Lerp H., Klaus S., Allgöwer S., Wronski T., Pfenninger M., Plath M. (2016): Phylogenetic analyses of gazelles reveal repeated transitions of key ecological traits and provide novel insights into the origin of the genus Gazella. Molecular Phylogenetics and Evolution, 98. Pp 1 – 10. ISSN 1055-7903
Romero P., Pfenninger M., Kano Y & A. Klussmann-Kolb (2016): Molecular phylogeny of the Ellobiidae (Gastropoda: Panpulmonata) supports independent terrestrial invasions. Molecular Phylogenetics and Evolution, 97. pp. 43-54. ISSN 1055-7903
Pfenninger M. and M. Plath (2016): Ist Evolution vorhersagbar? Biologie in unserer Zeit, 46. pp. 42-48. ISSN 1521-415X
Oppold A., Pedrosa J., Balint M., Diogo J.B., Ilkova J., Pestana J. & M. Pfenninger (2016): Support for the evolutionary speed hypothesis from intraspecific population genetic data in the non-biting midge ~Chironomus riparius~. Proceedings of the Royal Society B-Biological Sciences, 283 (1825). ISSN 0962-8452
Roembke J., Aira M., Backeljau T., Breugelmans K., Dominguez J., Funke E., Graf N., Hajibabaei M., Pérez-Losada M., Porto P.G., Schmelz R.M., Vierna J., Vizcaino A. & M. Pfenninger (2016): DNA barcoding of earthworms (Eisenia fetida/andrei complex) from 28 ecotoxicological test laboratories. Applied Soil Ecology. ISSN 0929-1393 (In Press)
Koch K., Algarb D., Searle J. B., Pfenninger M. & K Schwenk (2015): A voyage to Terra Australis: human-mediated dispersal of cats. BMC Evolutionary Biology, 15 (262). ISSN 1471-2148
Pfenninger M., Patel S., Arias-Rodriguez L, Feldmeyer B., Riesch R. & M. Plath (2015): Unique evolutionary trajectories in repeated adaptation to hydrogen sulphide-toxic habitats. Molecular Ecology, 24 (21). pp. 5446-5459. ISSN 0962-1083
Bock F., Kuch U., Pfenninger M. & R. Müller (2015): Standardized Laboratory Feeding of Larval Aedes japonicus japonicus (~Diptera: Culicidae~). Journal of Insect Science. ISSN 1536-2442
Patel S., Schell T., Eifert C, Feldmeyer B. & M. Pfenninger (2015): Characterizing a hybrid zone between a cryptic species pair of freshwater snails. Molecular Ecology, 24 (3). pp. 643-655. ISSN 0962-1083
Balint M., Bartha L., O'Hara R. B., Olson M.S., Otte J., Pfenninger M., Robertson A., Tiffin P. & I. Schmitt (2015): Relocation, high-latitude warming and host genetic identity shape the foliar fungal microbiome of poplars. Molecular Ecology, 24 (1). pp. 235-248. ISSN 0962- 1083
Khaliq I., Fritz S. A., Prinzinger R., Pfenninger M., Böhning-Gaese K. & C. Hof (2015): Global variation in thermal physiology of birds and mammals: evidence for phylogenetic niche conservatism only in the tropics. Journal of Biogeography, 42. pp. 2187-2196. ISSN 0305-0270
Feldmeyer B., Greshake B., Funke E., Ebersberger I. & M. Pfenninger (2015): Positive selection on developmental and sexual genes involved in species divergence of the genus Radix. BMC Evolutionary Biology, 15 (164). ISSN 1471-2148
Khaliq I., Hof C., Prinzinger R., Boehning-Gaese K. & M. Pfenninger (2014): Global variation in thermal tolerances and vulnerability of endotherms to climate change. Proceedings of the Royal Society B-Biological Sciences, 281. p. 20141097. ISSN 0962-8452
Merker S., Thomas S., Völker E., Perwitasari-Farajallah D., Feldmeyer B., Streit B. & M. Pfenninger (2014): Control region length dynamics potentially drives amino acid evolution in tarsier mitochondrial genomes. Journal of Molecular Evolution, 79. pp. 40-51. ISSN 0022- 2844
Pfenninger M., Weigand A. M., Balint, M. & Klussmann-Kolb, A. (2014): Misperceived invasion: the Lusitanian slug (Arion lusitanicus auct. non-Mabille or Arion vulgaris Moquin- Tandon 1855) is native to Central Europe. Evolutionary Applications, 7 (6). pp. 702-713. ISSN 1752-4571
Pfenninger M., Lerp H., Tobler M., Passow C., Kelley J., Funke E., Greshake B., Erkoc K., Berberich T., & M. Plath (2014): Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment. Nature Communications, 5. 3873. ISSN 2041-1723
Frosch C., Dutsov A., Zlatanova D., Valchev K., Reimers T. E. Steyer K., Pfenninger M. & C. Nowak (2014): Noninvasive genetic assessment of brown bear population structure in Bulgarian mountain regions. Mammalian Biology. ISSN 1616-5047
