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Research Infrastructures offer capacity to address scientific questions never attempted before: Are all taxa equal?

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Abstract

Research Infrastructures (RIs) are facilities, resources and services used by the scientific community to conduct research and foster innovation. LifeWatch ERIC has developed various virtual research environments, which include many virtual laboratories (vLabs) offering high computational capacity and comprehensive collaborative platforms that supporting the needs of digital biodiversity science. Over its 250 years of history, the taxonomic research community has developed a system for describing, classifying and naming taxa across multiple levels. For the marine biota, taxonomic information is organized and made publicly available through the World Register of Marine Species (WoRMS) that records more than 250,000 described valid species. Although scientists tend to assign an equal status (in terms of contribution to overall diversity) to each taxon used in taxonomy, biogeography, ecology and biodiversity, the question “ are all taxa equal? ” has never been tested at a global scale. We present evidence that this question can be addressed by applying relatedness indices (Taxonomic Distinctness) over the entire WoRMS metazoan tree. The RvLab, developed by the LifeWatchGreece RI, operating on a high-performance computer cluster, has been used to meet the high computational demands required for such an analysis at a global scale.
Research Infrastructures offer capacity to address scientific
questions never attempted before: Are all taxa equal?
Research Infrastructures (RIs) are facilities, resources and services used by the scientific
community to conduct research and foster innovation. LifeWatch ERIC has developed
various virtual research environments, which include many virtual laboratories (vLabs)
offering high computational capacity and comprehensive collaborative platforms that
supporting the needs of digital biodiversity science. Over its 250 years of history, the
taxonomic research community has developed a system for describing, classifying and
naming taxa across multiple levels. For the marine biota, taxonomic information is
organized and made publicly available through the World Register of Marine Species
(WoRMS) that records more than 250,000 described valid species. Although scientists tend
to assign an equal status (in terms of contribution to overall diversity) to each taxon used
in taxonomy, biogeography, ecology and biodiversity, the question “are all taxa equal?
has never been tested at a global scale. We present evidence that this question can be
addressed by applying relatedness indices (Taxonomic Distinctness) over the entire
WoRMS metazoan tree. The RvLab, developed by the LifeWatchGreece RI, operating on a
high-performance computer cluster, has been used to meet the high computational
demands required for such an analysis at a global scale.
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
Research Infrastructures offer capacity to address scientific questions never attempted
before: Are all taxa equal?
Christos ARVANITIDIS1, Richard M WARWICK2, Paul J SOMERFIELD3, Christina PAVLOUDI4,
Evangelos PAFILIS5, Anastassis OULAS6, Giorgos CHATZIGEORGIOU7, Vasilis
GEROVASILEIOU8, Theodoros PATKOS9, Nicolas BAILLY10, Francisco HERNANDEZ11, Bart
VANHOORNE12, Leen VANDEPITTE13, Ward APPELTANS14, Robert ADLARD15, Peter
ADRIAENS16, Ahn KEE-JEONG17, Ahyong SHANE18, Akkari NESRINE19, Belinda ALVAREZ20,
Gary ANDERSON21, Angel MARTIN22, Claudia ARANGO23, Tom ARTOIS24, Stephen
ATKINSON25, Ruud BANK26, Anthony D Barber27, Joao Paulo BARBOSA28, Ilse BARTSCH29,
Denise BELLAN-SANTINI30, Jimmy BERNOT31, Annalisa BERTA32, Rüdiger BIELER33, Isabel
BLASCO-COSTA34, Magda BŁAŻEWICZ35, Phil BOCK36, Ruth BÖTTGER-SCHNACK37, Philippe
BOUCHET38, Nicole BOURY-ESNAULT39, Geoff BOXSHALL40, Christopher B BOYKO41, Simone
NUNES BRANDÃO42, Rod BRAY43, Niel L BRUCE44, Stephen CAIRNS45,Tania N CAMPINAS
BEZERRA46, Paco CÁRDENAS47, Benny KK Chan48,Tin-Yam CHAN49, Lanna CHENG50, Morgan
CHURCHILL51, Charles O COLEMAN52, Allen G COLLINS53, Laure CORBARI54, Ralf
CORDEIRO55, Astrid CORNILS56, Keith A CRANDALL57, Thomas CRIBB58, Jean-Loup
d'HONDT59, Meg DALY60, Mikhail DANELIYA61, Jean-Claude DAUVIN62, Peter DAVIE63, Claude
DE BROYER64, Sammy DE GRAVE65, Valentin DE MAZANCOURT66, Nicole DE VOOGD67,
Peter DECKER68, Danielle DEFAYE69, Henk Dijkstra70, Martin DOHRMANN71, Daryl DOMNING72,
Rachel DOWNEY73, Inna DRAPUN74, Ursula EISENDLE-FLÖCKNER75, John EPLER76, Christine
EWERS-SAUCEDO77, Marien FABER78, Diego FIGUEROA79, Julian FINN80, Cene FIŠER81,
Gustavo FONSECA82, Ewan FORDYCE83, William FOSTER84, Frank J HOWARD85, Charles
FRANSEN86, Hidetaka FURUYA87, Horia GALEA88, Oscar GARCIA-ALVAREZ89, Rade GARIC90,
Rebeca GASCA91, Santiago GAVIRIA-MELO92, Sarah GERKEN93, Hendrik GHEERARDYN94,
David GIBSON95, João GIL96, Arjan GITTENBERGER97, Chris GLASBY98, Serge GOFAS99,
Samuel E GÓMEZ-NOGUERA100, David GONZÁLEZ-SOLÍS101, Dennis GORDON102, Michal
