1. Carreiro AR, Ramos JA, Mata VA, Almeida NM, Paiva VH, Lopes RJ (2023) DNA metabarcoding uncovers prey diversity overlap among tunas and seabirds of Eastern Tropical Atlantic: implications for an ecosystem-based management. Marine Environmental Research.
  2. Carreiro AR, Ramos JA, Mata VA, Almeida NM, Paiva VH, Lopes RJ (2023) Genetics show that Tuna species misidentification can be an underestimated issue in fish landings. Food Control 109473
  1. Carreiro AR, Ramos JA, Mata VA, Matos D, Santos I, Araújo PM, Rodrigues I, Almeida NM, Militão T, Saldanha S, Paiva VH, Lopes RJ (2022) High-throughput sequencing reveals prey diversity overlap between sympatric Sulids in the tropical Atlantic. Food Webs 33:e00258
  2. Santos I, Ramos JA, Ceia FR, Rodrigues I, Almeida N, Antunes S, Carreiro AR, Matos DM, Lopes RJ, Geraldes P, Paiva VH (2022) Sexual segregation in the foraging distribution, behaviour, and trophic niche of the endemic Boyd’s shearwater (Puffinus lherminieri boydi). Marine Biology 169: 144
  3. Movalli P, Koschorreck J, Treu G, Slobodnik J, Alygizakis N, Androulakakis A, Badry A, Baltag E, Barbagli F, Bauer K, Biesmeijer K, Borgo E, Cincinelli A, Claßen D, Danielsson S, Dekker RWRJ, Dietz R, Eens M, Espín S, Eulaers I, Frahnert S, Fuiz TI, García-Fernández AJ, Fuchs J Gkotsis G, Glowacka N, Gómez-Ramírez P, Grotti M, Hosner PA, Johansson U, Jaspers VJB, Koureas D, Krone O, Kubin E, Lefevre C, Leivits m, LoBrutto S, Lopes RJ, Lourenço R, Lymberakis P, Madslien K, Martellini T, Mateo R, Nika M, Osborn D, Oswald P, Pauwels O, Pereira MG, Pezzo F, Sánchez-Virosta P, Sarajlić N, Shore RF, Soler F, Sonne C, Thomaidis N, Töpfer T, Väinölä R, van den Brink N, Vrezec A, Walker L, Weigl S, Wernham C, Woog F, Zorrilla I, Duke G (2022) The role of natural science collections in the biomonitoring of environmental contaminants in apex predators in support of the EU’s zero pollution ambition. Environmental Sciences Europe 34: 88
  4. Toomey MB, Marques CI, Araújo PM, Huang D, Zhong S, Liu Y, Schreiner GD, Myers CA, Pereira P, Afonso S, Andrade P, Gazda MA, Lopes RJ, Viegas I, Koch R, Haynes ME, Smith DJ, Ogawa Y, Murphy D, Kopec RE, Parichy DM, Carneiro M, Corbo JC (2022) A mechanism for red coloration in vertebrates. Current Biology 32(19): 4201-4214
  5. Santos B, Pinho CJ, Santos B, Pinho CJ, Šťáhlavský F, Mata VA, Lopes RJ, Vasconcelos R (2022). Diet study of geckos reveals the first records of pseudoscorpions on Desertas Islands (Cabo Verde). Journal of Arachnology 50: 39–42
  6. Norte AC, Araújo PM, Augusto L, Guímaro H, Santos S, Lopes RJ, Núncio MS, Ramos JA, Lopes de Carvalho I (2022) Effects of stress exposure in captivity on physiology and infection in avian hosts: no evidence of increased Borrelia burgdorferi s.l. infectivity to vector ticks. Microbial Ecology 83(1):202-215
  1. Lopes RJ, Faria P, Gomes D, Freitas B, Malinger J. (2021) The Hummingbird Collection of the Natural History and Science Museum of the University of Porto (MHNC-UP), Portugal. Biodiversity Data Journal 9: e59913
  2. Hellgren O, Kelbskopf V, Ellis VA, Ciloglu A, Duc M, Huang X, Lopes RJ, Mata VA, Aghayan SA, Inci A, Drovetski SV (2021) Low MSP-1 haplotype diversity in the West Palearctic population of the avian malaria parasite Plasmodium relictum. Malaria Journal 20: 265
