Deliverables list

• D1.1. Database of sequence alignments for phylogeny reconstruction
• D1.2. Database of hypervariable neutral microsatellite loci for all the macrophyte (seagrass and algae) species and populations considered. Development of TAG loci for Z. noltii and Fucus spp
• D1.3. Web-based database containing network phylogenies and genetic diversity networks
• D2.1. Software toolbox v1.0
• D2.2. Report on correlation methods
• D2.3. Report on community detection methods
• D2.4. Software toolbox v2.0
• D3.1. Report on population network structure obtained from computer simulations
• D3.2. Computer algorithms modeling reticulate evolution
• D4.1. Report on intrapopulation relationships obtained by network methods for several species sampled according to standarized schemes
• D4.2. Report on compared biogeographic relationships in various species sampled according to standarized scheme and in similar geographic localities
• D5.1. Report on allometric scaling on phylogenetic trees
• D5.2. Report on network phylogenies and their properties
• D6.1. Communication lists and project website
• D6.2. Project meetings
• D6.3. Reports to the Commision
• D6.4. Final Plan for using and disseminating knowledge

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Publications

• A sequential algorithm for fast clique percolation. J.M. Kumpula, M. Kivelä, K. Kaski, and J. Saramäki
  Physical Review E 78, 026109 (2008), also at arXiv:0805.1449
  In complex network research clique percolation, introduced by Palla et al., is a deterministic
  community detectio ...
  [... more]
• An Expressed Sequence Tag (EST) Analysis of the Intertidal Brown Seaweeds Fucus serratus (L.) and F. vesiculosus (L.) (Heterokontophyta, Phaeophyceae) in Response to Abiotic Stressors. Pearson GA, Hoarau G, Lago-Leston A, Coyer JA, Kube M, Henckel K, Serrăo EA, Corre E, Stam WT, Olsen JL
  Marine Biotechnology, in press (2010)
  Expressed sequence tags (EST) responsive to abiotic stressors were studied in two Fucus species. From over 12000 EST f ...
  [... more]
• Critical behavior in an evolutionary Ultimatum Game with social structure. Eguíluz, Víctor M.; Tessone, Claudio J.
  Advances in complex systems 12, 221-232 (2009)
    Experimental studies have shown the ubiquity of altruistic behavior in human societies. The social structure is a fu ...
  [... more]
• Detecting modules in dense weighted networks with the Potts method. T. Heimo, J.M. Kumpula, K. Kaski, and J. Saramäki
  Journal of Statistical Mechanics, P08007 (2008), also at arXiv: 0804.3457
  We address the problem of multiresolution module detection in dense
  weighted networks, where the modular structur ...
  [... more]
• Differentiating hybridizing species in the Fucus complex. Billard E, Serrăo EA, Pearson GP, Destombe C, Valero M
  Marine Ecology Progress Series, in press.

  Intertidal rocky shores provide classical examples of hab ...

  [... more]
• Evolutionary and Ecological Trees and Networks. E. Hernandez-Garcia, E.A. Herrada, A.F. Rozenfeld, C.J.Tessone, V.M. Eguiluz, C.M. Duarte, S. Arnaud-Haond, E. Serrao
  Nonequilibrium Statistical Mechanics and Nonlinear Physics, ed. by O. Descalzi, O.A. Rosso and H.A. Larrondo, AIP Conference Proceedings Volume 913, American Institute of Physics (New York, 2007), pp. 78-83
  Evolutionary relationships between species are usually represented in phylogenies, i.e. evolutionary trees, which are ...
  [... more]
• FRANz: Reconstruction of wild multi-generation pedigrees. Markus Riester, Peter F. Stadler, Konstantin Klemm
  Bioinformatics 25:2134-2139 (2009)
  We present a software package for pedigree reconstruction in natural populations using co-dominant genom ...
  [... more]
• Habitat continuity and geographic distance predict population genetic differentiation in giant kelp. Alberto F, Raimondi PT, Reed DC, Coelho NC, Leblois R, Whitmer A, Serrăo EA
  Ecology 91 (2010), pp. 49-56

  Isolation by di ...

