Dr. Joaquín Muñoz (Last update: 10-01-2015 ) ddd      Doñana Biological Station (CSIC)

(Take my Thesis here)                          xxxxxxxxxxxxxxxxxxxxxxx   (Department of Wetland Ecology)

E-mail: quini@ebd.csic.es



Recent collaborations

What do I like to do in Molecular Ecology?

What have I published?

What am I working on?

How do I learn Molecular Ecology?

Things that can be interesting for you


The 'Evolution' of one specimen


África Gómez

Group of Evolutionary Biology (Univ. Hull - U.K.)

Lawrence J. Weider

Dept. of Biology (Univ. Oklahoma - U.S.A.)

Cino Pertoldi

Dept. of Biotechnology, Chemistry and Environmental Engeneering - Section of Biology and Environmental Science (Univ. Aalborg - Denmark)

Jordi Figuerola

Dept. of Wetland Ecology (Doñana Biological Station [CSIC] - Seville, Spain)















































* Currently I am invoved in a project funded by the European Union (Marie Curie Actions - IOF) to investigate the effect of cultural eutrophication on freshwater lakes (human population growth, adition of fertilizer, cut down of trees...) on the genetic compositioin and physiology of those inhabiting species. By using the waterflea Daphnia as model organism, we are analysing those genetic changes caused due to environmental changes, mainly by the high level of Phosphorous in the lakes and its potential adaptation to the new environment.

* During the last three years, I have been working and collaborating on projects related to the study of emergent diseases transmission networks (host-vector-pathogen interactions, the effect of feeding patterns), the behavior of vectors for those diseases (e.g., mosquitoes) taking into account their diet, host abundance as well as the abiotic factors in the ecosystem (tiger mosquito, efficiency of mosquito trapping, environmental factors involved on the mosquito population dynamics), and the effects of blood and intestintal parasitism on migratory birds (Sylvia borin).

* During last few years I have also studied the evolutionary implications of diapausing egg's dispersal on aquatic invertebrate populations. To understand the population dynamics and evolution of this invertebrate group, we used species of genus Artemia (Crustacea:Anostraca) as model organism (Thesis report). My Thesis dealt with two different lines: 'Population Genetics and Phylogeography: Relationships between aquatic birds/humans - aquatic invertebrates and their influence on genetic structure of their populations'; and 'Biological and Genetic Conservation: Relationships between native and invasive Artemia species, and other aquatic invertebrates'.

* Regarding Conservation Genetics of birds, I have investigated the genetic status of several species within the genus Turnix in order to clarify a possible reintroduction in Andalusia (South Spain) of the more related subspecies to the extinct Turnix sylvatica sylvatica (Torillo andaluz).

* On Evolutionary Biology and Phylogeography, I have also collaborated on the survey of island colonization events and Phylogeography of bats within the genus Plecotus (big-eared bat); and the relationship between the low genetic diversity in MHC genes and its phylogenetic relevance into a Falconidae group (falcons vs kestrel). One of my recent collaborations has resulted on the description of MHC Class II ß for the Eurasian coot (Fulica atra) as the non-passerine bird showing the highest diversity reported to date (Fulica atra MHC II).


PUBLICATIONS ( ¶ = equal contribution)

Ongoing manuscripts

34.- Joaquín Muñoz, Anurag Chaturvedi, Luc De Meester, Lawrence J Weider (2015) Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS). IN PREP.

33.- Joaquín Muñoz, Punidan D. Jeyasingh, Andy J. Green, Billy W. Culver, Priyanka Roy Chowdhury and Lawrence J. Weider (2015) Competition driven by cultural eutrophication in the keystone aquatic herbivore, Daphnia pulicaria: population-level effects. IN PREP.