  3. Andrade P, Gazda MA, Araújo PM, Afonso S, Lopes RJ, Marques C, Gilbert MTP, Carneiro M (2021) Molecular Parallelisms between Pigmentation in The Avian Iris and in the Integument of Ectothermic Vertebrates. PLOS Genetics 17(2):e1009404
  1. Silva LP, Mata VA, Lopes PB, Lopes RJ, Beja P (2020) High resolution multi-marker DNA metabarcoding reveals sexual dietary differentiation in a bird with minor dimorphism. Ecology & Evolution 10(19): 10364-10373
  2. Gazda MA*, Araújo PM*, Lopes RJ*, Toomey MB, Andrade P, Afonso S, Marques C, Nunes L, Pereira P, Trigo S, Hill GE, Corbo JC, Carneiro M (2020) A Genetic Mechanism for Sexual Dichromatism in Birds. Science 368(6496): 1270-1274 (* co-first authors)
  3. Gazda MA, Toomey MB, Araújo PM, Lopes RJ, Afonso S, Myers CA, Serres K, Kiser PD, Hill GE, Corbo JC, Carneiro M (2020). Genetic Basis of De Novo Appearance of Carotenoid Ornamentation in Bare-Parts of Canaries. Molecular Biology and Evolution 37(5): 1317-1328
  1. Silva LP, Mata VA, Lopes PB, Pereira P, Jarman SN, Lopes RJ, Beja P (2019) Advancing the integration of multi-marker metabarcoding data in dietary analysis of trophic generalists. Molecular Ecology Resources 19(6): 1420-1432
  2. Lopes RJ, Pinho CJ, Santos B, Seguro M, Mata VA, Egeter B, Vasconcelos R (2019) Intricate trophic links between threatened vertebrates confined to a small island in the Atlantic Ocean. Ecology & Evolution 9(8): 4994-5002
  3. Joulami L, Hamoumi R, Daief Z, Bazairi H, Lopes RJ (2019) Impact of shorebird predation on intertidal macroinvertebrates in a key Atlantic north African wintering site: an experimental approach. African Journal of Marine Science 41(1): 1-9.
  4. Lopes RJ, Ferreira JM, Moraes-Barros N (2019) A bold step towards effective monitoring of illegal wildlife trade. Conservation Biology 33(1): 7-8.
  5. Marko R, Neto JM, Lopes RJ, Collinson M, Koblik E, Fadeev I, Lohman Y, Aghayan S, Boano G, Pavia M, Perlman Y, Kiat Y, Ben DA, Voelker G, Drovetski S (2019) Geographic patterns of mtDNA and Z-linked sequence variation in the common chiffchaff. PLOS ONE 14 (1), e0210268.
  6. Pinho CJ, Santos B, Mata VA, Seguro M, Romeiras MM, Lopes RJ, Vasconcelos R (2018) What is the giant wall gecko having for dinner? Conservation genetics for guiding reserve management in Cabo Verde. Genes 9(12): 599.
  7. Rodrigues P, Micael J, Resendes R, Lopes RJ, Ramos JA, Cunha RT (2018) Genetic and morphometric variation of the Blackcap (Sylvia atricapilla) on the Azores Archipelago reveals a recent range expansion. Journal of Natural History 52: 2413-2435
  8. Drovetski SV, Fadeev IV, Rakovic M, Lopes RJ, Boano G, Pavia M, Koblik EA, Lohman YV, Red’kin YA, Aghayan SA, Reis S, Drovetskaya SS, Voelker G (2018) A test of the European Pleistocene Refugial Paradigm, using a Western Palearctic endemic bird species. Proceedings of the Royal Society B 285: 20181606
  9. Toomey M, Marques C, Andrade P, Araújo PM, Sabatino S, Gazda M, Afonso S, Lopes RJ, Corbo J, Carneiro M (2018) A non-coding region near Follistatin controls head color polymorphism in gouldian finch. Proceedings of the Royal Society B 285: 20181788.