  [... more]
• Highly polymorphic microsatellite loci for the Parsley frog (Pelodytes punctatus). van de Vliet MS, Diekmann OE, Serrăo ETA, Beja P
  Conservation Genetics, 10:665-668 (2009)
  This paper describes the development of microsatellite markers in a frog species (Pelodytes punctatus) from a temporar ...
  [... more]
• Highly polymorphic microsatellite loci for the western spadefood toad, Pelobates cultripes. van de Vliet MS, Diekmann OE, Serrăo ETA
  Conservation Genetics 10: 993-996 (2009)
  This paper described the development of microsatellite loci for the spadefood toad Pelobates cultripes, from a tempora ...
  [... more]
• Highly polymorphic microsatellite markers for the black striped pipefish, Syngnathus abaster. . Diekmann OE, Gouveia L, Serrăo EA, Van de Vliet MS (2009)
  Molecular Ecology Resources 9(6): 1460-1466.
  This paper describes the development of microsatellite markers in the pipefish Syngnathus abaster from seagrass meadow ...
  [... more]
• Highly polymorphic microsatellite markers for the short-snouted seahorse (Hippocampus hippocampus), . van de Vliet MS, Diekmann OE, Serrăo ETA (2009)
  Conservation Genetics Resources 1, 93-96 (2009)
  Species of the family Syngnathidae are increasingly being investigated for conservation purposes but also for mating ...
  [... more]
• Implications of mating system for genetic diversity of sister algal species: Fucus spiralis and Fucus vesiculosus . Perrin C, Daguin C, Van de Vliet M, Engel CR, Pearson GA, Serrăo EA
  European Journal of Phycology 42 (2007) , pp. 219-230

  The implications of mating s ...

  [... more]
• Isolation of highly polymorphic microsatellite loci for a species with a large genome size: Sharp-ribbed Salamander (Pleurodeles waltl).. van de Vliet MS, Diekmann OE, Serrăo EA, Beja P
  Molecular Ecology Resources 9: 425-428 (2009)
  This paper described the development of microsatellite loci for the sharp-ribbed salamander Pleurodeles waltl, from a ...
  [... more]
• Limited resolution and multiresolution methods in complex network community detection. J. Kumpula, J. Saramäki, K. Kaski, and J. Kertész
  Fluct. Noise Lett. 7, L209 (2007)
  Detecting community structure in real-world networks is a challenging problem. Recently,
  it has been shown that the ...
  [... more]
• Microsatellite markers for the giant kelp Macrocystis pyrifera. Alberto F, Whitmer A, Coelho A, Zippay M, Varela-Alvarez E, Raimondi PT, Reed D, Serrăo EA.
  Conservation Genetics. 10:1915-1917 (2009)

  We report the isolation and characte ...

  [... more]
• Network analysis identifies weak and strong links in a metapopulation system. Alejandro F. Rozenfeld, Sophie Arnaud-Haond, Emilio Hernández-García, Víctor M. Eguíluz, Ester A. Serrăo and Carlos M. Duarte
  Proceedings of the National Academy of Sciences of the USA (PNAS) 105, 18824-18829 (2008)
  The identification of key populations for conservation or eradication is a major challenge in population ecology, par ...
  [... more]
• Simple models for scaling in phylogenetic trees. Hernandez-Garcia, Emilio; Tugrul, Murat; Herrada, E. Alejandro; Eguíluz, V.M.; Klemm, Konstantin
  to appear in International Journal of Bifurcation and Chaos (IJBC)
  Many processes and models produce trees with depth scaling logarithmically with the number of leaves. Phylogenetic tr ...
  [... more]
• Universal scaling in the branching of the Tree of Life. E. Alejandro Herrada, Claudio J. Tessone, Konstantin Klemm, Víctor M. Eguíluz, Emilio Hernández-García, Carlos M. Duarte
  PLoS ONE 3, e2757 (2008)
  Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The T ...
  [... more]

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Data

• Cymodocea nodosa microsatellite data . Alberto F, Massa S, Manent P, Diaz-Almela E, Arnaud-Haond S, Duarte CM, Serrăo EA
  Journal of Biogeography 35, 1279 – 1294 (2008).

  Th ...

  [... more]
• D1.2. Database of hypervariable neutral microsatellite loci for all the macrophyte (seagrass and algae) species and populations considered. Development of TAG loci for Z. noltii and Fucus spp. CCMAR, CSIC, IFREMER (associated)
    This deliverable consists on datafiles for microsatellite and TAG loci developed for several seagrass and algae, nam ...
  [... more]
• D1.3. Web-based database containing network phylogenies and genetic diversity networks. CCMAR and IFISC/IMEDEA-UIB

  The EDEN project has developed novel methodologies to characterize genetic relationships among biological individ ...