GRABOWSKI103, Cinzia GRAVILI104, José M GUERRA-GARCÍA105, Roberto GUIDETTI106, Katja
GUILINI107, Kerry A HADFIELD108, Eduardo HAJDU109, Jacob HALLERMANN110, Ed
HENDRYCKS111, Bachiller HERRERA112, Ju-Shey HO113, Jens HØEG114, Bert HOEKSEMA115,
Oleksandr HOLOVACHOV116, Matthew D HOOGE117, John HOOPER118, Tammy HORTON119,
Roland HOUART120, Lauren HUGHES121, Matús HYŽNÝ122, Luiz IF MORETTI123, Tohru ISETO124,
Viatcheslav N Ivanenko125, Gerhard JARMS126, Damià JAUME127, Krzysztof JAZDZEWSKI128,
Ivana KARANOVIC129, Young-Hyo KIM130, Rachael KING131, Michelle KLAUTAU132, Jürgen
KOLB133, Alexey KOTOV134, Traudl KRAPP-SCHICKEL135, Antonina KREMENETSKAIA136,
Reinhardt KRISTENSEN137, Andreas KROH138, Sven KULLANDER139, Rafael LA PERNA140,
Gretchen LAMBERT141, Sara LECROY142, Daniel LEDUC143, Rafael LEMAITRE144, Anne-Nina
LÖRZ145, Jim LOWRY146, Enrique MACPHERSON147, Larry MADIN148, Christopher MAH149,
Tomasz MAMOS150, Renata MANCONI151, Gill MAPSTONE152, Paul E MAREK153, Bruce
Marshall154, David J MARSHALL155, Patrick MARTIN156, Sandra MCINNES157, Jan MEES158, Tõnu
MEIDLA159, Kenneth MELAND160, Kelly MERRIN161, Charles MESSING162, Dmitry MILJUTIN163,
Claudia MILLS164, Vadim MOKIEVSKY165, Tina MOLODTSOVA166, Françoise MONNIOT167, Rich
MOOI168, André C MORANDINI169, Rosana MOREIRA DA ROCHA170, Fabio MORETZSOHN171,
Jonas MORTELMANS172, Jeanne MORTIMER173, Luigi MUSCO174, Thomas A NEUBAUER175,
Eike NEUBERT176, Peter NG NEUHAUS177, Anh D NGUYEN178, Claus NIELSEN179, Teruaki
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
NISHIKAWA180, Jon NORENBURG181, Tim O'HARA182, Hisayo OKAHASHI183, Dennis
OPRESKO184, Masayuki OSAWA185, Yuzo OTA186, Gustav PAULAY187, Hannelore PAXTON188,
Vincent PERRIER189, William PERRIN190, Iorgu PETRESCU191, Bernard PICTON192, John F
PILGER193, Andrzej PISERA194, Dan POLHEMUS195, Gary POORE196, James D REIMER197,
Hans REIP198, Michael REUSCHER199, John W REYNOLDS200, Pilar RIOS LOPEZ201, Marc
RIUS202, Gary ROSENBERG203, Klaus RÜTZLER204, Alexander RZHAVSKY205, José SAIZ-
SALINAS206, Sandro SANTOS207, André F SARTORI208, Aya SATOH209, Heinrich SCHATZ210,
Bernd SCHIERWATER211, Andreas SCHMIDT-RHAESA212, Simon SCHNEIDER213, Christine
SCHÖNBERG214, André R SENNA215, Cristiana SEREJO216, Shabuddin SHAIK217, Shokoofeh
SHAMSI218, Jyotsna SHARMA219, William A SHEAR220, Noa SHENKAR221, Andrew SHINN222,
Megan SHORT223, Jacek SICINSKI224, Volker SIEGEL225, Petra SIERWALD226, Elizabeth
SIMMONS227, Frederic SINNIGER228, Duncan SIVELL229, Boris SKET230, Harry SMIT231, Nicole
SMOL232, Jesser F SOUZA-FILHO233, Jörg SPELDA234, Sérgio N STAMPAR235, Eric STIENEN236,
Pavel STOEV237, Sabine STÖHR238, Malin STRAND239, Eduardo SUÁREZ-MORALES240, Mindi
SUMMERS241, Billie J SWALLA242, Stefano TAITI243, Masaatsu TANAKA244, Anne H
TANDBERG245, Danny TANG246, Mark TASKER247, John TAYLOR248, Alexei TCHESUNOV249,
Harry ten HOVE250, Jan J ter POORTEN251, Jim THOMAS252, Erik V THUESEN253, Mike
THURSTON254, Ben THUY255, Juan T TIMI256, Antonio TODARO257, Xavier TURON258, Seth
TYLER259, Peter UETZ260, Sergiy UTEVSKY261, Jean VACELET262, Wim VADER263, Risto
VÄINÖLÄ264, Sancia ET van der MEIJ265, Ton van HAAREN266, Rob van SOEST267, Robert Van
SYOC268, Virág VENEKEY269, Ronald VONK270, Chris VOS271, Genefor WALKER-SMITH 272,
Chad T WALTER273, Les WATLING274, Matthew WAYLAND275, Thomas WESENER276,
Christopher WHIPPS277, Kristine WHITE278, Gary WILLIAMS279, Robin WILSON280, Nigel
WYATT282, Moriaki YASUHARA283, Joana ZANOL284, Wolfgang ZEIDLER285
1Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; arvanitidis@hcmr.gr
2Plymouth Marine Laboratory (PML), Plymouth, Devon, UK; RMW@pml.ac.uk
3Plymouth Marine Laboratory (PML), Plymouth, Devon, UK; PJSO@pml.ac.uk
4Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; cpavloud@hcmr.gr
5Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; pafilis@hcmr.gr
6Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; anastasioso@cing.ac.cy
7Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; chatzigeorgiou@hcmr.gr
8Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; vgerovas@hcmr.gr
9Institute of Computer Science (ICS), Foundation for Research and Technology - Hellas
(FORTH), Science and Technology Park of Crete, Vassilika Vouton, Heraklion, Greece;
patkos@ics.forth.gr
10Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; nbailly@hcmr.gr
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
11Flanders Marine Institute (VLIZ) Ostend, Belgium; tjess@vliz.be
12Flanders Marine Institute (VLIZ) Ostend, Belgium; bart.vanhoorne@vliz.be
13Flanders Marine Institute (VLIZ) Ostend, Belgium; leen.vandepitte@vliz.be
14Intergovernmental Oceanographic Commission of UNESCO, IOC Project Office for IODE,
Oostende, Belgium; w.appeltans@unesco.org
15Queensland Museum, Centre for Biodiversity, Australia; robert.adlard@qm.qld.gov.au
16Biology Department, University of Ghent, Belgium; p_adriaens@yahoo.com
17Chungnam National University, Department of Biology, Southern Korea; kjahn@cnu.ac.kr
18Australian Museum, Marine Invertebrates, Australia; Shane.Ahyong@austmus.gov.au
