prof. Mgr. et Mgr. Josef Bryja Ph.D.

Position head of the facility
Direction molecular ecology

+420 560 590 601

Research interests

  • evolutionary history, phylogeography, speciation, adaptation, phylogeny and systematics (mainly of small mammals),
  • biogeography, distribution of biodiversity in Africa,
  • molecular ecology of vertebrates (interactions between neutral and adaptive genetic variation, conservation genetics, immunogenetics),
  • ecology of mammals (population dynamics, structure of communities).

Running Projects

Phyloregions of sub-Saharan Africa: Small mammals as a suitable model group for unbiased quantification of evolutionary diversity and uniqueness (2023–2025)
COST - CA18134 Genomic BIodiversity Knowledge for Resilient Ecosystems (2019–2023)

Finished projects

INTER-COST: Conservation genetics and genomics of vertebrate species in Central European region (2020–2023)
Small mammals of Eastern African Mountains: evolutionary diversification and endemism in one of the world´s most important biodiversity hot-spots (2020–2022)
Evolution at steep elevational gradients: assessing the role of genetic and ecological factors in speciation process (2018–2020)
MEZEK: Mezinárodní spolupráce v ekologické a evoluční biologii obratlovců (2018–2020)
Evoluce hlodavců a jejich parazitů v otevřených biotopech východní Afriky (2015–2017)
BIOM: Vzdělávací centrum pro biodiverzitu – Mohelský mlýn (2015–2016)
Next-generation technologies in evolutionary genetics (2012–2015)
Comparative phylogeography of Zambezian region in Southeastern Africa using small mammals as a model (2010–2014)
Toll-like receptors in passerine birds: description, characterization of polymorphism and evolutionary consequences of allelic variation (2010–2014)
PROVAZ: PROpojení Vzdělávání A nových přístupů v Zoologicko-ekologickém výzkumu - od teorie k praxi (2011–2014)
Utilization of genetic resources for effective corservation of endangered species (2010–2012)
Biology of African mole-rats from mesic tropic areas (2008–2011)
Genetic structure of the freshwater pearl mussel in the Czech Republic (2009–2010)
Conservation genetics of selected vertebrates in the Western Balkans (2008–2009)
Intraspecific variability of populations of two cryptic bat species of genus Pipistrellus in Central Europe (2006–2008)
The role of MHC in sexual selection - observational and experimental study in three model vertebrate species (2006–2008)

Education

  • 1992-1997: undergraduate study in Systematic Zoology and Ecology – Masaryk University in Brno, Faculty of Science. Diploma thesis: Structure of communities of small terrestrial mammals in various habitats of the Protected Landscape Area of Poodří. (MSc.=Mgr.).
  • 1993-1998: undergraduate study in Molecular Biology and Genetics – Masaryk University in Brno, Faculty of Science. Diploma thesis: Preparation of truncated variant of gene coding for RXR alpha and its transfer to monoblast cell line BM2. (MSc.=Mgr.).
  • 1997-2000: Ph.D. study in Zoology – Masaryk University in Brno, Faculty of Science. Ph.D. thesis: Demographic characteristics of the common vole (Microtus arvalis) population in southern Moravia. (PhD.).

Employment

Institute of Vertebrate Biology, Czech Academy of Sciences, Brno (IVB):

  • 1997-1998: research assistant, Brno
  • 1998-2009: junior researcher, Department of Population Biology of IVB, Brno and Studenec (responsible for the running of the Laboratory of molecular genetics in Studenec)
  • 2010-present: senior researcher, head of the Research Facility of IVB in Studenec
  • 2011-2019: scientific secretary of IVB
  • 2012-present: head of the IVB´s Board

Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno:

  • 2003-2009: research assistant (part-time)
  • 2009-present: Associate Professor (part-time), Lectures: Molecular ecology, Genetic methods in zoology, Advances in zoology of vertebrates, supervising of M.Sc. and Ph.D. students.

International experience

  • 2004-2006: postdoctoral fellow, Centre de Biologie et Gestion des Populations, Montferriez sur Lez, France (projects on wildlife immunogenetics).
  • short visits and invited lectures at research institutes in France, Poland, Denmark, Belgium, Portugal, Italy, Slovenia, Romania, etc.,
  • numerous field expeditions in Africa, more than 1 year in total (Senegal, Mozambique, Kenya, Tanzania, Ethiopia, Madagascar).
  • 2009-2013: Member of the consortium ConGRESS (Conservation of Genetic Resources for Effective Species Survival), 7th Framework Programme of EC; 2012 – organization of two international workshops on conservation genetics (Slovakia, Hungary).
  • 2018 – CIBIO-InBIO – Research Centre in Biodiversity and Genetic Resources, Porto, Portugal (guest researcher, 6 months)
  • 2019 – university course of Molecular Ecology at Mekelle University (Ethiopia)
  • 2019 – main organizer of the 13th African Small Mammal Symposium in Ethiopia

Selected current collaborations

  • University of South Bohemia, České Budějovice, Czech Republic (R. Šumbera)
  • Centre de Biologie et Gestion des Populations, Montferrier sur Lez, France (M. Galan, N. Charbonnel, L. Granjon, G. Dobigny, C. Brouat)
  • Muséum national d´Histoire naturelle, Paris, France (V. Nicolas, C. Denys)
  • University of Antwerps, Belgium (H. Leirs)
  • Field Museum of Natural History, Chicago, USA (J. Kerbis Peterhans, T. Demos, A. Ferguson)
  • Royal Belgian Institute for Natural Sciences, Brussels, Belgium (E. Verheyen)
  • Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania (R. Makundi, A. Massawe)
  • Mekelle University, Ethiopia (Y. Meheretu)
  • A.N.Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia (L. Lavrenchenko)
  • CIBIO-InBIO – Research Centre in Biodiversity and Genetic Resources, Porto, Portugal (Z. Boratynski)

Other scientific activities

Actual Ph.D. students

Former Ph.D. students

  • Mazoch Vladimír, 2019: Phylogeography of small mammals in the Zambezian savannahs. University of South Bohemia, České Budějovice. (co-supervised by R. Šumbera)
  • Bartáková Veronika, 2018: The effects of non-native species on host-parasite relationships. Masaryk University, Brno. (co-supervised by M. Reichard)
  • Aghová Tatiana, 2018: Comparative phylogeography of the Somali-Maasai region in eastern Africa using selected rodent species as a model. Masaryk University, Brno. (co-supervised by R. Šumbera)
  • Čížková Dagmar, 2015: Major histocompatibility complex variation in the house mice hybrid zone. Masaryk University, Brno.
  • Wasimuddin, 2014: Genetic variation of selected pathogens in the house mouse hybrid zone. Masaryk University, Brno. (co-supervised by J.Gouy de Bellocq and J. Piálek)
  • Zemanová Barbora, 2014: Genetic structure of chamois populations in Central Europe. Masaryk University, Brno.
  • Fornůsková Alena, 2013: Genes of innate immunity and their significance in evolutionary ecology of free living rodents. Masaryk University Brno and Université Montpellier II. (co-supervised by J.F. Cosson)
  • Patzenhauerová-Konvičková Hana, 2013: Bathyergid rodents of mesic tropical regions: Phylogeography, kinship structure and mating systems. Masaryk University, Brno.
  • Promerová Marta, 2011: Major histocompatibility complex genes: their variation and impact on fitness in a socially monogamous passerine. Masaryk University, Brno. (co-supervised by T. Albrecht)
  • Poláková Radka, 2011: The effect of genetic factors on reproductive success in a socially monogamous songbird. Masaryk University, Brno. (co-supervised by T. Albrecht).
  • Říčanová Štěpánka, 2011: Phylogeography and conservation genetics of the European ground squirrel. University of South Bohemia, České Budějovice. (co-supervised by F.Sedláček)
  • Konečný Adam, 2009: Consequences of anthropogenic changes on rodent communities and populations: study cases on native and introduced species in Eastern Senegal. Masaryk University, Brno and Université Montpellier II. (co-supervised by J.M. Duplantier and J.F. Cosson)
  • Hájková Petra, 2008: Conservation genetics of the Eurasian otter. Masaryk University, Brno. (co-supervised by P.Jurajda)

