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Theories and models

Section edited by Laura Kubatko and Arne Traulsen

This section considers studies in mathematical modeling of evolutionary processes and research into theoretical areas.

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  1. Recent methodological advances allow better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the s...

    Authors: Sacha Laurent, Marc Robinson-Rechavi and Nicolas Salamin

    Citation: BMC Evolutionary Biology 2015 15:157

    Content type: RESEARCH COLLECTION

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  2. The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master...

    Authors: Renan Gross, Itzhak Fouxon, Doron Lancet and Omer Markovitch

    Citation: BMC Evolutionary Biology 2014 14:265

    Content type: Research article

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  3. The allele frequency spectrum (AFS) consists of counts of the number of single nucleotide polymorphism (SNP) loci with derived variants present at each given frequency in a sample. Multiple approaches have rec...

    Authors: John D Robinson, Alec J Coffman, Michael J Hickerson and Ryan N Gutenkunst

    Citation: BMC Evolutionary Biology 2014 14:254

    Content type: Research article

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  4. The value of a continuous character evolving on a phylogenetic tree is commonly modelled as the location of a particle moving under one-dimensional Brownian motion with constant rate. The Brownian motion model...

    Authors: Michael G Elliot and Arne Ø Mooers

    Citation: BMC Evolutionary Biology 2014 14:226

    Content type: Methodology Article

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  5. RNA or RNA-like polymers are the most likely candidates for having played the lead roles on the stage of the origin of life. RNA is known to feature two of the three essential functions of living entities (met...

    Authors: Balázs Könnyű and Tamás Czárán

    Citation: BMC Evolutionary Biology 2014 14:234

    Content type: Research article

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  6. Brain signaling requires energy. The cost of maintaining and supporting energetically demanding neurons is the key constraint on brain size. The dramatic increase in brain size among mammals and birds cannot b...

    Authors: Yuguo Yu, Jan Karbowski, Robert NS Sachdev and Jianfeng Feng

    Citation: BMC Evolutionary Biology 2014 14:178

    Content type: Research article

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  7. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is known that thousands of isoforms bind themselves through specific homophilic interact...

    Authors: Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang and Yan Zhu

    Citation: BMC Evolutionary Biology 2014 14:186

    Content type: Research article

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  8. The relationship between allopolyploidy and plant virus resistance is poorly understood. To determine the relationship of plant evolutionary history and basal virus resistance, a panel of Nicotiana species from d...

    Authors: John Gottula, Ramsey Lewis, Seiya Saito and Marc Fuchs

    Citation: BMC Evolutionary Biology 2014 14:149

    Content type: Research article

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  9. Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Access...

    Authors: Tsun-Tsao Huang, María Laura del Valle Marcos, Jenn-Kang Hwang and Julian Echave

    Citation: BMC Evolutionary Biology 2014 14:78

    Content type: Research article

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  10. As it becomes increasingly possible to obtain DNA sequences of orthologous genes from diverse sets of taxa, species trees are frequently being inferred from multilocus data. However, the behavior of many metho...

    Authors: Michael DeGiorgio, John Syring, Andrew J Eckert, Aaron Liston, Richard Cronn, David B Neale and Noah A Rosenberg

    Citation: BMC Evolutionary Biology 2014 14:67

    Content type: Research article

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  11. Host-parasite coevolution is generally believed to follow Red Queen dynamics consisting of ongoing oscillations in the frequencies of interacting host and parasite alleles. This belief is founded on previous t...

    Authors: Chaitanya S Gokhale, Andrei Papkou, Arne Traulsen and Hinrich Schulenburg

    Citation: BMC Evolutionary Biology 2013 13:254

    Content type: Research article

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  12. We wish to understand how sex and recombination affect endogenous retroviral insertion and deletion. While theory suggests that the risk of ectopic recombination will limit the accumulation of repetitive DNA i...

    Authors: Patrick Gemmell, Jotun Hein and Aris Katzourakis

    Citation: BMC Evolutionary Biology 2013 13:243

    Content type: Research article

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  13. It is often assumed that evolution takes place on very large timescales. Countering this assumption, rapid evolutionary dynamics are increasingly documented in biological systems, e.g. in the context of predat...

    Authors: Mathias Franz, Oliver Schülke and Julia Ostner

    Citation: BMC Evolutionary Biology 2013 13:235

    Content type: Research article

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  14. Reassortment between the RNA segments encoding haemagglutinin (HA) and neuraminidase (NA), the major antigenic influenza proteins, produces viruses with novel HA and NA subtype combinations and has preceded th...

    Authors: Melissa J Ward, Samantha J Lycett, Dorita Avila, Jonathan P Bollback and Andrew J Leigh Brown

    Citation: BMC Evolutionary Biology 2013 13:222

    Content type: Research article

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  15. The coexistence of macromolecular replicators and thus the stability of presumed prebiotic replicator communities have been shown to critically depend on spatially constrained catalytic cooperation among RNA-l...

    Authors: Balázs Könnyű and Tamás Czárán

    Citation: BMC Evolutionary Biology 2013 13:204

    Content type: Research article

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  16. Sex in higher diploids carries a two-fold cost of males that should reduce its fitness relative to cloning, and result in its extinction. Instead, sex is widespread and clonal species face early obsolescence. ...

    Authors: David Green and Chris Mason

    Citation: BMC Evolutionary Biology 2013 13:174

    Content type: Research article

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  17. Dispersal is a major factor in ecological and evolutionary dynamics. Although empirical evidence shows that the tendency to disperse varies among individuals in many organisms, the evolution of dispersal patte...

    Authors: Ariel Gueijman, Amir Ayali, Yoav Ram and Lilach Hadany

    Citation: BMC Evolutionary Biology 2013 13:125

    Content type: Research article

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  18. The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to inv...