32.- Josué Martínez-de la Puente, Joaquín Muñoz, Carles Aranda, Gioia Capelli, Stefania Cazzin, Silvia Ravagnan, Tomás Montalvo, Annapaola Rizzoli, Daniele Arnoldi, Ramón Soriguer, Jordi Figuerola (2015) Feeding patterns of the invasive Asian tiger mosquito Aedes albopictus and the native Culex pipiens in Southern Europe. UNDER REVIEW.

31.- Rafael Gutiérrez-López, Laura Gangoso, Josué Martínez-de la Puente, Jakob Fric, Pascual López-López, Mélanie Mailleux, Joaquín Muñoz, Boudjema Samraoui, Laïd Touati and Jordi Figuerola (2015) Blood parasite prevalence in a long-distance migratory raptor: Does characteristics of breeding habitat matter? UNDER REVIEW.

30.- Annapaola Rizzoli, Luca Bolzoni, Elizabeth Chadwick, Gioia Capelli, Montarsi Fabrizio, Michela Grisenti, Josue Martínez-de la Puente, Joaquin Muñoz, Jordi Figuerola, Ramon Soriguer, Gianfranco Anfora, Marco Di Luca and Roberto Rosa (2015) Understanding West Nile virus ecology in Europe: Culex pipiens host feeding preference in a hotspot of virus emergence. UNDER REVIEW.


29.- Josué Martínez-de la Puente, Joaquín Muñoz, Gioia Capelli, Fabrizio Montarsi, Ramón Soriguer, Daniele Arnoldi, Annapaola Rizzoli, Jordi Figuerola (2015) Avian malaria parasites in the last supper: identifying encounters between parasites and the invasive Asian mosquito tiger and native mosquito species in Italy. ACCEPTED.


28.- Cino Pertoldi, Kelly Elschot, Lous van de Zande, Andrzej Zalewski, Joaquín Muñoz, Aritz Ruiz-Gonzalez, Aksel Bo Madsen, Volker Loeschcke, Arjen de Groot and Rob Bijlsma (2014) Genetic variability of Central-Western European pine marten (Martes martes) populations. Acta Theriologica, 59: 503-510 (DOI 10.1007/s13364-014-0196-7). Website

27.- Miguel Alcaide ¶, Joaquin Muñoz ¶, Josué Martínez-de la Puente, Ramón Soriguer and Jordi Figuerola (2014) Extraordinary MHC class II ß diversity in a non-passerine, wild bird: the Eurasian coot Fulica atra (Aves: Rallidae). Ecology and Evolution, 4(6): 688-698 (DOI: 10.1002/ece3.974)

26.- Joaquín Muñoz ¶, Africa Gómez ¶, Jordi Figuerola, Francisco Amat, Ciro Rico and Andy J. Green (2014) Colonization and dispersal patterns of the invasive American brine shrimp Artemia franciscana (Branchiopoda: Anostraca) in the Mediterranean region. Hydrobiologia, 726: 25-41 (DOI: 10.1007/s10750-013-1748-6)


25.- Joaquín Muñoz, Francisco Amat, Andy J Green, Jordi Figuerola and Africa Gómez (2013) Bird migratory flyways influence the phylogeography of the invasive brine shrimp Artemia franciscana in its native American range. PeerJ 1: e200 () - SPECIAL CELEBRATION200th ARTICLE

24.- Martina Ferraguti, Josué Martínez-de la Puente, Joaquín Muñoz, David Roiz, Santiago Ruiz , Ramón Soriguer and Jordi Figuerola (2013) Avian Plasmodium in Culex and Ochlerotatus mosquitoes from Southern Spain: effects of season and host feeding source on parasite dynamics. PLoS ONE, 8(6): e66237 (doi:10.1371/journal.pone.0066237)

23.- Guillermo López, Joaquín Muñoz, Ramón Soriguer and Jordi Figuerola (2013) Increased endoparasite infection in late-arriving individuals of a trans-Saharan passerine migrant bird. PLoS ONE, 8(4): e61236 (doi:10.1371/journal.pone.0061236)


