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Selected Publications

Ravinet, M., Hynes, R., Poole, R., Cross, T. F., McGinnity, P., Harrod, C., Prodöhl, P.A. (2015). Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks. PLOS ONE 10(4) 1-22 : e0122825. doi: 10.1371/journal.pone.0122825. 

Reed, T., Prodöhl, P.A., Hynes, R., Cross, T.C., Ferguson, A., McGinnity, P. (2015). Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment. Heredity (29 April 2015): doi:10.1038/hdy.2015.29.

Boston, E. S. M., Montgomery, W. I., Hynes, R. & Prodöhl, P.A. (2015). New insights on postglacial colonization in Western Europe: the phylogeography of the Leisler's bat (Nyctalus leisleri). Proceedings of the Royal Society of London. Series B, Biological Sciences (early online date 25/02/2015) :

Bailie, D. A., Fitzpatrick, S., Connolly, M., Thiel, M., Hynes, R., Prodöhl, P. A., (2014). Genetic assessment of parentage in the caridean rock shrimp Rhynchocinetes typus based on microsatellite markers.  Journal of Crustacean Biology (available online June 2014) (doi: 10.1163/1937240X-00002254).

Aykanat, T., Johnston, S. E., Cotter, D., Cross, T. F., Poole, R., Prodöhl, P. A., Reed, T., Rogan, G., McGinnity, P., Primmer, C. R.  (2014).  Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evolutionary Biology 14:68. (doi: 10.1186/1471-2148-14-68). 

Ravinet, M., Harrod, C., Eizaguirre, C. and Prodöhl, P. A. (2014). Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonisation? Ecology and Evolution 4: 2488-2504. (doi:10.1002/ece3.853).

O’Malley, K. G., Cross, T. F., Bailie, D., Carlsson, J., Coughlan, J. P., Dillane, E., Prodöhl, P. A. and McGinnity, P. (2014). Circadian clock gene (OtsClock1b) variation and time of ocean return in Atlantic salmon Salmo salarFisheries Management and Ecology 21: 82-87. (10.1111/fme.12058).

Keenan, K., McGinnity, P., Cross, T., Crozier, W.W. & Prodöhl, P. A. (2013) diveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors. Methods in Ecology and Evolution 8: 782-788. (first published online 9 August 2013) - doi: 10.1111/2041-210X.12067.

Havelka, M., Hulák, M., Bailie, D. A., Prodöhl, P. A. and Flajšhans, M. (2013). Extensive Genome Duplications in Sturgeons: New Evidence from Microsatellite Data. Journal of Applied Ichthyology 29: 704-708. (first published online 22 April 2013) – doi: 10.1111/jai.12224.

Keenan, K., Bradley, C. R., Magee, J. J., Hynes, R. A., Kennedy, R. J., Crozier, W. W., Poole, R., Cross, T. F., McGinnity, P., Prodöhl, P. A. (2013). Beaufort trout MicroPlex: a high throughput multiplex platform comprising 38 informative microsatellite loci for use in resident and anadromous (sea trout) brown trout Salmo trutta genetics studies. Journal of Fish Biology 82:1789-804 - doi: 10.1111/jfb.12095.

Ravinet, M., Prodöhl. P. A. and Harrod, C. (2013). On Irish sticklebacks: morphological diversification in a secondary contact zone. Evolutionary Ecology Research 15: 271-294. 

Scott, D. D., Fitzpatrick, S., Bailie, D. A., Boston, E. S. M., Lundy, M. G., Buckley, D. j., Teeling, E. C., Montgomery, W. I. and Prodöhl, P. A. (2013). Isolation and characterization of eight polymorphic microsatellite loci for Natterer’s bat, Myotis nattereri (Vespertilionidae, Chiroptera). Conservation Genetics Resources 5: 643-645 (published online: 05 February 2013). doi: 10.1007/s12686-013-9871-2. 

Ravinet, M., Prodöhl. P. A. and Harrod, C. (2013). Parallel ecological, morphological and genetic divergence in lake-stream stickleback from a single novel catchment. Journal of Evolutionary Biology 26: 186-204. doi: 10.1111/jeb.12049. 