  [... more]
• Fucus vesiculosus SNP genotyping. . Canovas F, Mota C, Pearson G
  manuscript in preparation

  [... more]
• Posidonia microsatellite data . Arnaud-Haond S, Migliaccio M, Diaz-Almela E, Teixeira S, van de Vliet MS, Alberto F, Procaccini G, Duarte CM, Serrăo EA
  Vicariance patterns in the Mediterranean sea: East-West cleavage and low dispersal in the endemic seagrass Posidonia oceanica. Journal of Biogeography, 34, 963-976 (2007)

  [... more]
• Zostera marina microsatellites. Arnaud-Haond et al.
  manuscript in preparation

  Th ...

  [... more]
• Zostera noltii EST data. Massa S, Pearson GA, Serrao EA, Arnaud-Haond S
  manuscript in preparation

  The dwarf seagrass Zostera noltii do ...

  [... more]

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Software

• D2.4. Software toolbox v2.0. Mikko Kivelä, Sophie Arnaud-Haond, Jari Saramäki
  This package contains a Windows-ready executable for the EDEN Network analysis toolbox (EDENetwork). The current versi ...
  [... more]
• D3.2. Computer algorithms modeling reticulate evolution. Markus Riester

  The deliverable is a software package for pedigree reconstruction in natural populations using co-dominant genom ...

  [... more]
• FRANz: Pedigree reconstruction. Markus Riester

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Presentations at conferences, talks, ...

• Application de la théorie des réseaux en biologie évolutive (Applications of network theory in evolutionary ecology). Arnaud-Haond, S.
  Communication at the Séminaire ARBRE, Rennes, 23 March 2009. ...
  [... more]
• Can age explain macroevolution? . Tugrul, Murat; Keller-Schmidt, Stephanie; Eguíluz, Víctor M.; Hernández-García; Emilio; Klemm, Konstantin
  Poster presented at the International Workshop on 150 Years after Darwin: From Molecular Evolution to Language. Trends ...
  [... more]
• Ecological Diversity and Evolutionary Networks: The EDEN project. The Eden team
  Showcase of European Complexity Science Projects (CRP Forum). Dresden, Germany, 6 October 2007.
  Presentation of the EDEN project performed by Emilio Hernandez-Garcia at the Showcase of European Complexity Science P ...
  [... more]
• Evolution of lineages in the agent of Chagas disease, Trypanosoma cruzii, described with networks. Arnaud-Haond S, Rozenfeld AF.
  Talk given by Sophie Arnaud-Haond at IRD (Montpellier, France), 31th July 2007. ...
  [... more]
• From genes to species: Universal Scaling?. E. Alejandro Herrada, Claudio Juan Tessone, Konstantin Klemm, Víctor M. Eguíluz, Emilio HernándezGarcía, Carlos M. Duarte
  Talk by Alejandro Herrada at the Workshop on Dynamics and Evolution of Biological and Social Networks. Palma de Mallorc ...
  [... more]
• Genetic Similarity Networks in Populations and in Metapopulations. Emilio Hernandez-Garcia
  Talk by Emilio Hernández García at the Workshop on Dynamics and Evolution of Biological and Social Networks. Palma de Ma ...
  [... more]
• Genetic similarity networks: Weak and strong links in populations and in metapopulations. E. Hernández-García, A. F. Rozenfeld, S. Arnaud-Haond, V.M. Eguíluz, E. Serrăo and C. M. Duarte
  Poster and short talk presented by Emilio Hernández-García at the European Conference on Complex Systems (ECCS07). Dresd ...
  [... more]
• Metapopulation networks of the seagrass Posidonia oceanica.. Arnaud-Haond S, Rozenfeld AF, Hernández-García E, Serrao E.A., Duarte C.M.
  Talk given by Sophie Arnaud-Haond at MBARI, Monterrey (California, USA), 4th December 2007. ...
  [... more]
• Network analysis in population genetics, and example on preliminary analysis of various marine organisms (Zostera marina, Fucus sp., Laminaria digitata, Undaria sp.). Arnaud-Haond S., Moalic Y., Serrao E.A., Rozenfeld AF, Hernández-García E, Duarte C.M.
  Talk given by Arnaud-Haond at the Responsive Mode program Genetic Biodiversity in the Marine realm (RMP GBIRM), of the ...
  [... more]
• Networks of Genetic Similarity in Populations and in Metapopulations. Emilio Hernández-García Alejandro F. Rozenfeld, Sophie Arnaud-Haond, Víctor M. Eguíluz, Ester Serrăo and Carlos M. Duarte
  Poster presented at the International Conference on Modelling and Computation on Complex Networks and Related Topics, N ...
  [... more]
• Pedigree Reconstruction with FRANz. Markus Riester
  Talk about Pedigree Reconstruction in clonal plant populations at the "Doktoranden-Kolloquium",  BBZ Leipzig ...
  [... more]
• Population genetics networks: gene flow, source and sinks in the metapopulation system of the seagrass Posidonia oceanica. Arnaud-Haond S, Rozenfeld AF, Hernández-García E, Eguilúz, VM, Serrao E.A., Duarte C.M.
  Talk given by Sophie Arnaud-Haond at the ASLO aquatic science meeting, Santa Fe (New Mexico, USA), 4-9 February 2007. ...
  [... more]
• Prospects for network analysis in biogeography: an example on deep-sea vents. Moalic, Y., D. Desbruyčres, A. Rozenfeld, C. Bachraty, and S. Arnaud-Haond.
  Poster presented at the World conference on Marine Biodiversity, Valencia Spain 11-15 November 2008. ...
  [... more]
• Shapes of Phylogenetic Trees: Age Model and Likelihoods. Keller-Schmidt, Stephanie; Tugrul, Murat; Eguíluz, Víctor M.; Hernández-García; Emilio; Klemm, Konstantin
  Poster presented at the International Workshop on 150 Years after Darwin: From Molecular Evolution to Language. Trends ...
  [... more]
• Universal branching in phylogenetic trees. Emilio Hernandez-Garcia
  Invited talk at the International Conference on Modelling and Computation on Complex Networks and Related Topics, Net-W ...
  [... more]
• Universal scaling in phylogenetic branching. E. A. Herrada, C.J. Tessone, V. M. Eguíluz, E. Hernández-García and C. M. Duarte
  Poster and short talk presented by Emilio Hernández-García at the European Conference on Complex Systems (ECCS07). Dres ...
  [... more]
• Use of network tools to address the comparative biogeography of marine organisms. Arnaud-Haond S., Duarte C.M., Serrao E.A.
  Talk given by Sophie Arnaud-Haond at the Responsive Mode program Genetic Biodiversity in the Marine realm (RMP GBIRM), o ...
  [... more]