19Natural History Museum Vienna, Austria; nesrine.akkari@nhm-wien.ac.at
20Museum and Art Galleries of the Northern Territory, Australia; Belinda.glasby@gmail.com
21The University of Southern Mississippi; Department of Biological Sciences, USA;
gary.anderson@usm.edu
22Natural History Museum, London, UK; mvangel37@gmail.com
23Queensland Museum, Australia; claudia.arango@qm.qld.gov.au
24Hasselt University, Centrum voor Milieukunde; Research group Zoology: Biodiversity and
Toxicology, Belgium; tom.artois@uhasselt.be
25Oregon State University, Department of Microbiology, USA; atkinsos@science.oregonstate.edu
26Rijksuniversiteit Groningen, Faculty of Medical Sciences, Netherlands; ruud.bank@quicknet.nl
27British Myriapod and Isopod Group, Rathgar, Exeter Road, Ivybridge, Devon, UK;
abarber159@btinternet.com
28University of São Paulo, Instituto de Biociências, Brasil; jpppbarbosa@gmail.com
29Senckenberg Nature Research Society, Research Institute and Natural History Museum,
Germany; ibartsch@senckenberg.de
30Centre National de la Recherche Scientifique, Mediterranean Institute of marine and terrestrial
Biodiversity and Ecology, France; denise.bellan@imbe.fr
31Natural History Museum, Department of Life Sciences, UK; jbernot@gwmail.gwu.edu
32San Diego State University, Department of Biology, USA; aberta@mail.sdsu.edu
33Field Museum of Natural History, USA; rbieler@fieldmuseum.org
34Natural History Museum of Geneva, Geneva, Switzerland; isa.blasco.costa@gmail.com
35University of Lodz, Dept. Invertebrate Zoology & Hydrobiology, Laboratory of Polar Biology and
Oceanobiology, Poland; magdab@biol.uni.lodz.pl
36Museum Victoria, Melbourne, Australia; philbock1@gmail.com
37Helmholtz Centre for Ocean Research, Kiel, Germany; dschnack@geomar.de
38Muséum National d'Histoire Naturelle, Department Systematics and Evolution, France;
pbouchet@mnhn.fr
39Centre National de la Recherche Scientifique, Mediterranean Institute of marine and terrestrial
Biodiversity and Ecology, France; nicole.boury-esnault@orange.fr
40Natural History Museum, Department of Zoology, UK; g.boxshall@nhm.ac.uk
41American Museum of Natural History, Division of Invertebrate Zoology, USA;
cboyko@amnh.org
42Universidade Federal do Rio Grande do Norte, Centro de Ciências Exatas e da Terra,
Laboratório de Geologia e Geofísica Marinha e Monitoramento Ambiental, Natal, Brasil;
brandao.sn.100@gmail.com
43Natural History Museum, Department of Zoology, UK; r.bray@nhm.ac.uk
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44Queensland Museum, Museum of Tropical Queensland, Australia; niel.bruce@qm.qld.gov.au
45Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, USA; CAIRNSS@si.edu
46Ghent University, Faculty of Sciences, Biology Department, Marine Biology Section, Belgium;
tania.campinasbezerra@ugent.be
47Uppsala University, Department of Medicinal Chemistry, Division of Pharmacognosy, Sweden;
paco.cardenas@fkog.uu.se
48Academia Sinica, Biodiversity Research Centre, Taiwan; chankk@gate.sinica.edu.tw
49National Taiwan Ocean University, Institute of Marine Biology, Taiwan;
tychan@mail.ntou.edu.tw
50University of California, San Diego, Scripps Institution of Oceanography, USA;
lcheng@ucsd.edu
51University of Wyoming, Department of Geology and Geophysics, USA;
morgan.churchill@gmail.com
52Leibniz Institute for Evolution and Biodiversity, Museum für Naturkunde, Germany;
oliver.coleman@mfn-berlin.de
53Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, USA; COLLINSA@si.edu
54National Natural History Museum Paris, France; corbari@mnhn.fr
55Universidade Federal de Pernambuco, Brasil; ralfts@gmail.com
56Alfred Wegener Institute for Polar and Marine Research, Germany; Astrid.Cornils@awi.de
57George Washington University, Computational Biology Institute, USA; kcrandall@gwu.edu
58The University of Queensland, Centre for Marine Studies, Australia; T.Cribb@uq.edu.au
59Muséum National d'Histoire Naturelle, Département Milieux et Peuplements Aquatiques,
France; dhondt@mnhn.fr
60Ohio State University, Department of Evolution, Ecology and Organismal Biology, USA;
daly.66@osu.edu
61University of Helsinki, Finland; mdaneliya@gmail.com
62Normandie Univ, UNICAEN, Laboratoire Morphodynamique Continentale et Côtière, France;
jean-claude.dauvin@unicaen.fr
63Queensland Museum, Centre for Biodiversity, Australia; peter.davie@qm.qld.gov.au
64Belgian Academies of Sciences, Belgian National Committee on Antarctic Research, Belgium;
claude.debroyer@naturalsciences.be
65University of Oxford, Museum of Natural History, UK; sammy.degrave@oum.ox.ac.uk
66Muséum National d'Histoire Naturelle, Département Milieux et Peuplements Aquatiques,
France; valentin.demazancourt@laposte.net
67Naturalis Biodiversity Center, Netherlands; Nicole.deVoogd@naturalis.nl
68Senckenberg Nature Research Society, Germany; Peter.Decker@senckenberg.de
69National Natural History Museum Paris, France; ddefaye@mnhn.fr
70Naturalis Biodiversity Center, Department of Marine Zoology, Netherlands;
h.h.dijkstra@planet.nl
71Ludwig Maximilians University Munich, Faculty of Geosciences, Department of Earth and