  10. Costa J, Ramos JA, da Silva LP, Sérgio T, Andrade P, Araújo PM, Carneiro C, Correia E, Cortez P, Felgueiras M, Godinho C, Lopes RJ, Matos C, Norte C, Pereira PF, Rosa A, Heleno RH (2018) Rewiring of experimentally disturbed seed dispersal networks might lead to unexpected network configurations. Basic and Applied Ecology 30: 11-22.
  11. Lopes RJ, Correia J, Batalha H, Cardoso GC. Haemosporidian parasites missed the boat during the introduction of common waxbills (Estrilda astrild) in Iberia (2018) Parasitology 145(11): 1493-1498.
  12. Gazda MM, Andrade P, Afonso S, Dilytė J, Archer JP, Lopes RJ, Faria R, Carneiro M. Signatures of Selection on Standing Genetic Variation Underlie Athletic and Navigational Performance in Racing Pigeons. Molecular Biology and Evolution 35(5): 1176-1189.
  13. Lopes RJ, Mérida AM, Carneiro M (2017) Unleashing the Potential of Public Genomic Resources to Find Parasite Genetic Data. Trends in Parasitology 33(10): 750-753.
  14. Lopes RJ, Ferreira JM, Moraes-Barros N (2017) A critical comment to D´Cruze and Macdonald (2016). Nature Conservation 21: 159-161.
  15. Toomey MB, Lopes RJ, Araújo PM, Johnson JD, Gazda M, Afonso S, Mota PG, Koch RE, Hill GE, Corbo JC, Carneiro M (2017) The High-Density Lipoprotein Receptor, SCARB1, is required For Carotenoid Coloration in Birds. Proceedings of the National Academy of Science USA 114(20): 5219–5224.
  16. Lourenço PM, Catry T, Lopes RJ, Piersma T, Granadeiro J (2017) Invisible trophic links? Quantifying the importance of non-standard food sources for key intertidal avian predators in the Eastern Atlantic. Marine Ecology Progress Series 563: 219-232.
  17. Rodrigues P, Lopes RJ, Resendes R, Ramos JA, Cunha RT (2016) Genetic diversity of the Azores blackbirds reveal multiple founder events. Acta Ornithologica 51(2): 221-234.
  18. Lopes RJ, Gomez JA, Andreotti A, Andreoni M (2016) The Purple Swamphen or Gallinule (Porphyrio porphyrio) and humans, a forgotten history of past interactions. Society & Animals 24(6): 574-595.
  19. Lopes RJ, Johnson JD, Toomey MB, Ferreira MS, Araújo PM, Melo-Ferreira J, Andersson L, Hill GE, Corbo JC, Carneiro M (2016) Genetic basis for red coloration in birds. Current Biology 26(11): 1427-1434.
  20. Catry T, Pedro L, Lopes RJ, Carneiro C, Alves J, Costa J, Rguibi-Idrissi H, Bearhop S, Piersma T, Granadeiro J (2016) Structure and functioning of intertidal food webs along an avian flyway: a comparative approach using stable isotopes. Functional Ecology 30(3): 468-478.
  21. Catry T, Lourenço PM, Lopes RJ, Bocher P, Carneiro C, Alves JA, Delaporte P, Bearhop S, Piersma T, Granadeiro JP (2016) Use of stable isotopes fingerprints to assign wintering origin and trace shorebird movements across the East Atlantic Flyway. Basic and Applied Ecology 17(2): 177-187.
  22. Andrade P, Rodrigues P, Lopes RJ, Ramos JA, Cunha RT, Gonçalves D (2015) Ecomorphological patterns in Blackcap Sylvia atricapilla: insular versus mainland populations. Bird Study 62(4): 498-507.