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Dissemination

• Press relase commenting on the three NEST projects , including EDEN, in which the UIB is involved (in spanish).
  El Mundo - Baleares, 15 september 2006
  The local newspaper El Mundo - Baleares comments (in Spanish) on the particip ...
  [... more]
• Press releases on the paper ``Network analysis identifies weak and strong links in a metapopulation system´´, in PNAS, 2008 . several media
  Physicists and biologists from IFISC, IMEDEA, CCMAR and IFREMER highlight the importance of balearic populations of P ...
  [... more]

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Other (Reports, Project meetings, ...)

• D2.2. Report on correlation methods. Victor M. Eguiluz
  In this report we review recent advances in the analysis of fully connected networks with weighted links. The weight o ...
  [... more]
• D2.3. Report on community detection methods. TKK
  This report comprises publications related to identification of communities, produced within the EDEN project. Here, t ...
  [... more]
• D3.1. Report on population network structure obtained from computer simulations. Tomas Sintes
  The purpose of this deliverable is twofold: i) Develop a numerical model to study the space occupation and growth of c ...
  [... more]
• D4.1. Report on intrapopulation relationships obtained by network methods for several species sampled according to standarized schemes. CCMAR and IFISC/IMEDEA-UIB
   

  [... more]
• D4.2. Report on compared biogeographic relationships in various species sampled according to standarized scheme and in similar geographic localities.
   

  [... more]
• D5.1. Report on allometric scaling on phylogenetic trees. Palma and Leipzig
  Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The ...
  [... more]
• D5.2. Report on network phylogenies and their properties.
    The report consists of four publications advancing methods for network phylogeny reconstructions and demonstrating ...
  [... more]
• D6.1. Communication lists and project website. IMEDEA-UIB
  The EDEN web site is available at http://ifisc.uib.es/EDEN . The private part of the web site contains communication l ...
  [... more]
• D6.2. Project meetings. The EDEN team
  EDEN meetings are planned to take place every six months. They provide the opportunity for EDEN partners to interchang ...
  [... more]

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