Environmental Sciences, Paleontology and Geobiology, Germany; mdohrma@gmail.com
72Howard University, Department of Anatomy, Laboratory of Evolutionary Biology, USA;
ddomning@Howard.edu
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73Australia National University, Research School of Earth Sciences, Australia;
rachel.v.downey@gmail.com
74Russian Academy of Sciences, Russia; innadra@gmail.com
75Universität Salzburg, Austria; Ursula.Eisendle@sbg.ac.at
76WoRMS Editorial Board, Crawfordville, Florida, USA; johnepler3@comcast.net
77University of California, Davis, USA; ewers.christine@gmail.com
78WoRMS Editorial Board, Duivendrecht, Netherlands; marienfaber@hotmail.com
79University of Texas Rio Grande Valley, Department of Biology, USA; diego.figueroa@utrgv.edu
80Museum Victoria, Melbourne, Australia; jfinn@museum.vic.gov.au
81University of Ljubljana, Biotechnical Faculty, Department of Biology, Slovenia;
Cene.Fiser@bf.uni-lj.si
82Universidade Federal de São Paulo, Brasil; gfonseca.unifesp@gmail.com
83University of Otago, Department of Geology, New Zealand; ewan.fordyce@otago.ac.nz
84University of Cambridge, School of the Biological Sciences, Faculty of Biology, Department of
Zoology, UK; waf1@cam.ac.uk
85University of Florida, USA; jhfrank@ulf.edu
86Naturalis Biodiversity Center, Netherlands; charles.fransen@naturalis.nl
87Osaka University, Graduate School of Science and School of Science, Department of Biology,
Japan; hfuruya@bio.sci.osaka-u.ac.jp
88Hydrozoan Research Laboratory, Tourves, France; horia.galea@gmail.com
89University of Santiago de Compostela, Department of Zoology, Spain; ogarcia-
alvarez@edu.xunta.es
90University of Dubrovnik, Institute for Marine and Coastal Research, Dubrovnik, Croatia;
rade.garic@unidu.hr
91El Colegio de la Frontera Sur, Department of Aquatic Ecology, Chetumal, Mexico;
rgasca@ecosur.mx
92University of Vienna, Faculty of Life Sciences, Vienna Ecology Center, Department of
Limnology and Oceanography, Austria; santiago.gaviria@gmx.at
93University of Alaska Anchorage, Department of Biological Sciences, USA;
afsag@uaa.alaska.edu
94Hanyang University, Department of Life Sciences, Laboratory of Biodiversity, Seoul, Korea;
hendrik.gheerardyn@gmail.com
95Natural History Museum, Department of Zoology, UK; dig@nhm.ac.uk
96Consejo Superior de Investigaciones Científicas, Centre for Advanced Studies of Blanes,
Blanes, Spain; joaocfgil@gmail.com
97Naturalis Biodiversity Center, Department of Marine Zoology, Leiden, Netherlands;
gittenberger@yahoo.com
98Northern Territory Government, Natural Sciences, Museum & Art Gallery of the Northern
Territory, Darwin, Australia; chris.glasby@nt.gov.au
99University of Málaga, Faculty of Sciences, Departamento de Biología Animal, Malaga, Spain;
sgofas@uma.es
100Universidad Nacional Autonoma de Mexico, Instituto de Ciencias del Mar y Limnologia
Mazatlán, Mexico; samuelgomez@ola.icmyl.unam.mx
101El Colegio de la Frontera Sur, Department of Aquatic Ecology, Unidad Chetumal , Chetumal,
Mexico; dgonzale@ecosur.mx
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102National Institute of Water and Atmospheric Research, Wellington, New Zealand;
dennis.gordon@niwa.co.nz
103University of Lodz, Department of Invertebrate Zoology & Hydrobiology, Lodz, Poland;
michalg@biol.uni.lodz.pl
104University of Salento, Dipartimento di Scienze e Tecnologie Biologiche e Ambientali, National
Interuniversity Consortium For Marine Sciences, Laboratory of Zoology and Marine Biology,
Lecce, Italy; cinzia.gravili@unile.it
105University of Sevilla, Laboratorio di Biologia Marina, Seville, Spain; jmguerra@us.es
106University of Modena and Reggio Emilia, Department of Life Sciences, Modena, Italy;
roberto.guidetti@unimore.it
107Ghent University, Faculty of Sciences, Biology Department, Marine Biology Section, Ghent,
Belgium; katja.guilini@ugent.be
108North-West University, Department of Biological Sciences, Potchefstroom, South-Africa;
kerryh26@yahoo.com
109Universidade Federal do Rio de Janeiro, Museu Nacional, Rio de Janeiro, Brasil;
eduardo.hajdu@gmail.com
110University of Hamburg, Zoological Institute und Zoological Museum, Zoological Museum,
Hamburg, Germany; hallermann@zoologie.uni-hamburg.de
111Canadian Museum of Nature, Ottawa, Canada; EHENDRYCKS@mus-nature.ca
112Alfonso University of Alcalá, Department of Life Sciences, Madrid, Spain;
fosilete@gmail.com
113Department of Biological Sciences, California State University, Long Beach, USA;
hojushey@gmail.com
114University of Copenhagen, Biological Institute, Department of Cell Biology and Comparative
Zoology, Copenhagen, Denmark; jthoeg@bio.ku.dk
115Naturalis Biodiversity Center, Department of Marine Zoology, Leiden, Netherlands;
Bert.Hoeksema@naturalis.nl
116Swedish Museum of Natural History, Department of Zoology, Stockholm, Sweden;
holovachov@gmail.com
1176207 N Villard Avenue, Portland, USA; matt.hooge@gmail.com
118Queensland Museum, South Brisbane, Australia; john.hooper@qm.qld.gov.au
119University of Southampton, National Oceanography Centre, Ocean Biogeochemistry and
Ecosystems, Southampton, UK; tammy.horton@noc.ac.uk