Walker, S.M., Demiaszkiewicz, A. W., Kozak, M., Wedrychowicz, H., Teofanovac, D., Prodöhl, P., Brennan, G., Fairweather, I. Hoey, E. M. and Trudgett, A. (2013). Mitochondrial DNA haplotype analysis of liver fluke in bison from Bialowieza Primaeval Forest indicates domestic cattle as the likely source of infection. Veterinary Parasitology 191: 161– 164.

Walker, S. M., Prodöhl, P. A., Hoey, E. M., Fairweather, I., Hanna, R. E .E. and Trudgett, A. (2012). Substantial genetic divergence between morphologically indistinguishable populations of Fasciola suggests the possibility of cryptic speciation. International Journal of Parasitology 42: 1193-1199. doi:

Buckley, D. J., Lundy M. G., Boston, E. S. M., Scott, D. D., Gager, Y., Prodöhl, P. A., Marnell, F., Montgomery. W. I. and Teeling, E. C. (2012). The spatial ecology of the whiskered bat (Myotis mystacinus) at the western extreme of its range provides evidence of regional adaptation. Mammalian Biology 78: 198-204 (Available online 23 August 2012) - 

Boston, E. S. M., Puechmaille, S. J., Scott, D. D., Buckley, D. J., Lundy, M. G., Montgomery, I. W., Prodöhl, P. A. and Teeling, E. (2012). Empirical assessment of non-invasive population genetics in bats: comparison of DNA quality from faecal and tissue samples. Acta Chiropterologica 14: 45-52.

Boston, E. S. M., Roué, S. G., Montgomery, W. I. and Prodöhl, P. A. (2012). Kinship, parentage and temporal stability in nursery colonies of Leisler’s bat (Nyctalus leisleri). Behavioural Ecology 23: 1015-1021. doi: 10.1093/beheco/ars065.

McInerney, C. E., Allcock, A. L., Johnson, M. P. and Prodöhl, P. A. (2012). Ecological coherence in marine reserve network design: an empirical evaluation of sequential site selection using genetic structure. Biological Conservation 152: 262–270. 

Lundy, M. G., Buckley, D. J., Boston, E. S. M., Scott, D. D., Prodöhl P. A., Marnell, F., Teeling, E. C., Montgomery W.I. ( 2012). Behavioural context of multi-scale species distribution models assessed by radio-tracking. Basic and Applied Ecology 13: 188–195.

Ensing, D., Prodöhl, P. A., McGinnity, P., Boylan, P., O’Maoiléidigh, N., Crozier, W. W. (2011). Complex pattern of genetic structuring in the Atlantic salmon (Salmo salar L.) of the River Foyle system in north-west Ireland: disentangling the evolutionary signal from population stochasticity. Ecology and Evolution 1: 359-372 (doi:10.1002/ece3.32).

Nzoughet, J. K., Grant, I. Prodöhl, P. A., Hamilton, J., Botana, L., Elliott,. C. (2011). Evidence of Methylobacterium spp. andHyphomicrobium sp. in Azaspiracid toxin contaminated mussel tissues and assessment of the effect of Azaspiracid on their growth. Toxicon 58: 619-622 (doi:10.1016/j.toxicon.2011.09.012).

Baile, D. A., Hynes, R. and Prodöhl, P.A. (2011). Genetic parentage in the squat lobsters Munida rugosa and M. sarsi (Crustacea, Anomura, Galatheidae). Marine Ecological Progress Series 421: 173-181 (doi:10.3354/meps08895).

Boston E. S. M, Hanrahan N., Puechmaille S. J, Lundy M., Buckley D. J, Scott  D. D, Prodöhl P. A.,  Montgomery W.I, Teeling E. C. 2011 A rapid PCR-based assay for identification of cryptic Myotis spp (Myotis mystacinus, Myotis brandtii and Myotis alcathoe). Conservation Genetics Resources 3: 557-563 (doi: 10.1007/s12686-011-9404-9).