Publications

2023

Cuypers LN, Gryseels S, Van Houtte N, Baird SJE, Sabuni CA, Katakweba AS, van den Burg SRM, Bryja J, Leirs H, Goüy de Bellocq J (2023). Subspecific rodent taxa as the relevant host taxonomic level for mammarenavirus host specificity. Virology, 581: 116-127.
Dianat M, Voet I, Ortiz D, Goüy de Bellocq J, Cuypers LN, Kryštufek B, Bureš M, Čížková D, Bryjová A, Bryja J, Nicolas V, Konečný A (2023). Cryptic diversity of Crocidura shrews in the savannahs of Eastern and Southern Africa. Molecular Phylogenetics and Evolution, 180: 107708.
Dianat M, Konečný A, Lavrenchenko LA, Peterhans JCK, Demos TC, Nicolas V, Ortiz D, Bryja J (2023). How to cross the desert if you are small and need mountains? Out-of-Ethiopia dispersal in Afromontane shrews. Journal of Biogeography, :.
Gajdárová B, Belotti E, Bufka L, Volfová J, Wölfl S, Mináriková T, Hollerbach L, Duľa M, Kleven O, Kutal M, Nowak C, Ozoliņš J, Tám B, Bryja J, Koubek P, Krojerová-Prokešová J (2023). Long-term genetic monitoring of a reintroduced Eurasian lynx population does not indicate an ongoing loss of genetic diversity. Global Ecology and Conservation, 42: e02399.
Hánová A, Bryja J, Goüy de Bellocq J, Baird SJE, Cuypers L, Konečný A, Mikula O (2023). Historical demography and climatic niches of the Natal multimammate mouse (Mastomys natalensis) in the Zambezian region. Mammalian Biology, 103: 239-251.
Martynov AA, Zemlemerova ED, Kostin DS, Komarova VA, Gromov AR, Yihune M, Tsegaye A, Alexandrov DY, Bekele A, Bryja J, Lavrenchenko LA (2023). Uncovering the diversity of rodents and shrews in the Chebera Churchura National Park, Ethiopia. Mammalia, 87: 451-463.
Meheretu Y, Mikula O, Frynta D, Frýdlová P, Mulualem G, Lavrenchenko LA, Kostin DS, Elmi HSA, Šumbera R, Bryja J (2023). Phylogeny, biogeography, and integrative taxonomic revision of the Afro-Arabian rodent genus Ochromyscus (Muridae: Murinae: Praomyini). Zoological Journal of the Linnean Society, :.
Mizerovská D, Martynov AA, Mikula O, Bryjová A, Meheretu Y, Lavrenchenko LA, Bryja J (2023). Genomic diversity, evolutionary history, and species limits of the endemic Ethiopian laminate-toothed rats (genus Otomys, Rodentia: Muridae). Zoological Journal of the Linnean Society, :.
Mizerovská D, Špoutil F, Claude J, Lavrenchenko LA, Procházka J, Bryja J, Mikula O (2023). Parallel evolution of skull form in three rodent genera inhabiting steep elevational gradients of Ethiopian highlands. Evolutionary Biology, 50: 332-349.
Reichard M, Koblmüller S, Blažek R, Zimmermann H, Katongo C, Bryjová A, Bryja J (2023). Lack of host specialization despite selective host use in brood parasitic cuckoo catfish. Molecular Ecology, 32: 6070-6082.

2022

Bryja J, Meheretu Y, Boratyński Z, Zeynu A, Denys C, Mulualem G, Welegerima K, Bryjová A, Kasso M, Kostin DS, Martynov AA, Lavrenchenko LA (2022). Rodents of the Afar Triangle (Ethiopia): geographical isolation causes high level of endemism. Biodiversity and Conservation, 31: 629-650.
Cuypers LN, Sabuni C, Šumbera R, Aghová T, Lišková E, Leirs H, Baird SJE, Goüy de Bellocq J, Bryja J (2022). Biogeographical importance of the Livingstone Mountains in southern Tanzania: comparative genetic structure of small non-volant mammals. Frontiers in Ecology and Evolution, 9: 742851.
Krásová J, Mikula O, Lavrenchenko LA, Šumbera R, Meheretu Y, Bryja J (2022). A new rodent species of the genus Mus (Rodentia: Muridae) confirms the biogeographical uniqueness of the isolated forests of southern Ethiopia. Organisms Diversity & Evolution, 22: 491-509.
Mapaco L, Crespin L, Rodrigues D, Goüy de Bellocq J, Bryja J, Bourgarel M, Missé D, Caron A, Fafetine J, Cappelle J, Liégeois F (2022). Detection and genetic diversity of Mopeia virus in Mastomys natalensis from different habitats in the Limpopo National Park, Mozambique. Infection, Genetics and Evolution, 98: 105204.
Meheretu Y, Meinig H, Mikula O, Hermes N, Wale M, Tadele A, Kaipf I, Bryja J (2022). Small- and medium-sized mammals of the Kafa Biosphere Reserve, Ethiopia. African Journal of Ecology, 60: 433-446.
Meheretu Y, Tilahun T, Engdayehu G, Bosma L, Mulualem G, Craig EW, Bryja J, van Steenbergen F (2022). A snapshot of rodents and shrews of agroecosystems in Ethiopian highlands using camera traps. Mammalia, 86: 230-238.
Mikula O, Krásová J, Šumbera R, Bryja J (2022). Taxonomic position and biogeography of Mus callewaerti, the largest species of the subgenus Nannomys (Rodentia: Muridae). Lynx, 53: 271-290.
Uhrová M, Mikula O, Bennett NC, Van Daele P, Piálek L, Bryja J, Visser JH, Jansen van Vuuren B, Šumbera R (2022). Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius. Molecular Phylogenetics and Evolution, 167: 107337.
Votýpka J, Stříbrná E, Modrý D, Bryja J, Bryjová A, Lukeš J (2022). Unexpectedly high diversity of trypanosomes in small sub-Saharan mammals. International Journal for Parasitology, 52: 647-658.