120Royal Belgian Institute of Natural Sciences, Brussels, Belgium; roland.houart@skynet.be
121Natural History Museum, London; UK; l.hughes@nhm.ac.uk
122Comenius University in Bratislava, Department of geology and paleontology, Bratislava,
Slovakia; hyzny.matus@gmail.com
123Instituto Butantan, Laboratório de coleções zoológicas, São Paulo, Brasil; luiz-
moretti@hotmail.com
124Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan;
tohru_iseto@hotmail.com
125Lomonosov Moscow State University, Moscow, Russia; Ivanenko.slava@gmail.com
126University of Hamburg, Zoological Institute und Zoological Museum, Hamburg, Germany;
Gerhard.Jarms@zoologie.uni-hamburg.de
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127Universitat de les Illes Balears, Mediterranean Institute for Advanced Studies, Esporles,
Mallorca, Spain; damiajaume@imedea.uib-csic.es
128University of Lodz, Department of Invertebrate Zoology & Hydrobiology, Laboratory of Polar
Biology and Oceanobiology, Lodz, Poland; kryjaz@biol.uni.lodz.pl
129University of Hamburg, Zoological Institute und Zoological Museum, Zoological Museum,
Hamburg, Germany; ivana.karanovic@uni-hamburg.de
130Dankook University, Department of Life Sciences, Seoul, Southern Korea;
amphipod74@gmail.com
131South Australian Museum, Adelaide, Australia; Rachael.King@samuseum.sa.gov.au
132Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil; mklautau@gmail.com
133Massey University, Institute of Natural Sciences, Ecology and Conservation Group, Auckland,
New Zealand; kolbjuer@gmail.com
134Russian Academy of Sciences, A.N. Severtsov Institute of Ecology and Evolution, Moscow,
Russia; alexey-a-kotov@yandex.ru
135Zoologisches Forschungsinstitut und Museum Alexander Koenig, Bonn, Germany;
traudl.krapp@netcologne.de
136russian Academy of Sciences, P. P. Shirshov Institute of Oceanology, Moscow, Russia;
antoneene@gmail.com
137University of Copenhagen, Zoological Museum, Copenhagen, Denmark;
rmkristensen@snm.ku.dk
138Natural History Museum Vienna, Vienna, Austria; andreas.kroh@nhm-wien.ac.at
139Swedish Museum of Natural History, Stockholm, Sweden; sven.kullander@nrm.se
140University of Bari, Department of Earth Sciences, Bari, Italy; rafael.laperna@uniba.it
141University of Washington, Friday Harbor Laboratories, Friday Harbor, USA;
gretchen.lambert00@gmail.com
142The University of Southern Mississippi, Gulf Coast Research Laboratory, Ocean Springs,
USA; sara.lecroy@usm.edu
143National Institute of Water and Atmospheric Research, Wellington, New Zealand;
Daniel.Leduc@niwa.co.nz
144Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, Washington DC, USA; lemaitrr@si.edu
145National Institute of Water and Atmospheric Research, Wellington, New Zealand; Anne-
Nina.Loerz@t-online.de
146nstitute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine
Research (HCMR), Gouves, Heraklion, Crete, Greece; stephonyx@gmail.com
147Consejo Superior de Investigaciones Científicas, Centre for Advanced Studies of Blanes,
Blanes, Spain; macpherson@ceab.csic.es
148Woods Hole Oceanographic Institution, Woods Hole, USA; lmadin@whoi.edu
149Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, Washington DC, USA; brisinga@gmail.com
150University of Lodz, Department of Invertebrate Zoology & Hydrobiology, Lodz, Poland;
tmamos@biol.uni.lodz.pl
151Università degli studi di Sassari, Dipartimento di Zoologia e Genetica Evoluzionistica, Sassari,
Italy; r.manconi@uniss.it
152Natural History Museum, London, UK; gillm@nhm.ac.uk
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
153Virginia Polytechnic Institute and State University, Department of Entomology, Blacksburg,
USA; pmarek@vt.edu
154Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand;
BruceM@tepapa.govt.nz
155University Brunei Darussalam, Department of Biology, Rimba, Brunei;
david.marshall@ubd.edu.bn
156Royal Belgian Institute of Natural Sciences, Brussels, Belgium;
Patrick.Martin@naturalsciences.be
157Natural Environment Research Council, British Antarctic Survey, Cambridge, UK;
s.mcinnes@bas.ac.uk
158Flanders Marine Institute , Ostend, Belgium; jan.mees@vliz.be
159University of Tartu, Faculty of Biology and Geography, Tartu, Estonia; tonu.meidla@ut.ee
160University of Bergen, Department of Biology, Bergen, Norway; Kenneth.Meland@ifm.uib.no
161Museum Victoria, Melbourne, Australia; kellymerrin@hotmail.com
162Nova Southeastern University, Oceanographic Center, Dania Beach, USA;
messingc@nova.edu
163Senckenberg am Meer, German Centre for Marine Biodiversity Research, Wilhelmshaven,
Germany; d.milyutin@mail.de
164University of Washington, Friday Harbor Laboratories, Friday Harbor, USA;
cemills@u.washington.edu
165Russian Academy of Sciences, P. P. Shirshov Institute of Oceanology, Moscow, Russia;
vadim@ocean.ru
166Russian Academy of Sciences, P. P. Shirshov Institute of Oceanology, Moscow, Russia;
tina@ocean.ru
167National Natural History Museum Paris, Paris, France; monniot@mnhn.fr
168California Academy of Sciences, Department of Invertebrate Zoology & Geology, San
Francisco, USA; rmooi@calacademy.org
169Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo,