Ellis J. S., Gilbey J., Armstrong A., Balstad T., Cauwelier E., Cherbonnel C., Consuegra S., Coughlan J., Cross T. F., Crozier W., Dillane E., Ensing D., García de Leániz C., García-Vázquez E., Griffiths A. M., Hindar K., Hjorleifsdottir S., Knox D., Machado-Schiaffino G., McGinnity P., Meldrup D., Nielsen E. E., Olafsson K., Primmer C. R., Prodöhl P. A. , Stradmeyer L., Vähä J.-P., Verspoor E., Wennevik V., Stevens J. R. (2011). Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.). Genetica 139: 353-367 (doi: 10.1007/s10709-011-9554-4).

Fitzpatrick. S., Shivji, M. S., Chapman, D. D. and Prodöhl, P. A. (2011). Development and characterization of 10 polymorphic microsatellite loci for the blue shark, Prionace glauca, and their cross shark-species amplification. Conservation Genetic Resources 3:523-527 (doi 10.1007/s12686-011-9395-6).

Lundy, M. G., Teeling, E. C., Boston, E. M., Scott, D. D., Buckley, D. J., Prodöhl, P. A., Marnell, F. and Montgomery, W. I. (2011). The shape of sound: elliptic Fourier descriptors (EFD) discriminate the echolocation calls of Myotis bats (M. daubentonii, M. nattereri & M. mystacinus). Bioacoustics 20: 101-116.

McInerney, C.E., Allcock, A.L., Johnson, M.P., Bailie, D.A. and Prodöhl, P.A. (2011). Comparative genomic analysis explain difficulties with microsatellite marker development in molluscs. Heredity 106: 78-87 (doi:10.1038/hdy.2010.36).

Walker, S. M., Johnston, C., Hoey, E.M., Fairweather, I., Borgsteede, F., Gaasenbeek, C., Prodöhl, P. A. and Trudgett, A. (2011). Potential role of hares in the spread of liver fluke in the Netherlands. Veterinary Parasitology 177: 179-181 (doi:10.1016/j.vetpar.2010.11.043).

Walker, S. M., Johnston, C., Hoey, E.M., Fairweather, I., Borgsteede, F., Gaasenbeek, C., Prodöhl, P. A. and Trudgett, A. (2011). Population dynamics of the liver fluke, Fasciola hepatica: the effect of time and spatial separation on the genetic diversity of fluke populations in the Netherlands. Parasitology 138: 215-223 (doi: 10.1017/S0031182010001149).

Bailie, D. A., Fletcher, H. and Prodöhl, P. A. (2010). High incidence of cryptic repeated elements in microsatellite flanking regions of galatheid genomes and its evolutionary implications. Journal of Crustacean Biology 30(4): 664-672.

Boston, E. M., Buckley, D. J., Bekaert, M., Gager, Y., Lundy, M. G., Scott, D. D., Prodöhl, P. A., Montgomery, W. I., Marnell, F. and Teeling, E. C. (2010). The status of Ireland’s newest bat species, Myotis brandtii (Brandt’s bat). Acta Chiropterologica 12: 457-461 (doi: 10.3161/150811010X538025).

Farren, . A. Prodöhl, P. A., Laming. P. and Reid,  N. (2010). Distribution of the common lizard (Zootoca vivipara) and landscape favourability for the species in Northern Ireland. Amphibia-Reptilia 31 (3) 387-394 (doi:10.1163/156853810791769428).

Feldheim, K. A., Chapman, D. D., Sweet, D., Fitzpatrick, S., Prodöhl, P. A., Shivji, M. S. and Snowden, B. (2010). Shark virgin birth produces multiple, viable offspring. Journal of Heredity 101(3):374-377 (doi:10.1093/jhered/esp129).

McKeown, N. J., Hynes, R. A., Duguid, R. A., Ferguson, A. and Prodöhl, P. A. (2010). Phylogeographic structure of brown trout (Salmo trutta) in Britain and Ireland: glacial  refugia, post-glacial colonisation, and origins of sympatric populations. Journal of Fish Biology 76:319-347 (doi:10.1111/j.1095-8649.2009.02490.x).

