Marien, Jonathan Gershenzon, Paul J. Ode, Robin Heinen, Rieta Gols, Jacintha Ellers
2018 Journal of Chemical Ecology  
Phylogenetic reconstruction of the Cryptinae reveals that G. hortensis and G. proximus are 'sister'species, with G. agilis, and G.areator in particular evolving along more distant trajectories.  ...  We discuss the possibility that wingless Gelis species have evolved a suite of ant-like traits as a form, of mimicry to repel predators on the ground.  ...  Leon Westerd and Andre Gidding of Wageningen University for the rearing of P. brassicae, and Roel Wagenaar at NIOO for rearing of C. glomerata, A. nens and the Gelis species.  ... 
doi:10.1007/s10886-018-0989-2 pmid:30066038 fatcat:wv2jcaxkpfa27e5h5wb2kg522q

Stigmergic Optimization: Inspiration, Technologies and Perspectives [chapter]

Grosan Crina, Abraham Ajith
2006 Studies in Computational Intelligence  
We focused on ant colony optimization algorithm, bees behavior inspired algorithms, particle swarm optimization algorithm and bacterial foraging algorithm.  ...  This Chapter summarizes some of the well known stigmergic computational techniques inspired by nature, mainly for optimization problems developed by mimicking social insects' behavior.  ...  Perrotto and Lopez use ant colonies optimization for reconstruction of phylogenetic trees, which are developed in order to help unveil the evolutionary relationships among species, taking into account  ... 
doi:10.1007/978-3-540-34690-6_1 fatcat:hv5chn6blfcpncyu7fnbes24ri

Phylogenetic Relationships of Termitomyces aurantiacus Inferred from Internal Transcribed Spacers DNA Sequences

Shafiquzzaman Siddiquee, Kobun Rovina, Laila Naher, Kenneth F. Rodrigues, Md Akhter Uzzaman
2015 Advances in Bioscience and Biotechnology  
As an alternative, nuclear ribosomal DNA sequences consisting of the internal transcribed spacers (ITS1 and ITS2) and 5.8S rDNA were used to identify Malaysian isolates of Termitomyces sp.  ...  Fungus-growing termites cultivate species of the mutualistic basidiomycete genus Termitomyces on a substrate called the fungal comb.  ...  Acknowledgements The authors acknowledge the valuable contributions of the late Prof. Dr. Faridah Abdullah.  ... 
doi:10.4236/abb.2015.65035 fatcat:qduedwcuynekrgc7yib7wcdnfm

Insect Symbioses: A Case Study of Past, Present, and Future Fungus-growing Ant Research

Eric J. Caldera, Michael Poulsen, Garret Suen, Cameron R. Currie
2009 Environmental Entomology  
Indeed, the discovery that the ants actually use leaf fragments to manure a fungus did not come until the 1800s.  ...  Although biologists have been fascinated with fungus-growing ants since the resurgence of natural history in the modern era, the early stages of research focused mainly on the foraging behavior of the  ...  The application of molecular phylogenetics has also facilitated the reconstruction of the evolutionary history of the garden parasite.  ... 
doi:10.1603/022.038.0110 pmid:19791600 fatcat:mhrjrjprwfcalgbarxjtfqp6d4

Memetic Algorithms in Bioinformatics [chapter]

Regina Berretta, Carlos Cotta, Pablo Moscato
2012 Studies in Computational Intelligence  
They described several metaheuristics such as MAs, tabu search, ant colony optimization, self-organizing map-based computing approaches and chain growth algorithm PERM, highlighting their advantages and  ...  They consider the use of P-systems [73] , a computing model included in the ampler paradigm of membrane computing [74] .  ... 
doi:10.1007/978-3-642-23247-3_16 fatcat:cbhccq5bzzbyrbm7pxxhaa7pqu

Changing Paradigms in Insect Social Evolution: Insights from Halictine and Allodapine Bees

Michael P. Schwarz, Miriam H. Richards, Bryan N. Danforth
2007 Annual Review of Entomology  
We would also like to thank Doug Beckner for expert help in preparing the final figures.  ...  Phylogenetic studies using allozymes were the first attempts to reconstruct patterns of social evolution in halictine bees (53, 61) , but they were based on limited taxa because of the difficulty of preserving  ...  While Eickwort (26) did not explicitly map sociality onto his phylogenies, his trees were of immediate use in interpreting patterns of social evolution.  ... 
doi:10.1146/annurev.ento.51.110104.150950 pmid:16866635 fatcat:ph5fskfbvfbnthh4eizo3nnoty