Lerp H., Plath M., Wronski T., Bärmann E.V., Malczyk A., Resch R.R., Gasmy A.A. & M. Pfenninger (2014): Utility of island populations in reintroduction programs—relationships between Arabian gazelles (Gazella arabica) from the Farasan Archipelago and endangered mainland populations. Molecular Ecology, 23 (8). pp. 1910-1922. ISSN 0962-1083
Lerp H., Wronski T., Plath M., Schröter A. & M. Pfenninger (2013): Phylogenetic and population genetic analyses suggest a potential species boundary between Mountain (Gazella gazella) and Arabian Gazelles (G. arabica) in the Levant. Mammalian Biology, 78 (5). pp. 383-386. ISSN 1616-5047
Nemec S., Patel S., Nowak C. & M. Pfenninger (2013): Evolutionary determinants of population differences in population growth rate - habitat temperature interactions in Chironomus riparius. Oecologia, 172 (2). pp. 585-594. ISSN 0029-8549
Schmidt H., Greshake B., Feldmeyer B., Hankeln T. & M. Pfenninger (2013): Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges. BMC Genomics, 14. p. 384. ISSN 1471-2164
Plath M., Pfenninger M., Lerp H., Riesch, R., Eschenbrenner C., Slattery P., Bierbach D., Herrmann N., Schulte M., Arias-Rodriguez L., Indy J.R., Passow C. & M. Tobler (2013): Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments. Evolution, 67 (9). pp. 2647-2661. ISSN 0014-3820
Kuch U., Pfenninger M., & R. Müller (2013): Den Tigermücken auf der Spur - Von Hessen bis in den Himalaya: Gewinner des globalen Wandels unter der Lupe. Senckenberg Natur Forschung Museum, 143 (3/4). pp. 74-79. ISSN 0028-1301
Jansen M., Plath M. & M. Pfenninger (2013): Kommunikation und Artbildung neotropischer Frösche (Gattung Scinax): Bioakustische und genetische Variation zweier kryptischer Arten. TERRARIA/elaphe, 1/2013. pp. 116-117. ISSN ISSN 1613-1398
Pauls S.U., Nowak C., Balint M. & M. Pfenninger (2013): The impact of global climate change on genetic diversity within populations and species. Molecular Ecology, 22. pp. 925- 946. ISSN 0962-1083
Cordellier M., Pfenninger A., Streit B. & M. Pfenninger (2012): Assessing the effects of climate change on the distribution of pulmonate freshwater snail biodiversity. Marine Biology, 159 (11). pp. 2519-2531. ISSN 0025-3162
Weigand A.M., Pfenninger M., Jochum A. & A. Klussmann-Kolb (2012): Alpine crossroads or origin of genetic diversity? Comparative phylogeography of two sympatric microgastropod species. Public Library of Science One, 7 (5). e37089. ISSN 1932-6203
Nemec S., Hess M., Nowak C. & M. Pfenninger (2012): Experimental evidence for niche segregation in a sister species pair of non-biting midges. Hydrobiologia, 691. pp. 203-212. ISSN 0018-8158
Pérez-Losada M., Bloch R., Pfenninger M. & J. Domínguez (2012): Taxonomic assessment of Lumbricidae (Oligochaeta) earthworm genera using DNA barcodes. European Journal of Soil Biology, 48. pp. 41-47. ISSN 1164-5563
Nowak C., Vogt C., Oehlmann J., Pfenninger M., Schwenk K., Streit,, B., & N. Oetken (2012): Impact of genetic diversity and inbreeding on the life-history of Chironomus midges over consecutive generations. Chemosphere, 88 (8). pp. 988-993.
Pfenninger M., Balint M. & S.U. Pauls (2012): Methodological framework for projecting the potential loss of intraspecific genetic diversity due to global climate change. BMC Evolutionary Biology, 12. p. 224. ISSN 1471-2148
Haun T., Salinger M., Pachzelt,, A. & M. Pfenninger (2012): On the processes shaping small scale population structure in Radix balthica (Linnaeus 1758). Malacologia, 55 (2). pp. 219- 233.
Pulch H., Zajonz U. & M. Pfenninger (2012): Population connectivity of an endemic reef fish around Socotra Island. Tayf - the Soqotra Newsletter.
Jansen M., Bloch R., Schulze A. & M. Pfenninger (2011): Integrative inventory of Bolivia’s lowland anurans reveals hidden diversity. Zoologica Scripta, 40 (6). pp. 567-583. ISSN 0300-3256
Lerp H., Wronski T., Pfenninger M. & M. Plath (2011): A phylogeographic framework for the conservation of Saharan and Arabian dorcas gazelles (Artiodactyla: Bovidae). Organisms Diversity & Evolution, 11. pp. 317-329. ISSN 1439-6092
Weigand A.M., Simon A., Pfenninger M. & A. Klussmann-Kolb (2011): Comparative phylogeography of two sympatric microsnail species (Pulmonata, Carychiidae). In: BioSystematics Berlin 2011, 2011-02-24, Berlin, Germany.
