@article{RadchukReedTeplitskyetal.2019, author = {Radchuk, Viktoriia and Reed, Thomas and Teplitsky, Celine and van de Pol, Martijn and Charmantier, Anne and Hassall, Christopher and Adamik, Peter and Adriaensen, Frank and Ahola, Markus P. and Arcese, Peter and Miguel Aviles, Jesus and Balbontin, Javier and Berg, Karl S. and Borras, Antoni and Burthe, Sarah and Clobert, Jean and Dehnhard, Nina and de Lope, Florentino and Dhondt, Andre A. and Dingemanse, Niels J. and Doi, Hideyuki and Eeva, Tapio and Fickel, J{\"o}rns and Filella, Iolanda and Fossoy, Frode and Goodenough, Anne E. and Hall, Stephen J. G. and Hansson, Bengt and Harris, Michael and Hasselquist, Dennis and Hickler, Thomas and Jasmin Radha, Jasmin and Kharouba, Heather and Gabriel Martinez, Juan and Mihoub, Jean-Baptiste and Mills, James A. and Molina-Morales, Mercedes and Moksnes, Arne and Ozgul, Arpat and Parejo, Deseada and Pilard, Philippe and Poisbleau, Maud and Rousset, Francois and R{\"o}del, Mark-Oliver and Scott, David and Carlos Senar, Juan and Stefanescu, Constanti and Stokke, Bard G. and Kusano, Tamotsu and Tarka, Maja and Tarwater, Corey E. and Thonicke, Kirsten and Thorley, Jack and Wilting, Andreas and Tryjanowski, Piotr and Merila, Juha and Sheldon, Ben C. and Moller, Anders Pape and Matthysen, Erik and Janzen, Fredric and Dobson, F. Stephen and Visser, Marcel E. and Beissinger, Steven R. and Courtiol, Alexandre and Kramer-Schadt, Stephanie}, title = {Adaptive responses of animals to climate change are most likely insufficient}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-10924-4}, pages = {14}, year = {2019}, abstract = {Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications, to assess quantitatively whether phenotypic trait changes associated with climate change are adaptive in animals. A meta-analysis focussing on birds, the taxon best represented in our dataset, suggests that global warming has not systematically affected morphological traits, but has advanced phenological traits. We demonstrate that these advances are adaptive for some species, but imperfect as evidenced by the observed consistent selection for earlier timing. Application of a theoretical model indicates that the evolutionary load imposed by incomplete adaptive responses to ongoing climate change may already be threatening the persistence of species.}, language = {en} } @article{SallehRamosMadrigalPenalozaetal.2017, author = {Salleh, Faezah Mohd and Ramos-Madrigal, Jazmin and Penaloza, Fernando and Liu, Shanlin and Sinding, Mikkel-Holger S. and Patel, Riddhi P. and Martins, Renata and Lenz, Dorina and Fickel, J{\"o}rns and Roos, Christian and Shamsir, Mohd Shahir and Azman, Mohammad Shahfiz and Lim, Burton K. and Rossiter, Stephen J. and Wilting, Andreas and Gilbert, M. Thomas P.}, title = {An expanded mammal mitogenome dataset from Southeast Asia}, series = {Gigascience}, volume = {6}, journal = {Gigascience}, number = {8}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2047-217X}, pages = {1 -- 19}, year = {2017}, abstract = {Background: Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion:}, language = {en} } @article{WeyrichJeschekSchrapersetal.2018, author = {Weyrich, Alexandra and Jeschek, Marie and Schrapers, Katharina T. and Lenz, Dorina and Chung, Tzu Hung and Ruebensam, Kathrin and Yasar, Sermin and Schneemann, Markus and Ortmann, Sylvia and Jewgenow, Katarina and Fickel, J{\"o}rns}, title = {Diet changes alter paternally inherited epigenetic pattern in male Wild guinea pigs}, series = {Environmental Epigenetics}, volume = {4}, journal = {Environmental Epigenetics}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2058-5888}, doi = {10.1093/eep/dvy011}, pages = {12}, year = {2018}, abstract = {Epigenetic modifications, of which DNA methylation is the most stable, are a mechanism conveying environmental information to subsequent generations via parental germ lines. The paternal contribution to adaptive processes in the offspring might be crucial, but has been widely neglected in comparison to the maternal one. To address the paternal impact on the offspring's adaptability to changes in diet composition, we investigated if low protein diet (LPD) in F0 males caused epigenetic alterations in their subsequently sired sons. We therefore fed F0 male Wild guinea pigs with a diet lowered in protein content (LPD) and investigated DNA methylation in sons sired before and after their father's LPD treatment in both, liver and testis tissues. Our results point to a 'heritable epigenetic response' of the sons to the fathers' dietary change. Because we detected methylation changes also in the testis tissue, they are likely to be transmitted to the F2 generation. Gene-network analyses of differentially methylated genes in liver identified main metabolic pathways indicating a metabolic reprogramming ('metabolic shift'). Epigenetic mechanisms, allowing an immediate and inherited adaptation may thus be important for the survival of species in the context of a persistently changing environment, such as climate change.