2021

Bartáková V, Bryjová A, Nicolas V, Lavrenchenko LA, Bryja J (2021). Mitogenomics of the endemic Ethiopian rats: looking for footprints of adaptive evolution in sky islands. Mitochondrion, 57: 182-191.
Bletsa M, Vrancken B, Gryseels S, Boonen I, Fikatas A, Li Y, Laudisoit A, Lequime S, Bryja J, Makundi R, Meheretu Y, Akaibe BD, Mbalitini SG, Van de Perre F, Van Houtte N, Těšíková J, Wollants E, Van Ranst M, Pybus OG, Drexler JF, Verheyen E, Leirs H, Goüy de Bellocq J, Lemey P (2021). Molecular detection and genomic characterization of diverse hepaciviruses in African rodents. Virus Evolution, 7:1205 veab036.
Hánová A, Konečný A, Mikula O, Bryjová A, Šumbera R, Bryja J (2021). Diversity, distribution, and evolutionary history of the most studied African rodents, multimammate mice of the genus Mastomys: An overview after a quarter of century of using DNA sequencing. Journal of Zoological Systematics and Evolutionary Research, 59: 2500-2518.
Hánová A, Konečný A, Nicolas V, Denys C, Granjon L, Lavrenchenko LA, Šumbera A, Mikula O, Bryja J (2021). Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships. Molecular Phylogenetics and Evolution, 155: 107007.
Komarova VA, Kostin DS, Bryja J, Mikula O, Bryjová A, Čížková D, Šumbera R, Meheretu Y, Lavrenchenko LA (2021). Complex reticulate evolution of speckled brush‐furred rats (Lophuromys) in the Ethiopian centre of endemism. Molecular Ecology, 30: 2349-2365.
Krásová J, Mikula O, Šumbera R, Horáková S, Robovský J, Kostin DS, Martynov AA, Lavrenchenko LA, Bryja J (2021). The Rufous Sengi is not Elephantulus—Multilocus reconstruction of evolutionary history of sengis from the subfamily Macroscelidinae. Journal of Zoological Systematics and Evolutionary Research, 59: 918-932.
Krásová J, Mikula O, Bryja J, Baptista NL, Antonio T, Aghová T, Šumbera R (2021). Biogeography of Angolan rodents: the first glimpse based on phylogenetic evidence. Diversity and Distributions, 27: 2571-2583.
Meheretu Y, Granberg Å, Berhane G, Khalil H, Lwande OW, Mitiku M, Welegerima K, Goüy de Bellocq J, Bryja J, Abreha H, Leirs H, Ecke F, Evander M (2021). Prevalence of orthohantavirus-reactive antibodies in humans and peri-domestic rodents in Northern Ethiopia. Viruses, 13:1205 1054.
Mikula O, Nicolas V, Šumbera R, Konečný A, Denys C, Verheyen E, Bryjová A, Lemmon AR, Lemmon EM, Bryja J (2021). Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Molecular Phylogenetics and Evolution, 157: 107069.
Nicolas V, Mikula O, Lavrenchenko LA, Šumbera R, Bartáková V, Bryjová A, Meheretu Y, Verheyen E, Missoup AD, Lemmon AR, Moriarty Lemmon E, Bryja J (2021). Phylogenomics of African radiation of Praomyini (Muridae: Murinae) rodents: First fully resolved phylogeny, evolutionary history and delimitation of extant genera. Molecular Phylogenetics and Evolution, 163: 107263.
Onditi KO, Demos TC, Kerbis Peterhans JC, Chen ZZ, Bryja J, Lavrenchenko LA, Musila S, Verheyen E, Van de Perre F, Akaibe BD, de la Sancha NU, Jiang XL (2021). Historical biogeography, systematics, and integrative taxonomy of the non-Ethiopian speckled pelage brush-furred rats (Lophuromys flavopunctatus group). BMC Ecology and Evolution, 21:1205 89.
Voelker G, Huntley JW, Bryja J, Denys C, Šumbera R, Demos TC, Lavrenchenko L, Nicolas V, Gnoske TP, Kerbis Peterhans JC (2021). Molecular systematics and biogeographic history of the African climbing-mouse complex (Dendromus). Molecular Phylogenetics and Evolution, 161: 107166.

2020

Bryja J, Meheretu Y, Denys C, Taylor P, Leirs H (2020). The 13th African Small Mammal Symposium in Mekelle, Ethiopia, and the evolution of these meetings. Journal of Vertebrate Biology, 69:1205 E2002.
Craig EW, Stanley WT, Kerbis Peterhans JC, Bryja J, Meheretu Y (2020). Small terrestrial mammal distributions in Simien Mountains National Park, Ethiopia: a reassessment after 88 years. Journal of Mammalogy, 101: 634-647.
Cuypers LN, Baird SJE, Hánová A, Locus T, Katakweba AS, Gryseels S, Bryja J, Leirs H, Goüy de Bellocq J (2020). Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure?. Virus Evolution, 6:1205 veaa039.
Kerbis Peterhans JC, Hutterer R, Doty JB, Malekani JM, Moyer DC, Krásová J, Bryja J, Banasiak RA, Demos TC (2020). Four new species of the Hylomyscus anselli group (Mammalia: Rodentia: Muridae) from the Democratic Republic of Congo and Tanzania. Bonn Zoological Bulletin, 69: 55-831210 .
Konečný A, Hutterer R, Meheretu Y, Bryja J (2020). Two new species of Crocidura (Mammalia: Soricidae) from Ethiopia and updates on the Ethiopian shrew fauna. Journal of Vertebrate Biology, 69:1205 20064.
Kostin DS, Martynov AA, Komarova VA, Alexandrov DY, Yihune M, Kasso M, Bryja J, Lavrenchenko LA (2020). Rodents of Choke Mountain and surrounding areas (Ethiopia): the Blue Nile gorge as a strong biogeographic barrier. Journal of Vertebrate Biology, 69:1205 20016.
Lövy M, Lavrenchenko LA, Kostin DS, Martynov AA, Šumbera R, Bryja J, Okrouhlík J (2020). The effect of elevation on haematocrit in Ethiopian rodents. Journal of Vertebrate Biology, 69:1205 20011.
Martynov AA, Bryja J, Meheretu Y, Lavrenchenko LA (2020). Multimammate mice of the genus Mastomys (Rodentia: Muridae) in Ethiopia – diversity and distribution assessed by genetic approaches and environmental niche modelling. Journal of Vertebrate Biology, 69:1205 20006.
Mikula O, Nicolas V, Boratyński Z, Denys C, Dobigny G, Fichet-Calvet E, Gagaré S, Hutterer R, Nimo-Paintsil SC, Olayemi A, Bryja J (2020). Commensalism outweighs phylogeographical structure in its effect on phenotype of a Sudanian savanna rodent. Biological Journal of the Linnean Society, 129: 931-949.
Mizerovská D, Mikula O, Meheretu Y, Bartáková V, Bryjová A, Kostin DS, Šumbera R, Lavrenchenko LA, Bryja J (2020). Integrative taxonomic revision of the Ethiopian endemic rodent genus Stenocephalemys (Muridae: Murinae: Praomyini) with the description of two new species. Journal of Vertebrate Biology, 69:1205 20031.
Nicolas V, Fabre P, Bryja J, Denys C, Verheyen E, Missoup AD, Olayemi A, Katuala P, Dudu A, Colyn M, Kerbis Peterhans JC, Demos T (2020). The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity. Molecular Phylogenetics and Evolution, 144: 106703.

2019

Aghová T, Palupčíková K, Šumbera R, Frynta D, Lavrenchenko LA, Meheretu Y, Sádlová J, Votýpka J, Mbau JS, Modrý D, Bryja J (2019). Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny. BMC Evolutionary Biology, 19: 69.
Bartáková V, Bryja J, Šanda R, Bektas Y, Stefanov T, Choleva L, Smith C, Reichard M (2019). High cryptic diversity of bitterling fish in the southern West Palearctic. Molecular Phylogenetics and Evolution, 133: 1-11.
Bryja J, Colangelo P, Lavrenchenko LA, Meheretu Y, Šumbera R, Bryjová A, Verheyen E, Leirs H, Castiglia R (2019). Diversity and evolution of African Grass Rats (Muridae: Arvicanthis)—From radiation in East Africa to repeated colonization of northwestern and southeastern savannas. Journal of Zoological Systematics and Evolutionary Research, 57: 970-988.
Bryja J, Meheretu Y, Šumbera R, Lavrenchenko LA (2019). Annotated checklist, taxonomy and distribution of rodents in Ethiopia. Folia zoologica, 68: 117-213.
Kostin DS, Kasso M, Komarova VA, Martynov AA, Gromov AR, Alexandrov DY, Bekele A, Zewdie C, Bryja J, Lavrenchenko LA (2019). Taxonomic and genetic diversity of rodents from the Arsi Mountains (Ethiopia). Mammalia, 83: 237-247.
Krásová J, Mikula O, Mazoch V, Bryja J, Říčan O, Šumbera R (2019). Evolution of the Grey-bellied pygmy mouse group: highly structured molecular diversity with predictable geographic ranges but morphological crypsis. Molecular Phylogenetics and Evolution, 130: 143-155.
Krojerová-Prokešová J, Turbaková B, Jelenčič M, Bojda M, Kutal M, Skrbinšek T, Koubek P, Bryja J (2019). Genetic constraints of population expansion of the Carpathian lynx at the western edge of its native distribution range in Central Europe. Heredity, 122: 785-799.
Meheretu Y, Stanley WT, Craig EW, Goüy de Bellocq J, Bryja J, Leirs H, Pahlmann M, Günther S (2019). Tigray orthohantavirus infects two related rodent species adapted to different elevations in Ethiopia. Vector-Borne and Zoonotic Diseases, 19: 950-953.
Mizerovská D, Nicolas V, Demos TC, Akaibe D, Colyn M, Denys C, Kaleme PK, Katuala P, Kennis J, Kerbis Peterhans JC, Laudisoit A, Missoup AD, Šumbera R, Verheyen E, Bryja J (2019). Genetic variation of the most abundant forest‐dwelling rodents in Central Africa (Praomys jacksoni complex): Evidence for Pleistocene refugia in both montane and lowland forests. Journal of Biogeography, 46: 1466-1478.
Petružela J, Bryja J, Bryjová A, Katakweba A, Sabuni C, Baird SJE, Goüy de Bellocq J (2019). Evolutionary history of Pneumocystis fungi in their African rodent hosts. Infection, Genetics and Evolution, 75: 103934.