  23. Mata VA, Silva LP, Lopes RJ, Drovetski SV (2015) Strait of Gibraltar poses an effective barrier to host-specialized but not to host-generalized lineages of avian haemosporidia. International Journal for Parasitology 45(11): 711-719.
  24. Cardoso GC, Leitão AV, Funghi C, Batalha HR, Lopes RJ, Mota PG (2014) Similar preferences for ornamentation in opposite- and same- sex choice experiments. Journal of Evolutionary Biology 27(12): 2798-806.
  25. Rodrigues P, Lopes RJ, Micael J, Resendes R, Ramos JA, Cunha RT (2014) Genetic and morphometric diversity of the goldcrest (Regulus regulus) populations in the Azores. Zoology 117(6): 383–391.
  26. Cardoso GC, Batalha HR, Reis S, Lopes RJ (2014) Increasing sexual ornamentation during a biological invasion. Behavioral Ecology 25(4):916-923.
  27. SV Drovetski, SA Aghayan, VA Mata, Lopes RJ, NA Mode, JA Harvey, G Voelker (2014) Does the niche-breadth or trade-off hypothesis explain the abundance-occupancy relationship in avian haemosporidia? Molecular Ecology 23(13): 3322-3329.
  28. Pardal S, Alves JA, Rocha A, Lopes RJ, Potts P, Alves MJ, Zé-Zé L, Osório H, Amaro F, Pérez-Tris J, Masero J, Ramos JA, Mendes L (2014) Shorebird low spillover risk of mosquito-borne pathogens on major Iberian wetlands. Journal of Ornithology 155(2):549-554.
  29. Rodrigues P, Lopes RJ, Reis S, Resendes R, Ramos JA, Cunha RT (2014) Genetic diversity and morphological variation of the common chaffinch (Fringilla coelebs) in the Azores. Journal of Avian Biology 45: 167-178.
  30. Carvalho CF, Leitão AV, Funghi C, Batalha HR, Reis S, Mota PG, Lopes RJ, Cardoso GC (2013) Personality traits are related to ecology across a biological invasion. Behavioral Ecology 24:1081-1091.
  31. Rodrigues P, Lopes RJ, Drovetski SV, Reis S, Ramos JA, Cunha RT (2013) Phylogeography and genetic diversity of the Robin (Erithacus rubecula) in the Azores islands: evidence of a recent colonisation. Journal of Ornithology 154(4): 889-900.
  32. Lifjeld JT, Hoenen A, Johannessen LE, Laskemoen T, Lopes RJ, Rodrigues P, Rowe M (2013) The Azores bullfinch (Pyrrhula murina) has the same unusual and size-variable sperm morphology as the Eurasian bullfinch (Pyrrhula pyrrhula). Biological Journal of the Linnean Society 108: 677–687.
  33. Lopes RJ, JA Alves, JA Gill, TG Gunnarsson, JCEW Hooijmeijer, PM Lourenço, JA Masero, T Piersma, PM Potts, B Rabaçal, S Reis, JM Sánchez-Guzman, F Santiago-Quesada, A Villegas (2013) Do different subspecies of Black-tailed Godwit Limosa limosa overlap in Iberian wintering and staging areas? Validation with genetic markers. Journal of Ornithology 154(1): 35-40.
  34. Joulami L, Rguibi Idrissi H, Bazairi H, Lopes RJ, El Hamoumi R (2013) Study of the migratory waders phenology in the lagoon and salines of Sidi Moussa (Morocco). Bulletin de l’Institut Scientifique, Section Sciences de la Vie 35: 131-140.
  35. Ribeiro MA, Lopes RJ, Bowie RCK (2012) Historical demographic dynamics underlying local adaptation in the presence of gene flow. Ecology and Evolution 2(11): 2710-2721.