Ant versus Fungus versus Mutualism: Ant‐Cultivar Conflict and the Deconstruction of the Attine Ant‐Fungus Symbiosis

Ulrich G. Mueller
2002 American Naturalist  
Second, ant-cultivar conflict over fungal sexual reproduction exists if the fungi are able to escape from the symbiosis and live independently, as is implied by phylogenetic analyses of the fungi; this  ...  nests (symbiont drive) but that are detrimental to the survival of the whole colony.  ...  ) and resembles in all important details the tree found using maximum likelihood.  ... 
doi:10.1086/342084 pmid:18707454 fatcat:fxwseurzvfbvlafojecsktogu4

Phylogenomic Delimitation of Morphologically Cryptic Species in Globetrotting Nylanderia (Hymenoptera: Formicidae) Species Complexes

Jason L Williams, Y Miles Zhang, John S LaPolla, Ted R Schultz, Andrea Lucky, Gabriela P Camacho
2022 Insect Systematics and Diversity  
To elucidate the phylogenetic positions of these three complexes and delimit species boundaries within each, we used target enrichment of ultraconserved elements (UCEs) from 165 specimens representing  ...  Taxonomy is further complicated by Nylanderia being one of the most frequently intercepted ant genera at ports of entry worldwide, and at least 15 globetrotting species have widespread and expanding ranges  ...  The following institutions and individuals loaned or donated specimens used in this study: Archbold Biological Station (Mark Deyrup), Florida State Collection of Arthropods (Elijah Talamas), Ward Lab at  ... 
doi:10.1093/isd/ixab027 fatcat:rin4zlcjrveypdwhwwrez3sqd4

Evolution of Macromolecular Structure: A 'Double Tale' of Biological Accretion and Diversification

Derek Caetano-Anollés, Kelsey Caetano-Anollés, Gustavo Caetano-Anollés
2018 Science Progress  
Evolutionary genomics and network biology support the 'double tale' of structural module creation and validate an evolutionary principle of maximum abundance that drives the gain and loss of modules.  ...  In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organization.  ...  Research was supported by a National Science Foundation postdoctoral fellowship (award 1523549) to DCA and a grant from the USDA National Institute of Food and Agriculture (Hatch-1014249) to GCA.  ... 
doi:10.3184/003685018x15379391431599 fatcat:i4s3e2gmjrdedlzakhzzpu2fqa

Social trajectories and the evolution of social behavior

S. Helms Cahan, D. T. Blumstein, L. Sundstrom, J. Liebig, A. Griffin
2002 Oikos  
Social trajectories and the evolution of social behavior. -Oikos 96: 206-216.  ...  Developing a unified theory of social evolution has been a challenging process, hampered by the inherent complexity of social systems.  ...  Participants at the Summer School provided valuable feedback on the structure and applicability of the model.  ... 
doi:10.1034/j.1600-0706.2002.960202.x fatcat:mmveycoru5gaxpxum6uindptjy

Ant, Bee and Wasp Social Evolution ☆ [chapter]

Raghavendra Gadagkar
2017 Reference Module in Life Sciences  
In spite of the size of this order (more than 250,000 described species), only a small fraction (o10%) of the species is social, and thus of interest to us here.  ...  The discussion in this article thus refers to the evolution of eusociality in ants, bees, and wasps. It is also customary to distinguish two subgroups within the eusocial species.  ...  Based on our understanding of how ants, bees, and wasps utilize swarm intelligence, so-called ant colony optimization algorithms (AOL) are in regular use in the telecommunication industry, on the Internet  ... 
doi:10.1016/b978-0-12-809633-8.01024-4 fatcat:ovhj4pdddncgjjrflslit2idgu

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

Gustavo Caetano-Anollés, M Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés
2019 Evolutionary Bioinformatics  
The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels.  ...  In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization.  ...  Tree reconstruction involves optimizing the fit of data along the branches of all possible trees according to some optimality criterion and a model of character state change.  ... 
doi:10.1177/1176934319872980 pmid:31523127 pmcid:PMC6728656 fatcat:pundw72czjfwhc6gv2wnxktdvq
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