2018

Aghová T, Kimura Y, Bryja J, Dobigny G, Granjon L, Kergoat GJ (2018). Fossils know it best: Using a new set of fossil calibrations to improve the temporal phylogenetic framework of murid rodents (Rodentia: Muridae). Molecular Phylogenetics and Evolution, 128: 98-111.
Bartáková V, Bryja J, Reichard M (2018). Fine-scale genetic structure of the European bitterling at the intersection of three major European watersheds. BMC Evolutionary Biology, 18: 105.
Bryja J, Konvičková H, Bryjová A, Mikula O, Makundi R, Chitaukali WN, Šumbera R (2018). Differentiation underground: range-wide multilocus genetic structure of the silvery mole-rat does not support current taxonomy based on mitochondrial sequences. Mammalian Biology, 93: 82-92.
Bryja J, Kostin D, Meheretu Y, Šumbera R, Bryjová A, Kasso M, Mikula O, Lavrenchenko LA (2018). Reticulate Pleistocene evolution of Ethiopian rodent genus along remarkable altitudinal gradient. Molecular Phylogenetics and Evolution, 118: 75-87.
Goüy de Bellocq J, Wasimuddin W, Ribas A, Bryja J, Piálek J, Baird SJE (2018). Holobiont suture zones: Parasite evidence across the European house mouse hybrid zone. Molecular Ecology, 27: 5214-5227.
Konečný A, Popa O, Bartáková V, Douda K, Bryja J, Smith C, Popa LO, Reichard M (2018). Modelling the invasion history of Sinanodonta woodiana in Europe: tracking the routes of a sedentary aquatic invader with mobile parasitic larvae. Evolutionary Applications, 11: 1975-1989.
Králová T, Albrecht T, Bryja J, Hořák D, Johnsen A, Lifjeld JT, Novotný M, Sedláček O, Velová H, Vinkler M (2018). Signatures of diversifying selection and convergence acting on passerine Toll‐like receptor 4 in an evolutionary context. Molecular Ecology, 27: 2871-2883.
Mazoch V, Mikula O, Bryja J, Konvičková H, Russo I, Verheyen E, Šumbera R (2018). Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion. Mammalia, 82: 373-387.
Petružela J, Šumbera R, Aghová T, Bryjová A, Katakweba AS, Sabuni CA, Chitaukali WN, Bryja J (2018). Spiny mice of the Zambezian bioregion – phylogeny, biogeography and ecological differentiation within the Acomys spinosissimus complex. Mammalian Biology, 91: 79-90.
Sabuni C, Aghová T, Bryjová A, Šumbera R, Bryja J (2018). Biogeographic implications of small mammals from Northern Highlands in Tanzania with first data from the volcanic Mount Kitumbeine. Mammalia, 82: 360-372.
Šumbera R, Krásová J, Lavrenchenko LA, Mengistu S, Bekele A, Mikula O, Bryja J (2018). Ethiopian highlands as a cradle of the African fossorial root-rats (genus Tachyoryctes), the genetic evidence. Molecular Phylogenetics and Evolution, 126: 105-115.

2017

Aghová T, Šumbera R, Piálek L, Mikula O, McDonough MM, Lavrenchenko LA, Meheretu Y, Mbau JS, Bryja J (2017). Multilocus phylogeny of East African gerbils (Rodentia, Gerbilliscus) illuminates the history of the Somali-Masai savanna. Journal of Biogeography, 44: 2295-2307.
Bryja J, Šumbera R, Kerbis Peterhans JC, Aghová T, Bryjová A, Mikula O, Nicolas V, Denys C, Verheyen E (2017). Evolutionary history of the thicket rats (genus Grammomys) mirrors the evolution of African forests since late Miocene. Journal of Biogeography, 44: 182-194.
Horníček J, Menclová P, Popelková A, Rymešová D, Zárybnická M, Bryja J, Svobodová J (2017). Microsatellite analysis detects low rate of extra-pair paternity in Tengmalm’s owl, Aegolius funereus. Folia zoologica, 66: 22-28.
Janáč M, Bryja J, Ondračková M, Mendel J, Jurajda P (2017). Genetic structure of three invasive gobiid species along the Danube-Rhine invasion corridor: similar distributions, different histories. Aquatic Invasions, 12: 551-564.
Lavrenchenko LA, Nadjafova RS, Bekele A, Mironova TA, Bryja J (2017). Phylogenetic position of a monotypic Ethiopian endemic rodent genus Megadendromus (Rodentia, Nesomyidae). Mammalia, 81: 71-82.
Rymešová D, Králová T, Promerová M, Bryja J, Tomášek O, Svobodová J, Šmilauer P, Šálek M, Albrecht T (2017). Mate choice for major histocompatibility complex complementarity in a strictly monogamous bird, the grey partridge (Perdix perdix). Frontiers in Zoology, 14: 9.
Těšíková J, Bryjová A, Bryja J, Lavrenchenko LA, Goüy de Bellocq J (2017). Hantavirus strains in East Africa related to Western African hantaviruses. Vector-Borne and Zoonotic Diseases, 17: 278-280.

2016

Goüy de Bellocq J, Těšíková J, Meheretu Y, Čížková D, Bryjová A, Leirs H, Bryja J (2016). Complete genome characterisation and phylogenetic position of Tigray hantavirus from the Ethiopian white-footed mouse, Stenocephalemys albipes. Infection, Genetics and Evolution, 45: 242-245.
Mikula O, Šumbera R, Aghová T, Mbau JS, Katakweba AS, Sabuni CA, Bryja J (2016). Evolutionary history and species diversity of African pouched mice (Rodentia: Nesomyidae: Saccostomus). Zoologica Scripta, 45: 595-617.
Wasimuddin W, Bryja J, Ribas A, Baird SJE, Piálek J, Goüy de Bellocq J (2016). Testing parasite "intimacy": the whipworm Trichuris muris in the European house mouse hybrid zone. Ecology and Evolution, 6: 2688-2701.