  36. Santos SS, Pardal S, Proença DN, Lopes RJ, Ramos JA, Mendes L, Morais PV (2012) Diversity of cloacal microbial community in migratory shorebirds that use the Tagus estuary as stopover habitat and their potential to harbor and disperse pathogenic microorganisms. FEMS Microbiology Ecology 82(1): 63-74.
  37. Ventim R, Ramos JA, Osório H, Lopes RJ, Pérez-Tris J, Mendes L (2012) Avian malaria infections in western European mosquitoes. Parasitology Research 111(2): 637-645.
  38. Carvalho IL, Zé-Zé L, Alves AS, Pardal S, Lopes RJ, Mendes L, Núncio MS (2012) Borrelia garinii and Francisella tularensis subsp. holarctica detected in migratory shorebirds in Portugal. European Journal of Wildlife Research 58(5): 857-861.
  39. Töpfer T, Haring E, Birkhead TR, Lopes RJ, Liu Severinghaus, Martens J, Päckert M (2011) A molecular phylogeny of bullfinches Pyrrhula Brisson, 1760 (Aves: Fringillidae). Molecular Phylogenetics and Evolution 58(2): 271-282.
  40. Masero JA, Santiago-Quesada F, Sánchez-Guzmán JM, Villegas A, Abad-Gómez JM, Lopes RJ, Encarnação V, Corbacho C, Morán R (2011) Long lengths of stay, large numbers, and trends of the Black-tailed Godwit Limosa limosa in rice fields during spring migration. Bird Conservation International 21(1): 12-24.
  41. Chen S, Lin B, Baig M, Mitra B, Lopes RJ, Santos AM, Magee DA, Azevedo M, Tarroso P, Sasazaki S, Ostrowski S, Mahgoub O, Chaudhuri TK, Zhang Y, Costa V, Royo LJ, Goyache F, Luikart G, Boivin N, Fuller DQ, Mannen H, Bradley DG, Beja-Pereira A (2010) Zebu cattle are an exclusive legacy of the South Asia Neolithic. Molecular Biology and Evolution 27: 1-6.
  42. Lopes RJ, Hortas F, Wennerberg L (2008) Geographical segregation in Dunlin Calidris alpina populations wintering along the East Atlantic migratory flyway – evidence from mitochondrial DNA analysis. Diversity and Distributions 14: 732-741.
  43. Antao T, Lopes A, Lopes RJ, Beja-Pereira A, Luikart G (2008) LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9: 323.
  44. Tavares PC, Kelly A, Maia R, Lopes RJ, Serrão Santos R, Pereira ME, Duarte AC, Furness RW (2008) Variation in the mobilization of mercury into Black-winged Stilt Himantopus himantopus chicks in coastal saltpans, as revealed by stable isotopes. Estuarine Coastal and Shelf Science 77(1): 65-76.
  45. Silva-Santos P, Pardal MA, Lopes RJ, Múrias T, Cabral JA (2008). Testing the Stochastic Dynamic Methodology (StDM) as a management tool in a shallow temperate estuary of south Europe (Mondego, Portugal). Ecological Modelling 210: 377-402.
  46. Faria MS, Lopes RJ, Malcato J, Nogueira AJA, Soares AMVM (2008) In situ bioassays with Chironomus riparius larvae to biomonitor metal pollution in rivers and to evaluate the efficiency of restoration measures in mine areas. Environmental Pollution 151: 213-221.
  47. Tavares PC, Kelly A, Lopes RJ, Pereira ME, Duarte AC, Furness RW (2007) The influence of dietary specialization and trophic status on mercury levels in two species using common coastal wetlands, Himantopus himantopus and Sterna albifrons. Ardeola 54(2): 275-288.
  48. Simões BF, Rebelo H, Lopes RJ, Alves PC, Harris DJ (2007) Patterns of genetic diversity within and between Myotis d. daubentonii and M. d. nathalinae derived from cytochrome b mtDNA sequence data. Acta Chiropterologica 9(2): 379-389.