}, language = {en} } @article{RadchukKramerSchadtFickeletal.2019, author = {Radchuk, Viktoriia and Kramer-Schadt, Stephanie and Fickel, J{\"o}rns and Wilting, Andreas}, title = {Distributions of mammals in Southeast Asia: The role of the legacy of climate and species body mass}, series = {Journal of biogeography}, volume = {46}, journal = {Journal of biogeography}, number = {10}, publisher = {Wiley}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.13675}, pages = {2350 -- 2362}, year = {2019}, abstract = {Aim Current species distributions are shaped by present and past biotic and abiotic factors. Here, we assessed whether abiotic factors (habitat availability) in combination with past connectivity and a biotic factor (body mass) can explain the unique distribution pattern of Southeast Asian mammals, which are separated by the enigmatic biogeographic transition zone, the Isthmus of Kra (IoK), for which no strong geophysical barrier exists. Location Southeast Asia. Taxon Mammals. Methods We projected habitat suitability for 125 mammal species using climate data for the present period and for two historic periods: mid-Holocene (6 ka) and last glacial maximum (LGM 21 ka). Next, we employed a phylogenetic linear model to assess how present species distributions were affected by the suitability of areas in these different periods, habitat connectivity during LGM and species body mass. Results Our results show that cooler climate during LGM provided suitable habitat south of IoK for species presently distributed north of IoK (in mainland Indochina). However, the potentially suitable habitat for these Indochinese species did not stretch very far southwards onto the exposed Sunda Shelf. Instead, we found that the emerged landmasses connecting Borneo and Sumatra provided suitable habitat for forest dependent Sundaic species. We show that for species whose current distribution ranges are mainly located in Indochina, the area of the distribution range that is located south of IoK is explained by the suitability of habitat in the past and present in combination with the species body mass. Main conclusions We demonstrate that a strong geophysical barrier may not be necessary for maintaining a biogeographic transition zone for mammals, but that instead a combination of abiotic and biotic factors may suffice.}, language = {en} } @article{StillfriedFickelBoerneretal.2017, author = {Stillfried, Milena and Fickel, J{\"o}rns and B{\"o}rner, Konstantin and Wittstatt, Ulrich and Heddergott, Mike and Ortmann, Sylvia and Kramer-Schadt, Stephanie and Frantz, Alain C.}, title = {Do cities represent sources, sinks or isolated islands for urban wild boar population structure?}, series = {Journal of applied ecology : an official journal of the British Ecological Society}, volume = {54}, journal = {Journal of applied ecology : an official journal of the British Ecological Society}, number = {1}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0021-8901}, doi = {10.1111/1365-2664.12756}, pages = {272 -- 281}, year = {2017}, language = {en} } @article{WeyrichLenzFickel2018, author = {Weyrich, Alexandra and Lenz, Dorina and Fickel, J{\"o}rns}, title = {Environmental Change-Dependent Inherited Epigenetic Response}, series = {GENES}, volume = {10}, journal = {GENES}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes10010004}, pages = {15}, year = {2018}, abstract = {Epigenetic modifications are a mechanism conveying environmental information to subsequent generations via parental germ lines. Research on epigenetic responses to environmental changes in wild mammals has been widely neglected, as well as studies that compare responses to changes in different environmental factors. Here, we focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to either diet (~40\% less protein) or temperature increase (10 °C increased temperature). Because both experiments focused on the liver as the main metabolic and thermoregulation organ, we were able to decipher if epigenetic changes differed in response to different environmental changes. Reduced representation bisulfite sequencing (RRBS) revealed differentially methylated regions (DMRs) in annotated genomic regions in sons sired before (control) and after the fathers' treatments. We detected both a highly specific epigenetic response dependent on the environmental factor that had changed that was reflected in genes involved in specific metabolic pathways, and a more general response to changes in outer stimuli reflected by epigenetic modifications in a small subset of genes shared between both responses. Our results indicated that fathers prepared their offspring for specific environmental changes by paternally inherited epigenetic modifications, suggesting a strong paternal contribution to adaptive processes.