    Authors: Anne Kupczok and Jonathan P Bollback

    Citation: BMC Evolutionary Biology 2013 13:54

    Content type: Methodology article

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  19. There has been a considerable increase in studies investigating rates of diversification and character evolution, with one of the promising techniques being the BiSSE method (binary state speciation and extinc...

    Authors: Matthew P Davis, Peter E Midford and Wayne Maddison

    Citation: BMC Evolutionary Biology 2013 13:38

    Content type: Research article

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  20. Bacteriophage (viruses that infect bacteria) are of key importance in ecological processes at scales from biofilms to biogeochemical cycles. Close interaction can lead to antagonistic coevolution of phage and ...

    Authors: Hywel TP Williams

    Citation: BMC Evolutionary Biology 2013 13:17

    Content type: Research article

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  21. Gene duplications play an important role in the evolution of functional protein diversity. Some models of duplicate gene evolution predict complex forms of paralog divergence; orthologous proteins may diverge ...

    Authors: Cameron J Weadick and Belinda SW Chang

    Citation: BMC Evolutionary Biology 2012 12:206

    Content type: Research article

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  22. Changes in gene regulatory networks drive the evolution of phenotypic diversity both within and between species. Rewiring of transcriptional networks is achieved either by changes to transcription factor bindi...

    Authors: Alexander J Stewart, Robert M Seymour, Andrew Pomiankowski and Joshua B Plotkin

    Citation: BMC Evolutionary Biology 2012 12:173

    Content type: Research article

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  23. Sex-ratio distorting parasites are of interest due to their effects upon host population dynamics and their potential to influence the evolution of host sex determination systems. In theory, the ability to dis...

    Authors: Joseph E Ironside, Judith E Smith, Melanie J Hatcher and Alison M Dunn

    Citation: BMC Evolutionary Biology 2011 11:370

    Content type: Research article

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  24. Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evol...

    Authors: Johan A Grahnen, Priyanka Nandakumar, Jan Kubelka and David A Liberles

    Citation: BMC Evolutionary Biology 2011 11:361

    Content type: Research article

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  25. The human mating system is characterized by bi-parental care and faithful monogamy is highly valued in most cultures. Marriage has evolved as a social institution and punishment for extra pair mating (EPM) or ...

    Authors: Milind G Watve, Anuja Damle, Bratati Ganguly, Anagha Kale and Neelesh Dahanukar

    Citation: BMC Evolutionary Biology 2011 11:345

    Content type: Research article

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  26. Homing endonucleases (HEases) are a large and diverse group of site-specific DNAases. They reside within self-splicing introns and inteins, and promote their horizontal dissemination. In recent years, HEases h...

    Authors: Adi Barzel, Uri Obolski, Johann Peter Gogarten, Martin Kupiec and Lilach Hadany

    Citation: BMC Evolutionary Biology 2011 11:324

    Content type: Research article

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  27. Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades....

    Authors: Daniele Silvestro, Jan Schnitzler and Georg Zizka

    Citation: BMC Evolutionary Biology 2011 11:311

    Content type: Methodology article

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  28. A well-known characteristic of multi-locus data is that each locus has its own phylogenetic history which may differ substantially from the overall phylogenetic history of the species. Although the possibility...

    Authors: David Gerard, H Lisle Gibbs and Laura Kubatko

    Citation: BMC Evolutionary Biology 2011 11:291

    Content type: Methodology article

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  29. The evolutionary success of Wolbachia bacteria, infections of which are widespread in invertebrates, is largely attributed to an ability to manipulate host reproduction without imposing substantial fitness costs....

    Authors: Philip R Crain, James W Mains, Eunho Suh, Yunxin Huang, Philip H Crowley and Stephen L Dobson

    Citation: BMC Evolutionary Biology 2011 11:290

    Content type: Research article

    Published on:

  30. The ability to predict the function and structure of complex molecular mechanisms underlying cellular behaviour is one of the main aims of systems biology. To achieve it, we need to understand the evolutionary...

    Authors: Orkun S Soyer and Richard A Goldstein

    Citation: BMC Evolutionary Biology 2011 11:240

    Content type: Research article

    Published on:

  31. Anopheles gambiae mates in flight at particular mating sites over specific landmarks known as swarm markers. The swarms are composed of males; females typically approach a swarm, and leave in copula. This mating ...

    Authors: Abdoulaye Diabaté, Alpha S Yaro, Adama Dao, Moussa Diallo, Diana L Huestis and Tovi Lehmann

    Citation: BMC Evolutionary Biology 2011 11:184

    Content type: Research article

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  32. One of the classical questions in evolutionary biology is how evolutionary processes are coupled at the gene and species level. With this motivation, we compare the topological properties (mainly the depth sca...

    Authors: Alejandro Herrada, Víctor M Eguíluz, Emilio Hernández-García and Carlos M Duarte

    Citation: BMC Evolutionary Biology 2011 11:155

    Content type: Research article

    Published on:

  33. Accurate modelling of substitution processes in protein-coding sequences is often hampered by the computational burdens associated with full codon models. Lately, codon partition models have been proposed as a...

    Authors: Guy Baele, Yves Van de Peer and Stijn Vansteelandt

    Citation: BMC Evolutionary Biology 2011 11:145

    Content type: Research article

    Published on:

  34. Hepatitis C virus (HCV) is a rapidly-evolving RNA virus that establishes chronic infections in humans. Despite the virus' public health importance and a wealth of sequence data, basic aspects of HCV molecular ...

    Authors: Rebecca R Gray, Joe Parker, Philippe Lemey, Marco Salemi, Aris Katzourakis and Oliver G Pybus

    Citation: BMC Evolutionary Biology 2011 11:131

    Content type: Research article

    Published on:

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