  49. Faria MS, Lopes RJ, Nogueira AJA, Soares AMVM (2007) In situ and laboratory bioassays with Chironomus riparius larvae to assess toxicity of metal contamination in rivers: the relative toxic effect of sediment versus water contamination. Environmental Toxicology and Chemistry 26(9): 1968–1977.
  50. Martins I, Lopes RJ, Lillebo AI, Neto JM, Pardal MA, Ferreira JG, Marques JC (2007) Significant variations in the productivity of green macroalgae in a mesotidal estuary: Implications to the nutrient loading of the system and the adjacent coastal area. Marine Pollution Bulletin 54: 678-690.
  51. Lopes RJ, Pardal MA, Múrias T, Cabral JA, Marques JC (2006) Influence of macroalgal mats on abundance and distribution of Dunlin Calidris alpina in estuaries: A long-term approach. Marine Ecology Progress Series 323: 11-20.
  52. Lopes RJ, Marques JC, Wennerberg L (2006) Migratory connectivity and temporal segregation of Dunlin (Calidris alpina) in Portugal – evidence from morphology, ringing recoveries and mtDNA. Journal of Ornithology 147: 385-394.
  53. Silva-Santos P, Pardal MA, Lopes RJ, Múrias T, Cabral JA (2006) A Stochastic Dynamic Methodology (SDM) to the modelling of trophic interactions, with a focus on estuarine eutrophication scenarios. Ecological Indicators 6: 394-408.
  54. Múrias T, Cabral JA, Lopes RJ, Pardal M, Marques JC, Goss-Custard (2005) Competition for feeding in waders: A case study in an estuary of south temperate Europe (Mondego, Portugal). Hydrobiologia 544: 155-166.
  55. Lopes RJ, Múrias T, Cabral JC, Marques JC (2005) A ten year study of variation, trends and seasonality of shorebird community in the Mondego Estuary, Portugal. Waterbirds 28(1): 8-18.
  56. Tavares PC, Monteiro LR, Lopes RJ, Correia dos Santos MM, Furness RW (2005) Variation of Mercury Contamination in Chicks of Little Tern Sterna albifrons in Southwest Europe: Brood, Age, and Colony Related Effects. Bulletin of Environmental Contamination and Toxicology 74(1): 177-184.
  57. Tavares PC, Monteiro LR, Lopes RJ, Correia dos Santos MM, Furness RW (2004) Mercury in chicks of Black-winged Stilt (Himantopus himantopus) in coastal wetlands from south-western Europe: Inter-tissue and geographic variation. Bulletin of Environmental Contamination and Toxicology 72(3): 437-444.
  58. Múrias T, Cabral JC, Lopes RJ, Marques JC, Goss-Custard J (2003) Use of traditional salines by waders in the Mondego estuary (Portugal): A conservation perspective. Ardeola (2003) 49(2): 223-240.
  59. Lopes RJ, Pardal MA, Marques JC (2000) Impact of macroalgae blooms and wader predation on intertidal macroinvertebrates – experimental evidence in the Mondego estuary. Journal of Experimental Marine Biology and Ecology 28(2): 165-179.
  60. Cabral JA, Pardal MA, Lopes RJ, Múrias T, Marques JC (1999) The impact of macroalgal blooms on the use of the intertidal area and feeding behaviour of waders (Charadrii) in the Mondego estuary (Portugal). Acta Oecologica 20(4): 417-427.
  61. Lopes RJ, Cabral JA, Múrias T, Marques JC (1998) Contribution to the study of the diet of the Dunlin Calidris alpina and the Grey Plover Pluvialis squatarola in the Mondego estuary. Airo 9 (1/2): 27-32.
  62. Múrias T, Cabral JC, Lopes RJ, Marques JC (1997) Low-water use of the Mondego Estuary (West Portugal) by waders (Charadrii). Ardeola 44(1): 79-91.
  63. Cabral JA, Múrias T, Lopes RJ, Marques JC (1996) Macroalgae blooms and macrohabitat selection by waders: a study in Mondego Estuary (Western Portugal). Airo 7: 1-6.

@ Ricardo Jorge Lopes