Booth, W., Montgomery, W. I. and Prodöhl, P. A. (2009).  Spatial genetic structuring in a vagile species, the European wood mouse. Journal of Zoology 279:219-228 (doi:10.1111/j. 1469-7998.2009.00608.x).

Jørstad, K. E., Kristiansen, T. S., Farestveit, E., Agnalt, A.-L., Prodöhl, P. A., Hughes, M., Ferguson, A. and Taggart (2009). Survival of laboratory-reared juvenile European lobster (Homarus gammarus) from three brood sources in southwestern Norway. New Zealand Journal of Marine and Freshwater Research 43: 59.68.

Kenchington, E. L., Harding, G. C., Jones, M. W. and Prodöhl, P. A. (2009). Pleistocene glaciation events shape genetic structure across the range of the American lobster, Homarus americanus. Molecular Ecology 18:1654-1667(doi:10.1111/j.1365-294X.2009.04118.x).

McInerney, C. E., Allcock, A. L., Johnson, M. P. and Prodöhl, P. A. (2009). Understanding marine reserve function in a seascape genetic context: Nucella lapillus in Strangford Lough (Northern Ireland) as an example. Aquatic Biology 7:45-58 (doi: 10.3354/ab00177).

McInerney, C. E., Allcock, A. L., Johnson, M. P. and Prodöhl, P. A. (2009). Characterization of polymorphic microsatellites for the rough periwinkle gastropod, Littorina saxatilis (Olivi, 1792) and their cross-amplification in four congeners. Conservation Genetics 10:1989-1992 (doi:10.1007/s10592-009-9875-3).

Boston, E., Montgomery, W. I., and Prodöhl, P. A. (2008). Development and characterization of 11 polymorphic compound tetranucleotide microsatellite loci for the Leisler’s bat, Nyctalus leisleri (Vespertilionidae, Chiroptera). Conservation Genetics 10:1501-1504 (DOI 10.1007/s10592-008-9768-x).

Dillane, E., McGinnity, P., Coughlan, J. P., Cross, M. C., de Eyto, E., Kenchington, E., Prodöhl P. A. and Cross, T. F. (2008). Demographics and landscape features determine intra-river population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland. Molecular Ecology 17:4786-4800.

McInerney, C. E., Allcock, A. L., Johnson, M. P. and Prodöhl, P. A. (2008). Characterization of polymorphic microsatellites for the periwinkle gastropods, Littorina littorea (Linnaeus, 1758) and their cross-amplification in four congeners. Conservation Genetics 10:1417-1420 (doi:10.1007/s10592-008-9750-7).

Prodöhl, P. A. , Loughry, W. J. and McDonough, C. M. (2008). Genes and demes: population genetic analyses of the Xenarthra . In: The Biology of the Xenarthra (S. F. Vizcaíno & W. J. Loughry, eds.). University Press of Florida, Gainesville. pp 205-211.

Strugnell, J., Rogers, A. D., Prodöhl, P. A., Collins, M. A. and Allcock, A. L. (2008). The thermohaline expressway: the Southern Ocean as a centre of origin for deep-sea octopuses. Cladistics 24:1-8.

Walker, S. M., Makundi, A. E., Namuba, F. V., Kassuku, A. A., Keyyu, J., Hoey, E. M., Prodöhl, P. A., Stothard, J. R., E., and Trudgett, A. (2008). The distribution of Fasciola hepatica and Fasciola gigantica within an East African model – constraints associated with the intermediate host. Parasitology 135: 495-503.

Allcock, A. L., Strugnell, J. M., Prodöhl, P. Piatkowski, U. and Vecchione. M. (2007). A new species of Pareledone (Cephalopoda: Octopodidae) from Antarctic Peninsula Waters. Polar Biology 30: 883-893.

Booth, W., Montgomery, I.W. and Prodöhl, P. (2007). Polyandry by Wood mice in natural populations. Journal of Zoology 273: 176-182(7).

Chapman, D. C., Shivji, M. S., Louis, E., Sommer, L., Fletcher, H. and Prodöhl, P. A. (2007). Virgin birth in a hammerhead shark. Biology Letters 3(4): 425-427.