Jesse R., Grudinski M., Klaus S., Streit B. & M. Pfenninger (2011): Evolution of fresh water crab diversity in the Aegean region (Crustacea: Brachyura: Potamidae). Molecular Phylogenetics and Evolution, 59. pp. 22-33. ISSN 1055-7903
Pfenninger M., Salinger M., Haun, T., & B. Feldmeyer (2011: Factors and processes shaping the population structure and distribution of genetic variation across the species range of the freshwater snail Radix balthica (Pulmonata, Basommatophora). BMC Evolutionary Biology, 11 (135). pp. 1-15. ISSN 1471-2148
Jesse R., Vela E. & M. Pfenninger (2011): Phylogeography of a Land Snail Suggests Trans- Mediterranean Neolithic Transport. Public Library of Science One, 6 (6). e20734. ISSN 1932-6203
Feldmeyer B., Wheat C. W., Krezdorn N., Rotter B. & M. Pfenninger (2011): Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genomics, 12 (317). pp. 1-12. ISSN 1471-2164
Tills O., Rundle S. D., Salinger M., Haun T., Pfenninger M. & J. I. Spicer (2011): A genetic basis for intraspecific differences in developmental timing? Evolution & Development, 13 (6). pp. 542-548. ISSN 1525-142X
Weigand A. M., Jochum, A., Pfenninger M., Steinke D. & A. Klussmann-Kolb (2011): A new approach to an old conundrum-DNA barcoding sheds new light on phenotypic plasticity and morphological stasis in microsnails (Gastropoda, Pulmonata, Carychiidae). Molecular Ecology Resources, 11 (2). pp. 255-265. ISSN 1755-098X
Pfenninger M., Vela E., Jesse R., Aranzazu E. M., Magnin F., Martinez-Orti A. & F. Liberto (2010): Temporal speciation pattern in the western Mediterranean genus Tudorella P. Fischer, 1885 (Gastropoda, Pomatiidae) supports the Tyrrhenian vicariance hypothesis. Molecular Phylogenetics and Evolution, 54 (2). pp. 427-436. ISSN 1055-7903
Janke A. & M. Pfenninger (2010): Forschung und Service in einem Laborzentrum. Natur und Museum, 140 (9/10). pp. 254-255.
Klaus S., Schubart C., Streit, B. & M. Pfenninger (2010): When Indian crabs were not yet Asian - biogeographic evidence for Eocene contact of India and Southeast Asia. BMC Evolutionary Biology, 10. p. 287.
Jansen M., Bloch R., Schulze A. & M. Pfenninger (2010): Wie unterscheidet man Frösche, die sich nicht unterscheiden? Natur und Museum, 140 (9/10). pp. 260-261.
Feldmeyer B., Hoffmeier K. & M. Pfenninger (2010): The complete mitochondrial genome of Radix balthica (Pulmonata, Basommatophora), obtained by low coverage shot gun next generation sequencing. Molecular Phylogenetics and Evolution, 57 (3). pp. 1329-1333. ISSN 1055-7903
Nowak C., Vogt C., Pfenninger M., Streit B., Oehlmann J., Schwenk K. & M. Oetken, (2009): Rapid genetic erosion in pollutant-exposed experimental chironomid populations. Environmental Pollution, 157. pp. 881-886.
Depraz A., Hausser J. & Pfenninger M (2009): A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species with a sharp contact zone. BMC Evolutionary Biology, 9:171.
Pfenninger M. & C. Nowak (2008): Reproductive Isolation and Ecological Niche Partition among Larvae of the Morphologically Cryptic Sister Species Chironomus riparius and C. piger. Public Library of Science One, 3 (5). e2157. ISSN 1932-6203
Cordellier M. & M. Pfenninger (2009): Inferring the past to predict the future: climate modelling predictions and phylogeography for the freshwater gastropos Radix balthica (Pulmonata, Basommatophora). Molecular Ecology 18, 534-544
Salinger M. & M. Pfenninger (2009): Highly polymorphic microsatellite markers for Radix balthica (Linnaeus 1758). Molecular Ecology Resources, 9, 1152-1155
Jesse R., Pfenninger M., Fratini S., Scalici M., Streit B. & C. Schubart (2008): Disjunct distribution of the Mediterranean freshwater crab Potamon fluviatile – natural expansion or human introduction? Biological Invasions, 11, 2209-2221
Nowak C. & M. Pfenninger (2008): Reproductive isolation and ecological niche partition among the morphologically cryptic sister species Chironomus riparius and C. piger. PloS One 3, e2157
Depraz A., Cordellier M., Hausser J & M. Pfenninger (2008): Postglacial recolonisation at a snail’s pace (Trochulus villosus): confronting competing refugia hypotheses using model selection. Molecular Ecology 17, 2449-2462
Cordellier M. & M. Pfenninger (2008): Climate-driven range dynamics in the freshwater limpet Ancylus fluviatilis (Pulmonata, Basommatophora). Journal of Biogeography 35, 1580- 1592
Vela E., Magnin F., Pavon D. & M. Pfenninger (2008): Données phylogénétiques et paléobiogéographiques chez le gastéropode terrestre Tudorella sulcate (Draparnaud) en Algérie. Geodiversitas 30, 233-246