2015

Bartáková V, Reichard M, Blažek R, Polačik M, Bryja J (2015). Terrestrial fishes: rivers are barriers to gene flow in annual fishes from the African savanna. Journal of Biogeography, 42: 1832-1844.
Jacquet F, Denys C, Verheyen E, Bryja J, Hutterer R, Kerbis Peterhans JC, Stanley WT, Goodman SM, Couloux A, Colyn M, Nicolas V (2015). Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa. BMC Evolutionary Biology, 15: 71.
Jánová E, Bryja J, Čižmár D, Čepelka L, Heroldová M (2015). A new method for assessing food quality in common vole (Microtus arvalis) populations. European Journal of Wildlife Research, 61: 57-62.
Kaňuch P, Aghová T, Meheretu Y, Šumbera R, Bryja J (2015). New discoveries on the ecology and echolocation of the heart-nosed bat Cardioderma cor with a contribution to the phylogeny of Megadermatidae. African Zoology, 50: 53-57.
McDonough MM, Šumbera R, Mazoch V, Ferguson AW, Phillips CD, Bryja J (2015). Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa's Zambezi region. Molecular Ecology, 24: 5248-5266.
Meheretu Y, Šumbera R, Bryja J (2015). Enigmatic Ethiopian endemic rodent Muriculus imberbis (Rüppell 1842) represents a separate lineage within genus Mus. Mammalia, 79: 15-23.
Popa OP, Bartáková V, Bryja J, Reichard M, Popa LO (2015). Characterization of nine microsatellite markers and development of multiplex PCRs for the Chinese huge musel Anodonta (Sinanodonta) woodiana Lea, 1834 (Mollusca, Bivalvia). Biochemical Systematics and Ecology, 60: 234-237.
Vinkler M, Bainová H, Bryjová A, Tomášek O, Albrecht T, Bryja J (2015). Characterisation of Toll-like receptors 4, 5 and 7 and their genetic variation in the grey partridge. Genetica, 143: 101-112.
Winternitz JC, Promerová M, Poláková R, Vinkler M, Schnitzer J, Munclinger P, Babik W, Radwan J, Bryja J, Albrecht T (2015). Effects of heterozygosity and MHC diversity on patterns of extra-pair paternity in the socially monogamous scarlet rosefinch. Behavioral Ecology and Sociobiology, 69: 459-469.
Zemanová B, Hájková P, Hájek B, Martínková N, Mikulíček P, Zima J, Bryja J (2015). Extremely low genetic variation in endangered Tatra chamois and evidence for hybridization with an introduced Alpine population. Conservation Genetics, 16: 729-741.

2014

Bainová H, Králová T, Bryjová A, Albrecht T, Bryja J, Vinkler M (2014). First evidence of independent pseudogenization of Toll-like receptor 5 in passerine birds. Developmental and Comparative Immunology, 45: 151-155.
Bryja J, Mikula O, Šumbera R, Meheretu Y, Aghová T, Lavrenchenko LA, Mazoch V, Oguge N, Mbau JS, Welegerima K, Amundala N, Colyn M, Leirs H, Verheyen E (2014). Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa. BMC Evolutionary Biology, 14: 256.
Bryja J, Mikula O, Patzenhauerová H, Oguge NO, Šumbera R, Verheyen E (2014). The role of dispersal and vicariance in the Pleistocene history of an East African mountain rodent, Praomys delectorum. Journal of Biogeography, 41: 196-208.
Fornůsková A, Petit E, Bartonička T, Kaňuch P, Butet A, Řehák Z, Bryja J (2014). Strong matrilineal structure in common pipistrelle bats (Pipistrellus pipistrellus) is associated with variability in echolocation calls. Biological Journal of the Linnean Society, 113: 1115-1125.
Fornůsková A, Bryja J, Vinkler M, Macholán M, Piálek J (2014). Contrasting patterns of polymorphism and selection in bacterial-sensing toll-like receptor 4 in two house mouse subspecies. Ecology and Evolution, 4: 2931-2944.
Vinkler M, Bainová H, Bryja J (2014). Protein evolution of Toll-like receptors 4, 5 and 7 within Galloanserae birds. Genetics Selection Evolution, 46: 72.

2013

Bartáková V, Reichard M, Janko K, Polačik M, Blažek R, Reichwald K, Cellerino A, Bryja J (2013). Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique. BMC Evolutionary Biology, 13: 196.
Buzan EV, Bryja J, Zemanová B, Kryštufek B (2013). Population genetics of chamois in the contact zone between the Alps and the Dinaric Mountains: uncovering the role of habitat fragmentation and past management. Conservation Genetics, 14: 401-412.
Ćosić N, Říčanová Š, Bryja J, Penezić A, Ćirović D (2013). Do rivers and human-induced habitat fragmentation affect genetic diversity and population structure of the European ground squirrel at the edge of its Pannonian range?. Conservation Genetics, 14: 345-354.
Fornůsková A, Vinkler M, Pages M, Galan M, Jousselin E, Cerqueira F, Morand S, Charbonnel N, Bryja J, Cosson J (2013). Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE). BMC Evolutionary Biology, 13: 194.
Hoban S, Gaggiotti O, Bertorelle G, Arntzen P, Bryja J, Fernandes M, Frith K, Galbusera P, Godoy JA, Hauffe HC, Hoelzel R, Nichols R, Perez-Espona S, Primmer C, Russo IM, Segelbacher G, Siegismund HR, Sihvonen M, Sjoegren-Gulve P, Vernesi C, Vila C, Bruford MW (2013). Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): a software for choosing the appropriate number of markers and samples. Methods in Ecology and Evolution, 4: 299-303.
Hoban SM, Arntzen JW, Bertorelle G, Bryja J, Fernandes M, Frith K, Gaggiotti OE, Galbusera P, Godoy JA, Hauffe HC, Hoelzel AR, Nichols RA, Pérez-Espona S, Primmer CR, Russo I, Segelbacher G, Siegismund HR, Sihvonen M, Sjögren-Gulve P, Vernesi C, Vila C, Bruford MW (2013). Conservation Genetic Resources for Effective Species Survival (ConGRESS): Bridging the divide between conservation research and practice. Journal for Nature Conservation, 21: 433-437.
Hoban SM, Hauffe HC, Pérez-Espona S, Arntzen JW, Bertorelle G, Bryja J, Frith K, Gaggiotti OE, Galbusera P, Godoy JA, Hoelzel AR, Nichols RA, Primmer CR, Russo I, Segelbacher G, Siegismund HR, Sihvonen M, Vernesi C, Vila C, Bruford MW (2013). Bringing genetic diversity to the forefront of conservation policy and management. Conservation genetics resources, 5: 593-598.
Konečný A, Estoup A, Duplantier J, Bryja J, Ba K, Galan M, Tatard C, Cosson J (2013). Invasion genetics of the introduced black rat (Rattus rattus) in Senegal, West Africa. Molecular Ecology, 22: 286-300.
Patzenhauerová H, Šklíba J, Bryja J, Šumbera R (2013). Parentage analysis of Ansell’s mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal. Molecular Ecology, 22: 4988-5000.
Promerová M, Králová T, Bryjová A, Albrecht T, Bryja J (2013). MHC class IIB Exon 2 Polymorphism in the Grey Partridge (Perdix perdix) is shaped by selection, recombination and gene conversion. PLoS ONE, 8: e69135.
Říčanová Š, Koshev Y, Říčan O, Ćosić N, Ćirović D, Sedláček F, Bryja J (2013). Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe. Molecular Ecology, 22: 4256-4269.