22.- Joaquín Muñoz, Santiago Ruiz, Ramón Soriguer, Miguel Alcaide, Duarte S. Viana, David Roiz and Jordi Figuerola (2012) Feeding patterns of potential West Nile virus transmission vectors in Southwest Spain. PLoS ONE, 7(6): e39549 (doi:10.1371/journal.pone.0039549)

21.- Laura Gangoso, Miguel Alcaide, Juan M. Grande, Joaquín Muñoz, Sandra L. Talbot, Sara A. Sonsthagen, G. Kevin Sage and Jordi Figuerola (2012) Colonizing the world in spite of reduced MHC variation. Journal of Evolutionary Biology, 25(7): 1438-1447 (doi: 10.1111/j.1420-9101.2012.02529.x)

20.- David Roiz, Ana Vázquez, Roberto Rosà, Joaquín Muñoz, Daniele Arnoldi, Fausta Roso, Jordi Figuerola, Antonio Tenorio and Annapaola Rizzoli (2012) Blood meal analysis, flavivirus screening and influence of meteorological variables on the dynamics of potential mosquito vectors of West Nile virus in Trentino (Northern Italy). Journal of Vector Ecology, 37(1): 20-28. Website

19.- David Roiz, Marion Roussel, Joaquín Muñoz, Santiago Ruiz, Ramón Soriguer and Jordi Figuerola (2012) Efficacy of mosquito traps for collecting potential West Nile mosquito vectors in a natural Mediterranean wetland. The American Journal of Tropical Medicine and Hygiene, 86(4): 642-648 (DOI: 10.4269/ajtmh.2012.11-0326)



18.- Joaquín Muñoz, Roger Eritja, Miguel Alcaide, Tomás Montalvo, Ramón C. Soriguer and Jordi Figuerola (2011) Host-feeding patterns of native Culex pipiens and invasive Aedes albopictus mosquitoes (Diptera: Culicidae) in urban zones from Barcelona, Spain. Journal of Medical Entomology, 48(4): 956-960. Website


17.- Joaquín Muñoz ¶, Africa Gómez ¶, Andy J. Green, Jordi Figuerola, Francisco Amat and Ciro Rico (2010) Evolutionary origin and phylogeography of the diploid obligate parthenogen Artemia parthenogenetica (Branchiopoda: Anostraca). PLoS ONE, 5(8): e1932. (DOI: 10.1371/journal.pone.0011932)

16.- Joaquín Muñoz and Fernando Pacios (2010) Global biodiversity and geographical distribution of diapausing aquatic invertebrates: The case of the cosmopolitan brine shrimp Artemia (Branchiopoda: Anostraca). Crustaceana, 83(4): 465-480. DOI: 10.1163/001121610X489449 (A. franciscana MAP_2008; A. persimilis MAP_2008; A. salina MAP_2008; A. tibetiana MAP_2008; A. sinica MAP_2008)

15.- Joaquín Muñoz (2010) Diversity and distribution of diapausing aquatic invertebrates in inland wetlands: An ecosystem conservation viewpoint. Journal for Nature Conservation, 18(1): 55-62. DOI: 10.1016/j.jnc.2009.02.006


14.- Miguel Alcaide, Ciro Rico, Santiago Ruiz, Ramón Soriguer, Joaquín Muñoz and Jordi Figuerola (2009) Disentangling vector-borne transmision networks: auniversal DNA barcoding method to identify vertebrate hosts from arthropod bloodmeals. PLoS ONE, 4(9): e7092. DOI: 10.1371/journal.pone.0007092 (access to a detailed protocol)

13.- Javier Juste, Rasit Bilgin, Joaquín Muñoz and Carlos Ibáñez (2009) Mitochondrial DNA signatures at different spatial scales: from the effects of the Straits of Gibraltar to population structure in the meridional serotine bat (Eptesicus isabellinus). Heredity, 103: 178-187. Website