}, language = {en} } @article{GuerreroFickelBenhaiemetal.2020, author = {Guerrero, Tania P. and Fickel, J{\"o}rns and Benhaiem, Sarah and Weyrich, Alexandra}, title = {Epigenomics and gene regulation in mammalian social systems}, series = {Current zoology}, volume = {66}, journal = {Current zoology}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-5507}, doi = {10.1093/cz/zoaa005}, pages = {307 -- 319}, year = {2020}, abstract = {Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEls, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.}, language = {en} } @article{BayerlKrausNowaketal.2018, author = {Bayerl, Helmut and Kraus, Robert H. S. and Nowak, Carsten and Foerster, Daniel W. and Fickel, J{\"o}rns and K{\"u}hn, Ralph}, title = {Fast and cost-effective single nucleotide polymorphism (SNP) detection in the absence of a reference genome using semideep next-generation Random Amplicon Sequencing (RAMseq)}, series = {Molecular ecology resources}, volume = {18}, journal = {Molecular ecology resources}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.12717}, pages = {107 -- 117}, year = {2018}, abstract = {Biodiversity has suffered a dramatic global decline during the past decades, and monitoring tools are urgently needed providing data for the development and evaluation of conservation efforts both on a species and on a genetic level. However, in wild species, the assessment of genetic diversity is often hampered by the lack of suitable genetic markers. In this article, we present Random Amplicon Sequencing (RAMseq), a novel approach for fast and cost-effective detection of single nucleotide polymorphisms (SNPs) in nonmodel species by semideep sequencing of random amplicons. By applying RAMseq to the Eurasian otter (Lutra lutra), we identified 238 putative SNPs after quality filtering of all candidate loci and were able to validate 32 of 77 loci tested. In a second step, we evaluated the genotyping performance of these SNP loci in noninvasive samples, one of the most challenging genotyping applications, by comparing it with genotyping results of the same faecal samples at microsatellite markers. We compared (i) polymerase chain reaction (PCR) success rate, (ii) genotyping errors and (iii) Mendelian inheritance (population parameters). SNPs produced a significantly higher PCR success rate (75.5\% vs. 65.1\%) and lower mean allelic error rate (8.8\% vs. 13.3\%) than microsatellites, but showed a higher allelic dropout rate (29.7\% vs. 19.8\%). Genotyping results showed no deviations from Mendelian inheritance in any of the SNP loci. Hence, RAMseq appears to be a valuable tool for the detection of genetic markers in nonmodel species, which is a common challenge in conservation genetic studies.}, language = {en} } @article{HagemannConejeroStillfriedetal.2022, author = {Hagemann, Justus and Conejero, Carles and Stillfried, Milena and Mentaberre, Gregorio and Castillo-Contreras, Raquel and Fickel, J{\"o}rns and Lopez-Olvera, Jorge Ram{\´o}n}, title = {Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {833}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier Science}, address = {Amsterdam [u.a.]}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.155126}, pages = {10}, year = {2022}, abstract = {Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.}, language = {en} } @article{PatelWutkeLenzetal.2017, author = {Patel, Riddhi P. and Wutke, Saskia and Lenz, Dorina and Mukherjee, Shomita and Ramakrishnan, Uma and Veron, Geraldine and Fickel, J{\"o}rns and Wilting, Andreas and F{\"o}rster, Daniel W.}, title = {Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes}, series = {Journal of Heredity}, volume = {108}, journal = {Journal of Heredity}, number = {4}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {0022-1503}, doi = {10.1093/jhered/esx017}, pages = {349 -- 360}, year = {2017}, abstract = {The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species' distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).}, language = {en} }