2012

Bryja J, Mazoch V, Patzenhauerová H, Mateke C, Zima Jr. J, Šklíba J, Šumbera R (2012). Revised occurrence of rodents from the tribe Praomyini (Muridae) in Zambia based on mitochondrial DNA analyses: implications for biogeography and conservation. Folia zoologica, 61: 268-283.
Heroldová M, Bryja J, Jánová E, Suchomel J, Homolka M (2012). Rodent damage to natural and replanted mountain forest regeneration. Scientific World Journal, 2012: 872536.
Malé PG, Martin J, Galan M, Deffontaine V, Bryja J, Cosson J, Michaux J, Charbonnel N (2012). Discongruence of Mhc and cytochrome b phylogeographical patterns in Myodes glareolus (Rodentia: Cricetidae). Biological Journal of the Linnean Society, 105: 881-899.
Meheretu Y, Čížková D, Těšíková J, Welegerima K, Tomas Z, Kidane D, Girmay K, Schmidt-Chanasit J, Bryja J, Günther S, Bryjová A, Leirs H, Goüy de Bellocq J (2012). High diversity of RNA viruses in rodents, Ethiopia. Emerging Infectious Diseases, 18: 2047-2050.
Poláková R, Schnitzer J, Vinkler M, Bryja J, Munclinger P, Albrecht T (2012). Effect of extra-pair paternity and parental quality on brood sex ratio in the scarlet rosefinch Carpodacus erythrinus. Folia zoologica, 61: 225-232.
Promerová M, Babik W, Bryja J, Albrecht T, Stuglik M, Radwan J (2012). Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine—CE-SSCP and 454 pyrosequencing. Molecular Ecology Resources, 12: 285-292.
Reichard M, Spence R, Bryjová A, Bryja J, Smith C (2012). Female rose bitterling prefer MHC-dissimilar males: experimental evidence. PLoS ONE, 7: e40780.
Seifertová M, Bryja J, Vyskočilová M, Martínková N, Šimková A (2012). Multiple Pleistocene refugia and postglacial colonization in the European chub (Squalius cephalus) revealed by combined use of nuclear and mitochondrial markers. Journal of Biogeography, 39: 1024-1040.
Šumbera R, Mazoch V, Patzenhauerová H, Lövy M, Šklíba J, Bryja J, Burda H (2012). Burrow architecture, family composition and habitat characteristics of the largest social African mole-rat: the giant mole-rat constructs really giant burrow systems. Acta Theriologica, 57: 121-130.
Wasimuddin W, Čížková D, Ribas A, Piálek J, Goüy de Bellocq J, Bryja J (2012). Development and characterization of multiplex panels of microsatellite markers for Syphacia obvelata, a parasite of the house mouse (Mus musculus), using a high throughput DNA sequencing approach. Molecular and Biochemical Parasitology, 185: 154-156.
Wasimuddin W, Čížková D, Bryja J, Albrechtová J, Hauffe HC, Piálek J (2012). High prevalence and species diversity of Helicobacter spp. detected in wild house mice. Applied and Environmental Microbiology, 78: 8158-8160.

2011

Čížková D, Goüy de Bellocq J, Baird SJE, Piálek J, Bryja J (2011). Genetic structure and contrasting selection pattern at two major histocompatibility complex genes in wild house mouse populations. Heredity, 106: 727-740.
Demontis D, Czarnomska SD, Hájková P, Zemanová B, Bryja J, Loeschcke V, Pertoldi C (2011). Characterization of 151 SNPs for population structure analysis of the endangered Tatra chamois (Rupicapra rupicapra tatrica) and its relative, the Alpine chamois (R. r. rupicapra). Mammalian Biology, 76: 644-645.
Jánová E, Heroldová M, Konečný A, Bryja J (2011). Traditional and diversified crops in South Moravia (Czech Republic): Habitat preferences of common vole and mice species. Mammalian Biology, 76: 570-576.
Procházka P, Stokke BG, Jensen H, Fainová D, Bellinvia E, Fossoy F, Vikan JR, Bryja J, Soler M (2011). Low genetic differentiation among reed warbler Acrocephalus scirpaceus populations across Europe. Journal of Avian Biology, 42: 103-113.
Promerová M, Vinkler M, Bryja J, Poláková R, Schnitzer J, Munclinger P, Albrecht T (2011). Occurrence of extra-pair paternity is connected to social male’s MHC-variability in the scarlet rosefinch Carpodacus erythrinus. Journal of Avian Biology, 42: 5-10.
Reichard M, Bryja J, Polačik M, Smith C (2011). No evidence for host specialization or host-race formation in the European bitterling (Rhodeus amarus), a fish that parasitizes freshwater mussels. Molecular Ecology, 20: 3631-3643.
Říčanová Š, Bryja J, Cosson J, Gedeon C, Choleva L, Ambros M, Sedláček F (2011). Depleted genetic variation of the European ground squirrel in Central Europe in both microsatellites and the major histocompatibility complex gene: implications for conservation. Conservation Genetics, 12: 1115-1129.
Zemanová B, Hájková P, Bryja J, Zima Jr. J, Hájková A, Zima J (2011). Development of multiplex microsatellite sets for noninvasive population genetic study of the endangered Tatra chamois. Folia zoologica, 60: 70-80.

2010

Agbali M, Reichard M, Bryjová A, Bryja J, Smith C (2010). Mate choice for nonadditive genetic benefits correlate with MHC dissimilarity in the rose bitterling (Rhodeus ocellatus). Evolution, 64: 1683-1696.
Bartonička T, Kaňuch P, Bímová B, Bryja J (2010). Olfactory discrimination between two cryptic species of bats Pipistrellus pipistrellus and P. pygmaeus. Folia zoologica, 59: 175-182.
Bryja J, Granjon L, Dobigny G, Patzenhauerová H, Konečný A, Duplantier J, Gauthier P, Colyn M, Durnez L, Lalis A, Nicolas V (2010). Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay. Molecular Ecology, 19: 4783-4799.
Bryja J, Smith C, Konečný A, Reichard M (2010). Range-wide population genetic structure of the European bitterling (Rhodeus amarus) based on microsatellite and mitochondrial DNA analysis. Molecular Ecology, 19: 4708-4722.
Bryja J, Uhrin M, Kaňuch P, Bémová P, Martínková N, Zukal J (2010). Mitochondrial DNA confirms low genetic variation of the greater mouse-eared bats, Myotis myotis, in Central Europe. Acta Chiropterologica, 12: 73-81.
Bužan EV, Kryštufek B, Bryja J (2010). Microsatellite markers confirm extensive population fragmentation of the endangered Balkan palaeoendemic Martino’s vole (Dinaromys bogdanovi). Conservation Genetics, 11: 1783-1794.
Heroldová M, Pejčoch M, Bryja J, Jánová E, Suchomel J, Tkadlec E (2010). Tula virus in populations of small terrestrial mammals in a rural landscape. Vector-Borne and Zoonotic Diseases, 10: 599-603.
Hulva P, Fornůsková A, Chudárková A, Evin A, Allegrini B, Benda P, Bryja J (2010). Mechanisms of radiation in a bat group from the genus Pipistrellus inferred by phylogeography, demography and population genetics. Molecular Ecology, 19: 5417-5431.
Charbonnel N, Bryja J, Galan M, Deter J, Tollenaere C, Chaval Y, Morand S, Cosson J (2010). Negative relationships between cellular immune response, Mhc class II heterozygosity and secondary sexual trait in the montane water vole. Evolutionary Applications, 3: 279-290.
Jánová E, Nesvadbová J, Heroldová M, Bryja J (2010). Effectiveness of two trapping protocols for studying the demography of common voles. Hystrix, eItalian Journal of Mammalogy.
Kaňuch P, Fornůsková A, Bartonička T, Bryja J, Řehák Z (2010). Do two cryptic pipistrelle bat species differ in their autumn and winter roosting strategies within the range of sympatry?. Folia zoologica, 59: 102-107.
Konečný A, Koubek P, Bryja J (2010). Indications of higher diversity and abundance of small rodents in human-influenced Sudanian savannah than in the Niokolo Koba National Park (Senegal). African Journal of Ecology, 48: 718-726.
Patzenhauerová H, Bryja J, Šumbera R (2010). Kinship structure and mating system in a solitary subterranean rodent, the silvery mole-rat. Behavioral Ecology and Sociobiology, 64: 757-767.