Brasil; acmorand@ib.usp.br
170Universidade Federal do Paraná, Departamento de Zoologia, São José dos Pinhais, Brasil;
rmrocha@ufpr.br
171Texas A&M University, Texas A&M University-Corpus Christi, Department of Life Sciences,
Corpus Christi, USA; mollusca@gmail.com
172Flanders Marine Institute, Ostend, Belgium; jonas.mortelmans@vliz.be
173University of Florida, Department of Biology, Gainesville, USA; mortimer@ufl.edu
174Stazione Zoologica 'Anton Dohrn' of Naples, Integrative Marine Ecology, Naples, Italy;
luigi.musco@szn.it
175Justus Liebig University, Department of Animal Ecology & Systematics, Giessen, Germany;
thomas.a.neubauer@allzool.bio.uni-giessen.de
176Naturhistorisches Museum der Burgergemeinde, Bern, Switzerland; eike.neubert@nmbe.ch
177National University of Singapore, Faculty of Science, Department of Biological Science,
Singapore; peterng@nus.edu.sg
178Institute of Ecology and Biological Resources, Hanoi, Viet Nam; ducanh410@yahoo.com
179University of Copenhagen, Zoological Museum, Copenhagen, Denmark; Cnielsen@snm.ku.dk
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180Toho University, Faculty of Science, Department of Biology, Laboratory of Taxonomy, Tokyo,
Japan; nishikawateruaki@gmail.com
181Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, Washington DC, USA; NORENBUR@si.edu
182Museum Victoria, Melbourne, Australia; tohara@museum.vic.gov.au
183The University of Hong Kong, School of Biological Sciences, Hong Kong, China;
hisaseal@gmail.com
184Oak Ridge National Laboratory, Toxicology and Hazard Assessment Group, Oak Ridge, USA;
dmopresko@hotmail.com
185Shimane University, Research Center for Coastal Lagoon and Environments, Shimane, Japan;
osawam@soc.shimane-u.ac.jp
186University of Ryukyus, Graduate School of Engineering and Science, Senbaru, Japan;
yota1164@gmail.com
187University of Florida, Florida Museum of Natural History, Gainesville, USA;
paulay@flmnh.ufl.edu
188Macquarie University, Faculty of Science, Department of Biological Sciences, North Ryde,
Australia; hannelore.paxton@mq.edu.au
189Université Claude Bernard Lyon 1, Lyon, France; vincent.perrier@univ-lyon1.fr
190National Oceanic and Atmospheric Administration, Fisheries Service, Southwest Fisheries
Science Center, Protected Resources Division, Santa Cruz, USA; William.Perrin@noaa.gov
191Muzeul National de Istorie Naturala Grigore Antipa, Bucharest, Romania; iorgup@antipa.ro
192National Museums of Northern Ireland, Ulster Museum, Holywood, UK;
Bernard.Picton@nmni.com
193Agnes Scott College, Biology Department, Decatur, USA; jpilger@agnesscott.edu
194Polish Academy of Sciences, Institute of Paleobiology, Warsaw, Poland; apis@twarda.pan.pl
195Bishop Museum, Honolulu, Hawaii, USA; bugman@bishopmuseum.org
196Museum Victoria, Melbourne, Australia; gpoore@museum.vic.gov.au
197University of Ryukyus, Senbaru, Japan; jreimer@sci.u-ryukyu.ac.jp
198Senckenberg Nature Research Society, Research Institute and Natural History Museumm,
Frankfurt am Mainm, Germany; reip@myriapoden-info.de
199Harte Research Institute for Gulf of Mexico Studies, Texas A&M University-Corpus Christi,
Corpus Christi, USA; Michael.Reuscher@tamucc.edu
200Oligochaetology Laboratory, Kitchener, Canada; john.reynolds1@sympatico.ca
201Spanish Ministry of Economy and Competiveness, Instituto Español de Oceanografía, Centro
Oceanográfico de Gijón, Gijón, Spain; pilar.rios.lopez@gmail.com
202University of Southampton, National Oceanography Centre, School of Ocean & Earth Science,
Southampton, UK; M.Rius@soton.ac.uk
203Drexel University, Academy of Natural Sciences, Philadelphia, USA;
rosenberg.ansp@drexel.edu
204Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, Washington DC, USA; RUETZLER@si.edu
205Russian Academy of Sciences, A.N. Severtsov Institute of Ecology and Evolution, Moscow,
Russia; rzhavskij@mail.ru
206University of the Basque country, Department of zoology and animal cell dynamics, Vizcaya,
Spain; ji.saiz@ehu.es
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207Universidade Federal de Santa Maria, Laboratório de Carcinologia, Santa Maria, Brasil;
sandro.santos30@gmail.com
208National Museum of Natural History, Department Systematics and Evolution, Paris, France;
andrefsartori@gatesscholar.org
209University of Ryukyus, Faculty of Science, Senbaru, Japan; ayasatohjp@gmail.com
210University of Innsbruck, Faculty of Biology Institute of Zoology, Innsbruck, Austria;
heinrich.schatz@uibk.ac.at
211School of veterinary medicine, Institute of animal ecology and cell biology, ITZ, Ecology and
Evolution, Hannover, Germany; bernado@trichoplax.com
212Centrum für Naturkunde (CeNak), Centre of Natural History- Zoologisches Museum,
Hamburg, Germany; andreas.schmidt-rhaesa@uni-hamburg.de
213University of Cambridge, CASP, Cambridge, UK; simon.schneider@casp.cam.ac.uk
214University of Western Australia, Perth, Australia; christine.schonberg@uwa.edu.au
215Centro Universitário de Volta Redonda, Volta Redonda, Brasil; senna.carcinologia@gmail.com
216Universidade Federal do Rio de Janeiro, Museu Nacional, Rio de Janeiro, Brasil;
csserejo@acd.ufrj.br
