@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{PaijmansFickelCourtioletal.2016,
  author    = {Paijmans, Johanna L. A. and Fickel, J{\"o}rns and Courtiol, Alexandre and Hofreiter, Michael and Foerster, Daniel W.},
  title     = {Impact of enrichment conditions on cross-species capture of fresh and degraded DNA},
  series = {Molecular ecology resources},
  volume    = {16},
  journal   = {Molecular ecology resources},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12420},
  pages     = {42 -- 55},
  year      = {2016},
  abstract  = {Abstract By combining high-throughput sequencing with target enrichment ('hybridization capture'), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on nonmodel species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success is not yet thoroughly understood. We evaluated the impact of a key parameter - hybridization temperature - on the capture success of mitochondrial genomes across the carnivoran family Felidae. Capture was carried out for a range of sample types (fresh, archival, ancient) with varying levels of sequence divergence between bait and target (i.e. across a range of species) using pools of individually indexed libraries on Agilent SureSelect™ arrays. Our results suggest that hybridization capture protocols require specific optimization for the sample type that is being investigated. Hybridization temperature affected the proportion of on-target sequences following capture: for degraded samples, we obtained the best results with a hybridization temperature of 65 °C, while a touchdown approach (65 °C down to 50 °C) yielded the best results for fresh samples. Evaluation of capture performance at a regional scale (sliding window approach) revealed no significant improvement in the recovery of DNA fragments with high sequence divergence from the bait at any of the tested hybridization temperatures, suggesting that hybridization temperature may not be the critical parameter for the enrichment of divergent fragments.},
  language  = {en}
}
@article{CuiLoeberAlquezarPlanasetal.2016,
  author    = {Cui, Pin and L{\"o}ber, Ulrike and Alquezar-Planas, David E. and Ishida, Yasuko and Courtiol, Alexandre and Timms, Peter and Johnson, Rebecca N. and Lenz, Dorina and Helgen, Kristofer M. and Roca, Alfred L. and Hartman, Stefanie and Greenwood, Alex D.},
  title     = {Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome},
  series = {PeerJ},
  volume    = {4},
  journal   = {PeerJ},
  publisher = {PeerJ Inc.},
  address   = {London},
  issn      = {2167-8359},
  doi       = {10.7717/peerj.1847},
  pages     = {29},
  year      = {2016},
  abstract  = {Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.},
  language  = {en}
}