2009

Albrecht T, Vinkler M, Schnitzer J, Poláková R, Munclinger P, Bryja J (2009). Extra-pair fertilizations contribute to selection on secondary male ornamentation in a socially monogamous passerine. Journal of Evolutionary Biology, 22: 2020-2030.
Bryja J, Kaňuch P, Fornůsková A, Bartonička T, Řehák Z (2009). Low population genetic structuring of two cryptic bat species suggests their migratory behaviour in continental Europe. Biological Journal of the Linnean Society, 96: 103-114.
Clift LE, Andrlíková P, Frolíková M, Stopka P, Bryja J, Flanagan BF, Johnson PM, Dvořáková-Hortová K (2009). Absence of spermatozoal CD46 protein expression and associated rapid acrosome reaction rate in striped field mice (Apodemus agrarius). Reproductive Biology and Endocrinology, 7: 1-91210 .
Kryštufek B, Bryja J, Bužan EV (2009). Mitochondrial phylogeography of the European ground squirrel, Spermophilus citellus, yields evidence on refugia for steppic taxa in the southern Balkans. Heredity, 103: 129-135.
Promerová M, Albrecht T, Bryja J (2009). Extremely high MHC class I variation in a population of a long-distance migrant, the Scarlet Rosefinch (Carpodacus erythrinus). Immunogenetics, 61: 451-461.
Reichard M, Ondračková M, Bryjová A, Smith C, Bryja J (2009). Breeding resource distribution affects selection gradients on male phenotypic traits: experimental study on lifetime reproductive success in the bitterling fish (Rhodeus amarus). Evolution, 63: 377-390.
Vinkler M, Bryjová A, Albrecht T, Bryja J (2009). Identification of the first toll-like receptor gene in passerine birds: TLR4 orthologue in zebra finch (Taeniopygia guttata). Tissue Antigens, 74: 32-41.

2008

Bryja J, Patzenhauerová H, Albrecht T, Mošanský L, Stanko M, Stopka P (2008). Varying levels of female promiscuity in four Apodemus mice species. Behavioral Ecology and Sociobiology, 63: 251-260.
Deter J, Bryja J, Chaval Y, Galan M, Henttonen H, Laakkonen J, Voutilainen L, Vapalahti O, Vaheri A, Salvador AR, Morand S, Cosson J, Charbonnel N (2008). Association between the DQA MHC class II gene and Puumala virus infection in Myodes glareolus, the bank vole. Infection, Genetics and Evolution, 8: 450-458.
Heroldová M, Tkadlec E, Bryja J, Zejda J (2008). Wheat or barley? Feeding preferences affect distribution of three rodent species in agricultural landscape. Applied Animal Behaviour Science, 110: 354-362.
Jánová E, Heroldová M, Bryja J (2008). Conspicuous demographic and individual changes in a population of the common vole in a set-aside alfalfa field. Annales Zoologici Fennici, 45: 39-54.
Nicolas V, Bryja J, Akpatou B, Konečný A, Lecompte E, Colyn M, Lalis A, Couloux A, Denys C, Granjon L (2008). Comparative phylogeography of two sibling species of forest-dwelling rodent (Praomys rostratus and P. tullbergi) in West Africa: different reactions to past forest fragmentation. Molecular Ecology, 17: 5118-5134.
Reichard M, Smith C, Bryja J (2008). Seasonal change in the opportunity for sexual selection. Molecular Ecology, 17: 642-651.
Řehák Z, Bartonička T, Bryja J, Gaisler J (2008). New records of the Alcathoe bat, Myotis alcathoe in Moravia (Czech Republic). Folia zoologica, 57: 465-469.
Tollenaere C, Bryja J, Galan M, Cadet P, Deter J, Chaval Y, Berthier K, Ribas Salvador A, Voutilainen L, Laakkonen J, Henttonen H, Cosson J, Charbonnel N (2008). Multiple parasites mediate balancing selection at two MHC class II genes in the fossorial water vole: insights from multivariate analyses and population genetics. Journal of Evolutionary Biology, 21: 1307-1320.
Tóthová A, Knoz J, Sonnek R, Bryja J, Vaňhara J (2008). Taxonomic problems in the subgenus Meloehelea Wirth of the genus Atrichopogon Kieffer (Diptera: Ceratopogonidae) inferred from both morphological and molecular characters. Entomologica Fennica, 19: 1-12.

2007

Albrecht T, Schnitzer J, Kreisinger J, Exnerová A, Bryja J, Munclinger P (2007). Extrapair paternity and the opportunity for sexual selection in long-distant migratory passerines. Behavioral Ecology, 18: 477-486.
Bryja J, Kment P (2007). True bugs (Heteroptera) of the Bukovské vrchy Hills (Poloniny National Park, Slovakia). Acta Musei Moraviae. Scientiae biologicae = Časopis Moravského muzea. Vědy biologické, iScientiae biologicae92: 1-51.
Bryja J, Charbonnel N, Berthier K, Galan M, Cosson J (2007). Density-related changes in selection pattern for major histocompatibility complex genes in fluctuating populations of voles. Molecular Ecology, 16: 5084-5097.
Hájková P, Pertoldi C, Zemanová B, Roche K, Hájek B, Bryja J, Zima J (2007). Genetic structure and evidence for recent population decline in Eurasian otter populations in the Czech and Slovak Republics: implications for conservation. Journal of Zoology, 272: 1-9.
Heroldová M, Bryja J, Zejda J, Tkadlec E (2007). Structure and diversity of small mammal communities in agriculture landscape. Agriculture, Ecosystems and Environment, 120: 206-210.
Kaňuch P, Fornůsková A, Bartonička T, Bryja J (2007). Multiplex panels of polymorphic microsatellite loci for two cryptic bat species of the genus cross-species amplification within the family Vespertilionidae. Molecular Ecology Notes, 7: 871-873.
Kaňuch P, Hájková P, Řehák Z, Bryja J (2007). A rapid PCR-based test for species identification of two cryptic bats Pipistrellus pipistrellus and P. pygmaeus and its application on museum and dropping samples. Acta Chiropterologica, 9: 277-282.
Kment P, Bryja J (2007). Description of Nasocoris lautereri sp. nov. from the Balkan peninsula, with a review of the genus Nasocoris (Hemiptera: Heteroptera: Miridae: Phylinae). Zootaxa, 1633: 39-61.
Loiseau A, Konečný A, Galan M, Bryja J, Cosson J, Brouat C (2007). New polymorphic microsatellite loci for rodents of the genus Mastomys using PCR multiplexing, and cross-species amplification in Myomys and Praomys. Molecular Ecology Notes, 7: 684-687.
Poláková R, Vyskočilová M, Martin J, Mays Jr. HL, Hill GE, Bryja J, Albrecht T (2007). A multiplex set of microsatellite markers for the scarlet rosefinch (Carpodacus erythrinus). Molecular Ecology Notes, 7: 1375-1378.

2006

Bencová V, Kašpar T, Bryja J (2006). Sezónní a meziroční změny skladby potravy kalouse ušatého (Asio otus) na jižní Moravě. Tichodroma, 18: 65-71.
Bryja J, Kment P (2006). Ploštice (Heteroptera) Chráněné krajinné oblasti Kokořínsko. Bohemia centralis, 27: 267-2941210 .
Bryja J, Galan M, Charbonnel N, Cosson J (2006). Duplication, balancing selection and trans-species evolution explain the high levels of polymorphism of the DQA MHC class II gene in voles (Arvicolinae). Immunogenetics, 58: 191-202.
Hájková P, Zemanová B, Bryja J, Hájek B, Roche K, Tkadlec E, Zima J (2006). Factors affecting success of PCR amplification of microsatellite loci from otter faeces. Molecular Ecology Notes, 6: 559-562.
Kment P, Bryja J (2006). Revised occurrence of Heterotoma species (Heteroptera: Miridae) in the Czech Republic and Slovakia with remarks on nomenclature, diagnostic characters and ecology. Acta Musei Moraviae. Scientiae biologicae = Časopis Moravského muzea. Vědy biologické, iScientiae biologicae91: 7-52.
Tóthová A, Bryja J, Bejdák P, Vaňhara J (2006). Molecular markers used in phylogenetic studies of Diptera with a methodological overview. Acta Universitatis Carolinae, Biologica, 50: 125-133.