217Acharya Nagarjuna University, Department of Zoology and Aquaculture, Andhra Pradesh,
India; shabu.biologist@gmail.com
218Charles Sturt University, Sydney, Australia; sshamsi@csu.edu.au
219University of Texas at San Antonio, San Antonio, USA; jsharma06@gmail.com
220Hampden-Sydney College, Hampden Sydney, USA; wshear@hsc.edu
221Tel-Aviv University, Faculty of Life Sciences, Department of Zoology, Tel-Aviv, Israel;
noa.shenkar@gmail.com
222WoRMS Editorial Board, Fish Vet Group Asia Limited, University of Stirling, Stirling, UK;
andy.shinn@fishvetgroup.com
223Deakin University, Geelong, Australia; mshort@deakin.edu.au
224University of Lodz, Department of Invertebrate Zoology & Hydrobiology, Laboratory of Polar
Biology and Oceanobiology, Lodz, Poland; sicinski@biol.uni.lodz.pl
225Johann Heinrich von Thünen-Institut, Institute of Sea Fisheries, Braunschweig, Germany;
volker.siegel@ti.bund.de
226Field Museum of Natural History, Chicago, USA; psierwald@fieldmuseum.org
227Field Museum of Natural History, Chicago, USA; esimmons@fieldmuseum.org
228University of Ryukyus, Tropical Biosphere Research Center, Sesoko Station, Sesoko Island,
Japan; fredsinniger@hotmail.com
229Natural History Museum, Department of Life Sciences, London, UK; d.sivell@nhm.ac.uk
230University of Ljubljana, Biotechnical Faculty, Department of Biology, Ljubljana, Slovenia;
boris.sket@bf.uni-lj.si
231Naturalis Biodiversity Center, Leiden, Netherlands; Harry.Smit@naturalis.nl
232Ghent University, Faculty of Sciences, Biology Department, Nematology, Ghent, Belgium;
Nic.Smol@UGent.be
233Universidade Federal de Pernambuco, Museu de Oceanografia "Dr. Petrônio Alves Coelho",
Recife, Brasil; jesser_fidelis@yahoo.com.br
234Bavarian State Collection of Zoology, Munich, Germany; spelda@zsm.mwn.de
235Universidade Estadual Paulista "Júlio de Mesquita Filho", Laboratório de Evolução e
Diversidade Aquática, Marília, Brasil; stampar@assis.unesp.br
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
236Vlaamse overheid, Beleidsdomein Leefmilieu, Natuur en Energie, Instituut voor Natuur- en
Bosonderzoek, Afdeling Biodiversiteit en Natuurlijk Milieu, Onderzoeksgroep
Ecosysteemdiversiteit, Brussels, Belgium; eric.stienen@inbo.be
237Bulgarian Academy of Sciences, National Museum of Natural History, Sofia, Bulgaria;
pavel.e.stoev@gmail.com
238Swedish Museum of Natural History, Department of Zoology, Stockholm, Sweden;
sabine.stohr@nrm.se
239Swedish University of Agricultural Sciences, Swedish Species Information Centre, Uppsala,
Sweden; Malin.Strand@slu.se
240El Colegio de la Frontera Sur, Lerma Campeche, Mexico; esuarez@ecosur.mx
241University of Maine, School of Biology and Ecology, Orono, USA; mindi.summers@maine.edu
242University of Washington, Biology Department, Seattle, USA; bjswalla@u.washington.edu
243Italian National Research Council, Istituto per lo Studio degli Ecosistemi - Sede di Firenze,
Florence, Italy; stefano.taiti@ise.cnr.it
244Kagoshima University, Department of Earth and Environmental Sciences, Kagoshima, Japan;
echiura.sipuncula@gmail.com
245University of Bergen, Bergen Museum, Bergen, Norway; pansdamen@gmail.com
246Orange County Sanitation District, Environmental Laboratory & Ocean Monitoring Division,
Fountain Valley, USA; copepods@graduate.uwa.edu.au
247Joint Nature Conservation Committee, Peterborough, UK; mltasker@aol.com
248Natural History Museum, Department of Zoology, London, UK; j.taylor@nhm.ac.uk
249Lomonosov Moscow State University, Moscow, Russia; avtchesunov@yandex.ru
250Naturalis Biodiversity Center, Leiden, Netherlands; Harry.tenHove@naturalis.nl
251WoRMS Editorial Board, 1223 AM, Hilversum, Netherlands; terpoorten@chello.nl
252Nova Southeastern University, Oceanographic Center, Dania Beach, USA;
thomasjd@nova.edu
253The Evergreen State College, Laboratory One, Olympia, USA; thuesene@evergreen.edu
254University of Southampton, National Oceanography Centre, Southampton, UK;
mhth@noc.ac.uk
255University of Göttingen, Geological Museum, Göttingen, Germany; nebyuht@yahoo.com
256Universidad Nacional de Mar del Plata, Facultad de Ciencias Exactas y Naturales,
Departamento de Biología, Buenos Aires, Argentina; jtimi@mdp.edu.ar
257University of Modena e Reggio Emilia, Modena, Italy; todaro.antonio@unimo.it
258Consejo Superior de Investigaciones Científicas, Centre for Advanced Studies of Blanes,
Blanes, Spain; xturon@ceab.csic.es
259University of Maine, School of Biology and Ecology, Orono, USA; styler@maine.edu
260Virginia Commonwealth University, Center for the Study of Biological Complexity, Richmond,
USA; peter@uetz.us
261Kharkiv National University, Department of Zoology and Animal Ecology, Kharkiv, Ukrain;
serge.utevsky@karazin.ua
262Centre National de la Recherche Scientifique, Mediterranean Institute of marine and terrestrial
Biodiversity and Ecology, Marseille, France; jean.vacelet@imbe.fr
263University of Tromso, Tromso, Norway; wim.vader@uit.no
264University of Helsinki, Finnish Museum of Natural History, Helsinki, Finland;
risto.vainola@helsinki.fi
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265Naturalis Biodiversity Center, Leiden, Netherlands; sancia.vandermeij@naturalis.nl