12.- Joaquín Muñoz , Andy J. Green, Jordi Figuerola, Francisco Amat and Ciro Rico (2009) Characterization of polymorphic microsatellite markers in the brine shrimp Artemia (Branchiopoda, Anostraca). Molecular Ecology Resources, 9: 547-550. Website


11.- Cino Pertoldi , Joaquín Muñoz , Aksel Bo Madsen, John Stuart F. Barker, D.H. Andersen, H.J. Baagoe, Metter Birch and Volker Loeschcke (2008) Genetic variability in the mitochondrial DNA of the Danish Pine marten. Journal of Zoology, 276: 168-175. Website

10.- Catalina Monzón-Argüello, Joaquín Muñoz, Adolfo Marco, Luis Felipe López-Jurado and Ciro Rico (2008) Twelve new polymorphic microsatellite markers from the loggerhead sea turtle (Caretta caretta) and cross-species amplification on other marine turtle species. Conservation Genetics, 9: 1045-1049. Website

9.- Javier Montero-Pau, Africa Gómez and Joaquín Muñoz (2008) Application of an inexpensive and high-throughput genomic DNA extraction method for the molecular ecology of zooplanktonic diapausing eggs. Limnology and Oceanography: Methods, 6: 218-222. OPEN ACCESS: http://aslo.org/lomethods/free/2008/0218.pdf (access to a detailed protocol)

8.- Joaquín Muñoz ¶, Africa Gómez ¶, Andy J. Green, Jordi Figuerola, Francisco Amat and Ciro Rico (2008) Phylogeography and local endemism of the native Mediterranean brine shrimp Artemia salina (Branchiopoda: Anostraca). Molecular Ecology, 17: 3160-3177. Website

7.- Cino Pertoldi, Stuart F. Barker, Aksel Bo Madsen, Hanne Jørgensen, Ettore Randi, Joaquín Muñoz, Hans J. Baagoe and Volker Loeschcke (2008) Spatio-temporal population genetics of the Danish pine marten (Martes martes). Biological Journal of the Linnean Society, 93: 457-464. Website

6.- Juan Arroyo, Abelardo Aparicio, Rafael G. Albaladejo, Joaquín Muñoz and Rita Braza (2008) Genetic structure and population differentiation of the Mediterranean pioneer spiny broom Calicotome villosa across the Strait of Gibraltar. Biological Journal of the Linnean Society, 93: 39–51. Website



5.- Joaquín Muñoz (2007) Biodiversity conservation including uncharismatic species. Biodiversity and Conservation, 16: 2233-2235. Website


4.- Cino Pertoldi, Juan J. Negro, Joaquín Muñoz, Filippo Barbanera and Héctor Garrido (2006) Introduction or reintroduction? Last resorts for the latest bird to become extint in Europe, the Andalusian hemipode Turnix sylvatica sylvatica. Biodiversity and Conservation, 15: 3895-3908. Website


3.- Juste J, Ibáñez C, Muñoz J, Trujillo D, Benda P, Karatas A and Ruedi M (2004) Mitochondrial phylogeography of the long-eared bat (Plecotus) in the Mediterranean Palaearctic and Atlantic Islands. Molecular Phylogenetics and Evolution, 31(3): 1114-1126. Website


2.- Juste J, Ibáñez C, Trujillo D, Muñoz J and Ruedi M (2003) Phylogeography of Barbastelle bats (Barbastella barbastellus) in the western Mediterranean and the Canary Islands. Acta Chiropterologica, 5(2): 165-175. Website

1.- García-Mudarra JL, Juste J and Muñoz J (2003) Aplicación de técnicas moleculares a la Biología: ¿Qué nos dicen de los Quirópteros?. Barbastella. SECEMU Journal, Núm. II Dic.: 24-28.


In Research Projects:

* Project funded by the Secretaría General de Agrigultura, Pesca y Alimentación (MAPA): ‘Genetic structure of the populations of the Serotine bat (Eptesicus serotinus) as the main reservoir of the rabies virus EBLV1’. Year 2002.