2005

Bryja J, Galan M, Charbonnel N, Cosson J (2005). Analysis of major histocompatibility complex class II gene in water voles using capillary electrophoresis-single stranded conformation polymorphism. Molecular Ecology Notes, 5: 173-176.
Bryja J, Stopka P (2005). Facultative promiscuity in a presumably monogamous mouse Apodemus microps. Acta Theriologica, 50: 189-196.
Bryja J, Nesvadbová J, Heroldová M, Jánová E, Losík J, Trebatická L, Tkadlec E (2005). Common vole (Microtus arvalis) population sex ratio: biases and process variation. Canadian Journal of Zoology - Revue Canadienne de Zoologie, 83: 1391-1399.
Heroldová M, Jánová E, Bryja J, Tkadlec E (2005). Set-aside plots - source of small mammal pests?. Folia zoologica, 54: 337-350.
Kment P, Bryja J, Hradil K, Jindra Z (2005). New and interesting records of true bugs (Heteroptera) from the Czech Republic and Slovakia 3. Klapalekiana, 41: 157-2131210 .
Kment P, Bryja J, Jindra Z (2005). New records of true bugs (Heteroptera) of the Balkan peninsula. Acta entomologica slovenica, 13: 9-20.
Reichard M, Bryja J, Ondračková M, Dávidová M, Kaniewska P, Smith C (2005). Sexual selection for male dominance reduces opportunities for female mate choice in the European bitterling (Rhodeus sericeus). Molecular Ecology, 14: 1533-1542.

2004

Bryja J, Kment P (2004). Ploštice (Heteroptera) Bukovských vrchů (NP Poloniny). Folia faunistica Slovaca, 9: 31-41.
Hájková P, Hájek B, Zemanová B, Roche K, Toman A, Bryja J (2004). Genetická variabilita a populačno-genetická štruktúra subpopulácií vydry riečnej (Lutra lutra) v výskumnom projekte Českej a Slovenskej republike. Bulletin Vydra, 12001.
Hájková P, Zemanová B, Hájek B, Roche K, Kučerová M, Bryja J, Zima J (2004). Stanovenie početnosti a štruktúry populácie vydry riečnej (Lutra lutra) neinvazívnou genetickou metódou - správa o prebiehajúcom výskumnom projekte. Bulletin Vydra, 12001.
Heroldová M, Zejda J, Zapletal M, Obdržálková D, Jánová E, Bryja J, Tkadlec E (2004). Importance of winter rape for small rodents. Rostlinná  výroba, 50: 175-181.

2003

Bryja J, Konečný A (2003). Fast sex identification in wild mammals using PCR amplification of the Sry gene. Folia zoologica, 52: 269-274.
Jánová E, Heroldová M, Bryja J, Tkadlec E (2003). Metodické problémy při určování stáří hlodavců na základě hmotnosti očních čoček. Lynx, 34: 29-38.
Jánová E, Heroldová M, Nesvadbová J, Bryja J, Tkadlec E (2003). Age variation in a fluctuating population of the common vole. Oecologia, 137: 527-532.
Kment P, Bryja J, Jindra Z, Hradil K, Baňař P (2003). New and interesting records of true bugs (Heteroptera) from the Czech Republic and Slovakia 2. Klapalekiana, 39: 257-3061210 .

2002

Bartonička T, Řehák Z, Wolf P, Bryja J (2002). Drobní savci CHKO Litovelské Pomoraví. Část 1. Netopýři - Chiroptera. Lynx, 33: 35-46.
Bryja J, Heroldová M, Zejda J (2002). Effects of deforestation on structure and diversity of small mammal communities in the Moravskoslezské Beskydy Mts (Czech Republic). Acta Theriologica, 47: 295-306.
Bryja J, Kment P (2002). New and interesting records of plant bugs (Heteroptera: Miridae) from the Czech and Slovak Republics. Klapalekiana, 38: 1-101210 .
Bryja J, Kment P, Hradil K (2002). Ploštice (Heteroptera) Rokytenských slepenců. Přírodovědný sborník Západomoravského muzea v Třebíči=Acta Scientiarum Naturalium Musei Moraviae Occidentalis, 40: 33-60.
Bryja J, Řehák Z, Vermouzek Z, Wolf P, Bartonička T (2002). Drobní savci CHKO Litovelské Pomoraví. Část 2. Hmyzožravci a hlodavci - Insectivora et Rodentia. Lynx, 33: 79-87.
Bryja J, Řehák Z (2002). Další doklady současné expanze areálu myšice temnopásé (Apodemus agrarius) na Moravě. Lynx, 33: 69-77.
Konečný A, Bryja J (2002). Hmyzožravci a hlodavci v ČR - souhrn nepublikovaných faunistických dat z diplomových prací obhájených na Přírodovědecké fakultě MU v Brně. Lynx, 33: 133-140.
Kula E, Bryja J (2002). Comparison of various sampling methods for evaluation of biodiversity of true bugs (Heteroptera) in a birch forest. Ekológia, 21: 137-147.

2001

Bryja J, Tkadlec E, Nesvadbová J, Gaisler J, Zejda J (2001). Comparison of enumeration and Jolly-Seber estimation of population size in the common vole Microtus arvalis. Acta Theriologica, 46: 279-285.
Bryja J, Beneš B (2001). The harvest mouse (Micromys minutus) in the mountains of the Czech Republic. Časopis Slezského zemského muzea., iSérie A: Vědy přírodní50: 113-116.
Bryja J, Heroldová M, Zejda J (2001). Drobní zemní savci (Insectivora, Rodentia) vrcholových partií Moravskoslezských Beskyd. Časopis Slezského zemského muzea., iSérie A: Vědy přírodní50: 105-112.
Bryja J, Kment P (2001). The present state of knowledge of true bugs (Heteroptera) in the Protected Landscape Area of Poodří (Czech Republic). Klapalekiana, 37: 1-361210 .
Kment P, Bryja J (2001). New and interesting records of true bugs (Heteroptera) from the Czech Republic and Slovakia. Klapalekiana, 37: 231-2481210 .
Lososová Z, Danihelka J, Chytrý M, Hluchý M, Vítek P, Marek J, Škorpík M, Bezděk J, Průdek P, Poisel J, Lauterer P, Bagar M, Kment P, Bryja J, Janšta P (2001). Předběžné výsledky monitoringu biodiverzity vinic a přilehlých lesostepních lokalit CHKO Pálava a NP Podyjí. Thayensia, 4: 205-2081210 .

2000

Bryja J, Zukal J (2000). Small mammal communities in newly planted biocorridors and their surroundings in southern Moravia (Czech Republic). Folia zoologica, 49: 191-197.
Bryja J, Kula E (2000). A novel multiple approach to the biodiversity evaluation - example of the fractionated community of bugs Heteroptera). Ekológia, 19: 225-244.

1999

Bryja J, Zemanová K, Šmarda J (1999). Antileukemické účinky proteinu RXR. Klinická biochemie a metabolismus, 7: 17.
Bryja J (1999). Nejvýše položený nález myšice temnopásé (Apodemus agrarius Pallas, 1771) na území České republiky. Časopis Slezského zemského muzea., iSérie A: Vědy přírodní48: 223-226.
Šmarda J, Zemanová K, Bryja J, Šmardová J, Kozubík A, Hofmanová J, Nemajerová A, Ševčíková S, Kohoutek J, Vodička P (1999). Retinoid X receptor suppresses transformation by the v-myb oncogene. Journal of Leukocyte Biology, 66: 1039-1048.

1998

Bryja J, Řehák Z (1998). Drobní savci CHKO Poodří a blízkého okolí: 1. Insectivora, Rodentia. Časopis Slezského zemského muzea., iSérie A: Vědy přírodní47: 123-131.
Bryja J, Řehák Z (1998). Community of small terrestrial mammals (Insectivora, Rodentia) in dominant habitats of the Protected Landscape Area of Poodří (Czech Republic). Folia zoologica, 47: 249-260.
Bryja J, Řehák Z (1998). Diet composition of two owl species in the Odra river floodplain (Czech Republic). Buteo, 10: 97-102.
Řehák Z, Bryja J (1998). Drobní savci CHKO Poodří a blízkého okolí: 2. Chiroptera. Časopis Slezského zemského muzea., iSérie A: Vědy přírodní47: 133-142.