266Eurofins Aquasense, Amsterdam, Netherlands; TonVanHaaren@eurofins.com
267Naturalis Biodiversity Center, Leiden, Netherlands; rob.vansoest@naturalis.nl
268California Academy of Sciences, San Francisco, USA; Bvansyoc@calacademy.org
269Universidade Federal do Pará, Guama, Brasil; virag_venekey@yahoo.com.br
270Naturalis Biodiversity Center, Leiden, Netherlands; ronald.vonk@naturalis.nl
271Merellaan 13, Scherpenheuvel, Belgium; chris.vos1@telenet.be
272University of Tasmania, School of Zoology, Hobart, Australia; geneforws@yahoo.com.au
273Smithsonian Institution, National Museum of Natural History, Department of Invertebrate
Zoology, Washington DC, USA; walterc@si.edu
274University of Hawaii, Department of Biology, Honolulu, USA; watling@hawaii.edu
275University of Cambridge, School of the Biological Sciences, Faculty of Biology, Department of
Zoology, Cambridge, UK; mw283@cam.ac.uk
276Zoologisches Forschungsinstitut und Museum Alexander Koenig, Bonn, Germany;
twesener@uni-bonn.de
277State University of New York, College of Environmental Science and Forestry, Syracuse, USA;
cwhipps@esf.edu
278University of Ryukyus, Senbaru, Japan; white.kristinen@gmail.com
279California Academy of Sciences, Department of Invertebrate Zoology & Geology, San
Francisco, USA; gwilliams@calacademy.org
280Museum Victoria, Melbourne, Australia; rwilson@museum.vic.gov.au
281Natural History Museum, London, UK; N.Wyatt@nhm.ac.uk
282The University of Hong Kong, Faculty of Science, The Swire Institute of Marine Science, Hong
Kong, China; moriakiyasuhara@gmail.com
283Universidade Federal do Rio de Janeiro, Departamento de Zoologia, Laboratório de
Poliquetas, Rio de Janeiro, Brasil; joanazanol@ufrj.br
284South Australian Museum, Department of Invertebrates, Adelaide, Australia;
wolfgang.zeidler@samuseum.sa.gov.au
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
Research Infrastructures (RIs) are facilities, resources and services used by the scientific
community to conduct research and foster innovation. LifeWatch ERIC has developed various
virtual research environments, which include many virtual laboratories (vLabs) offering high
computational capacity and comprehensive collaborative platforms that supporting the needs of
digital biodiversity science.
Over its 250 years of history, the taxonomic research community has developed a system for
describing, classifying and naming taxa across multiple levels. For the marine biota, taxonomic
information is organized and made publicly available through the World Register of Marine
Species (WoRMS) that records more than 250,000 described valid species. Although scientists
tend to assign an equal status (in terms of contribution to overall diversity) to each taxon used in
taxonomy, biogeography, ecology and biodiversity, the question are all taxa equal?has never
been tested at a global scale. We present evidence that this question can be addressed by
applying relatedness indices (Taxonomic Distinctness) over the entire WoRMS metazoan tree.
The RvLab, developed by the LifeWatchGreece RI, operating on a high-performance computer
cluster, has been used to meet the high computational demands required for such an analysis at
a global scale.
PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.26819v1 | CC BY 4.0 Open Access | rec: 1 Apr 2018, publ: 1 Apr 2018
... However, this axiom has been tested only once before, on the United Kingdom's marine animal phyla, showing the inconsistency of the traditional Linnaean classification between different major groups [58]. In Arvanitidis et al. [59], the average taxonomic distinctness index ( +) and its variation (Lambda+) were calculated on a matrix deriving from the complete World Register of Marine Species [60], containing more than 250,000 described species of marine animals. It is the R-vLab web application, along with its HPC high RAM back-end components (on bigmem, see Section The IMBBC HPC Facility: From a Single Server to a Tier 2 System) that made such a calculation possible. ...
Article
Full-text available
High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and 2 0s and 1s in marine molecular research upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade's experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility's future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
Natuur en Energie, Instituut voor Natuur-en Bosonderzoek
  • Beleidsdomein Vlaamse Overheid
  • Leefmilieu
Vlaamse overheid, Beleidsdomein Leefmilieu, Natuur en Energie, Instituut voor Natuur-en Bosonderzoek, Afdeling Biodiversiteit en Natuurlijk Milieu, Onderzoeksgroep Ecosysteemdiversiteit, Brussels, Belgium; eric.stienen@inbo.be
Mexico; esuarez@ecosur.mx 241 University of Maine
  • El Colegio De La Frontera
  • Lerma Sur
  • Campeche
El Colegio de la Frontera Sur, Lerma Campeche, Mexico; esuarez@ecosur.mx 241 University of Maine, School of Biology and Ecology, Orono, USA; mindi.summers@maine.edu 242 University of Washington, Biology Department, Seattle, USA; bjswalla@u.washington.edu