* Project funded by the Consejería de Medio Ambiente - Junta de Andalucía: ‘Structure and genetic variability of the wild populatitons of Gypaetus barbatus (bearded vulture)’. Year 2001.

* Project of Medidas Compensatorias Correspondientes a la Autovía A-381 JEREZ-LOS BARRIOS, funded by GIASA: ‘Development of studies on the biology and genetic structure of tree and shrub populations’. Year 2000.



* To identify the genetic structure of two Artemia species, A. salina and A. parthenogenetica diploid, populations along their range of distribution, emphasizing on the Mediterranean Basin. At the same time, we would like to identify the genetic strucuture in the Mediterranean populations invaded by the exotic species A. franciscana.

- Molecualr marker used: Sequences of a fragment of the mitochondrial gene Cytochrome Oxidase Subunit I (COI).


* To determinate the Artemia species inhabiting in different salterns (hypersline aquatic ecosystems) using molecular tools applied to DNA obtained from cysts (resting eggs). With this approach it could be possible to make a more exhaustive census of the different salterns in Iberian Peninsula and other Mediterranean countries. This project includes the survey of the cyst bank in the saltern muds which are currently invaded by Artemia franciscana.

- Molecular markers used: Using sequences of COI for the different Artemia species, we will develop specific probes to be assessed with the technic TaqMan on a Real Time PCR. This approach will allow to differentiate between Artemia species in a mixed cyst sample (i.e. populations with more than one species inhabiting).


* Analyses of the gene flow between populations of the different Artemia species.

- Molecular marker: We will develop specific hypervariable markers, microsatellites.


* To analyse the influence of birds, as the main dispersal vectors, on the Artemia populations, their genetic structure and gene flow.

- Recording the abundance dataset of bird species which visit the different salterns (or lagoons) during their migratory movements, and the dataset of gene flow between populations, we could obtain the correlation between the migratory routes of those bird species and the gene flow of Artemia populations.



* PHYLOGENY Software: http://evolution.genetics.washintong.edu/phylip/software.html

* : http://lgb.unige.ch/arlequin/

* BEAST: http://beast.bio.ed.ac.uk/

* EVOLDIR: http://evol.mcmaster.ca/brian/evoldir.html

* CRANDALL LAB: hhttp://InBio.byu.edu/Faculty/kac/crandall_lab/Computer.html

* DnaSP: http://www.ub.es/dnasp/

* EUTHERIA: http://www.tolweb.org/tree?group=Eutheria&contgroup=Mammalia

* OLIGOS Design: http://www.biocenter.helsinki.fi/bi/bare-1_html/oligos.htm

* GENEFLOW Software: http://www.nceas.ucsb.edu/nceas-web/projects/2057/nceas-paper3/software/

* GENEPOP: http://genepop.curtin.edu.au/

TOP or more...

* GEODIS: http://darwin.uvigo.es/

* COLLAPSE: http://darwin.uvigo.es/

* MODELTEST: http://darwin.uvigo.es/

* TCS: http://darwin.uvigo.es/

* DNASTAR: http://www.dnastar.com/web/r3.php

* MAC_CLADE: http://www.macclade.org/macclade.html

* : http://www.mesquiteproject.org/mesquite/mesquite.html

* Mr. BAYES: http://mrbayes.csit.fsu.edu.index.php

TOP or more...

* : http://www.ncbi.nlm.nih.gov/

* TAXONOMY Software: http://taxonomy.zoology.gla.ac.uk/software/software.html

* : http://www.paup.csit.fsu.edu/downl.html

* PHYLIP: http://genetics.washintong.edu/phylip.html

* PRIMER 3: http://frodo.wi.mit.edu/primer3/

* : http://www.biodiversidadmolecular.es/

* TREE Web Page: http://www.tolweb.org/tree/