Ferguson, A., Fleming, I., Hindar, K., Skaala, Ø., McGinnity, P., Cross, T. and Prodöhl, P. (2007). Farm Escapes. In The Genetics of Atlantic Salmon: Implications for Conservation (Verspoor, E., Nielsen, J.L. & Stradmeyer, L., eds.). Blackwell, Oxford. pp 357-388.

Jørstad, K. E., Prodöhl, P. A., Agnalt, A.-L., Hughes, M., Farestveit, E. and Ferguson, A. F. (2007). Comparison of genetic and morphological methods to detect the presence of American lobsters, Homarus americanus H. Milne Edwards, 1837 (Astacidea: Nephropidae) in Norwegian waters. Hidrobiology 590: 103-114.

Walker, S. M., Prodöhl, P. A., Fletcher, H. L., Hanna, R. E. B., Kantzoura, . V., Hoey, E. M. and Trudgett, A. (2007). Evidence for multiple mitochondrial lineages of Fasciola hepatica (liver fluke) within infrapopulations from cattle and sheep. Parasitology Research 101(1): 117-125.

Booth, W. Bogdanowicz, S. M., Prodöhl, P. A., Harrison, R. G., Schal, C., and Vargo, L. (2006). Identification and characterization of 10 polymorphic microsatellite loci in the German cockroach, Blattella germanica . Molecular Ecology Notes 7(4): 648-650.

Duguid, R. A., Ferguson, A. and Prodöhl, P. A. (2006). Reproductive isolation and genetic differentiation of ferox trout from sympatric brown trout in Loch Awe and Loch Laggan, Scotland. Journal of Fish Biology 69: 89-114.

Jørstad, K.E., Prodöhl, P.A., Kristiansen, T.S., Hughes, M., Farestveit, E., Taggart, J.B., Agnalt, A.-L., and Ferguson, A. (2005). Communal larval rearing of European lobster (Homarus gammarus): family identification by microsatellite DNA profiling and offspring fitness. Aquaculture 247, 275– 285.

Loughry, W.J., Prodöhl, P. A. and McDonough, C. M. (2005). The inadequacy of observation: Understanding armadillo biology with molecular markers. Recent Res. Devel. Ecol. 3, 55-73.

Bremner-Harrison, S.; Prodöhl, P. A. and Elwood, R. W. (2004). Behavioural trait assessment as a release criterion: boldness predicts early death in a reintroduction programme of captive programme of captive-bred swift fox (Vulpex velox). Animal conservation 7: 1-8.

Chapman, D. D., Prodöhl, P. A., Gelsleichter, J., Manire, C. and Shivji. M. (2004). Predominance of genetic monogamy by females in a hammerhead shark, Sphyrna tiburo: Implications for shark conservation. Molecular Ecology 13: 1965-1974.

Jørstad, K.E., Prodöhl, P. A., Agnalt, A.-L., Hughes, M., Apostolidis, A., Triantaphyllidis, A., Farestveit, E., Kristiansen, T., Mercer, J. and Svåsand, T. (2004). Sub-Arctic populations of European lobster (Homarus gammarus) in Northern Norway. Environmental Biology of Fishes, 69: 223-231

McGinnity, P., Prodöhl, P., Maoiléidigh, N. Ó., Hynes, R., Cotter, D., Baker, N., O’Hea, B. and Ferguson A. (2004). Differential lifetime success and performance of native and non-native Atlantic salmon examined under communal natural conditions. Journal of Fish Biology, 65: 1-15.

McGinnity, P., Prodöhl, P., Ferguson, A., Hynes, Ó Maoiléidigh, R. N., Baker, N., Cotter, D., O’Hea, B., Cooke, D., Rogan, G., Taggart, J. and Cross, T. (2003). Fitness reduction and potential extinction of wild populations of Atlantic salmon Salmo salar as a result of interactions with escaped farm salmon. Proceedings of the Royal Society B, 270: 2443-2450.

Wattier R. A., Prodöhl P. A. and Maggs, C. A. 2000. DNA isolation protocol for red seaweed (rhodophyta). Plant Molecular Biology Reporter, 18 (3): 275-281 2000.

Loughry, W. J., Prodöhl, P. A., McDonough, C. M., Nelson, W. S., and Avise, J. C. 1998. Correlates of reproductive success in a population of nine-banded armadillos: a preliminary report. Canadian Journal of Zoology, 76:1815-1821.

Loughry, W. J., Prodöhl, P. A., McDonough, C. M. and Avise, J. C. (1998). The adaptive value of polyembryony. American Scientist, 86:274-279.

Prodöhl, P. A. , Loughry, W. J., McDonough, C. M., Nelson, W. S., Thompson, E. A. and Avise, J. C. 1998. Genetic maternity and paternity in a local population of armadillos assessed by microsatellite DNA markers and field data. American Naturalist, 151:7-19.

Prodöhl, P. A. , Walker, A. F., Hynes, R., Taggart, J. B. and Ferguson, A. (1997). Genetically monomorphic brown trout (Salmo trutta L.) populations as revealed by mitochondrial DNA, multi-locus and single-locus minisatellite  (VNTR) analyses. Heredity. 79: 208-213.

Prodöhl, P. A. , Loughry, W. J., McDonough, C. M., Nelson, W. N. and Avise, J. C. 1996. Molecular documentation of polyembryony and the micro-spatial dispersion of clonal sibships in the nine-banded armadillo, Dasypus novemcinctus. Proceedings of the Royal Society B. 263: 1643-1649.

Nelson, W. S., Prodöhl P. A. and Avise, J. C. 1996. Development and application of long-PCR for the assay of full-length animal mitochondrial DNA. Molecular Ecology. 5:807-810.

Taggart, J. B., Prodöhl, P. A. and Ferguson, A. (1995). Genetic markers for Atlantic salmon (Salmo salar L.): Single locus inheritance and joint segregation analysis of minisatellite (VNTR) DNA loci. Animal Genetics. 26: 13-20.

Prodöhl, P. A. , Taggart, J. B. and Ferguson, A. (1995). A panel of single locus minisatellite DNA probes for application to problems in salmonid aquaculture. Aquaculture. 137: 87-97.

Laikre, L., Prodöhl, P. A., Jorde, P. E. and Ryman, N. (1995). Genetic variability at minisatellite and allozyme loci in brown trout (Salmo trutta) - A comparison. Hereditas. 123: 191-195.

Ferguson, A., Taggart. J. B., Prodöhl, P. A., McMeel, O., Thompson, C., Stone, C., McGinnity, P. and Hynes, R. (1995). The application of molecular markers to the study and conservation of fish populations. Journal of Fish Biology. 47: 103-126.

Ferguson, A., Hynes, R., Prodöhl, P. A. and Taggart, J. B. (1995). Molecular approaches to the study of genetic variation in salmonid species. Nordic Journal of Freshwater. 71: 23-32.

Prodöhl, P. A. , Taggart, J. B. and Ferguson, A. (1994). Single locus inheritance and joint segregation analysis of minisatellite DNA single locus probes in the brown trout (Salmo trutta L). Heredity. 73, 556-566.

Prodöhl, P. A. , Taggart, J. B. and Ferguson, A. (1994). Cloning of highly variable minisatellite DNA single locus probes for brown trout (Salmo trutta L.) from a phagemid library. In: Genetics & Evolution of Aquatic Organisms (edited by A. Beaumont). Chapman & Hall, London. 263-270.

Prodöhl, P. A. , Taggart, J. B. and Ferguson, A. (1992). Genetic variability within and among sympatric brown trout (Salmo trutta L) populations: multi-locus DNA fingerprint analysis. Hereditas 117: 45-50.

Taggart, J. B., Hynes, R. A., Prodöhl, P. A. and Ferguson A. (1992). A simplified protocol for routine total DNA isolation from salmonid fishes. Journal of Fish Biology 40: 963-965.

Prodöhl, P. A. and Levy, J. A. (1989). Genetic study of Atherinidae of fishes of Mangueira Lagoon (RS - Brazil). Comp. Biochem. Physiol. 94B (3):423-426.