@article{WiltingPatelPfestorfetal.2016,
  author    = {Wilting, A. and Patel, R. and Pfestorf, Hans and Kern, C. and Sultan, K. and Ario, A. and Penaloza, F. and Kramer-Schadt, S. and Radchuk, Viktoriia and Foerster, D. W. and Fickel, J{\"o}rns},
  title     = {Evolutionary history and conservation significance of the Javan leopard Panthera pardus melas},
  series = {Journal of zoology : proceedings of the Zoological Society of London},
  volume    = {299},
  journal   = {Journal of zoology : proceedings of the Zoological Society of London},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0952-8369},
  doi       = {10.1111/jzo.12348},
  pages     = {239 -- 250},
  year      = {2016},
  abstract  = {The leopard Panthera pardus is widely distributed across Africa and Asia; however, there is a gap in its natural distribution in Southeast Asia, where it occurs on the mainland and on Java but not on the interjacent island of Sumatra. Several scenarios have been proposed to explain this distribution gap. Here, we complemented an existing dataset of 68 leopard mtDNA sequences from Africa and Asia with mtDNA sequences (NADH5+ ctrl, 724bp) from 19 Javan leopards, and hindcasted leopard distribution to the Pleistocene to gain further insights into the evolutionary history of the Javan leopard. Our data confirmed that Javan leopards are evolutionarily distinct from other Asian leopards, and that they have been present on Java since the Middle Pleistocene. Species distribution projections suggest that Java was likely colonized via a Malaya-Java land bridge that by-passed Sumatra, as suitable conditions for leopards during Pleistocene glacial periods were restricted to northern and western Sumatra. As fossil evidence supports the presence of leopards on Sumatra at the beginning of the Late Pleistocene, our projections are consistent with a scenario involving the extinction of leopards on Sumatra as a consequence of the Toba super volcanic eruption (similar to 74kya). The impact of this eruption was minor on Java, suggesting that leopards managed to survive here. Currently, only a few hundred leopards still live in the wild and only about 50 are managed in captivity. Therefore, this unique and distinctive subspecies requires urgent, concerted conservation efforts, integrating insitu and ex situ conservation management activities in a One Plan Approach to species conservation management.},
  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{PatelFoersterKitcheneretal.2016,
  author    = {Patel, Riddhi P. and F{\"o}rster, Daniel W. and Kitchener, Andrew C. and Rayan, Mark D. and Mohamed, Shariff W. and Werner, Laura and Lenz, Dorina and Pfestorf, Hans and Kramer-Schadt, Stephanie and Radchuk, Viktoriia and Fickel, J{\"o}rns and Wilting, Andreas},
  title     = {Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist},
  series = {Royal Society Open Science},
  volume    = {3},
  journal   = {Royal Society Open Science},
  publisher = {Royal Society},
  address   = {London},
  issn      = {2054-5703},
  doi       = {10.1098/rsos.160350},
  pages     = {741 -- 752},
  year      = {2016},
  abstract  = {Background. The bay cat Catopuma badia is endemic to Borneo, whereas its sister species the Asian golden cat Catopuma temminckii is distributed from the Himalayas and southern China through Indochina, Peninsular Malaysia and Sumatra. Based onmorphological data, up to five subspecies of the Asian golden cat have been recognized, but a taxonomic assessment, including molecular data and morphological characters, is still lacking. Results. We combined molecular data (whole mitochondrial genomes), morphological data (pelage) and species distribution projections (up to the Late Pleistocene) to infer how environmental changes may have influenced the distribution of these sister species over the past 120 000 years. The molecular analysis was based on sequenced mitogenomes of 3 bay cats and 40 Asian golden cats derived mainly from archival samples. Our molecular data suggested a time of split between the two species approximately 3.16 Ma and revealed very low nucleotide diversity within the Asian golden cat population, which supports recent expansion of the population. Discussion. The low nucleotide diversity suggested a population bottleneck in the Asian golden cat, possibly caused by the eruption of the Toba volcano in Northern Sumatra (approx. 74 kya), followed by a continuous population expansion in the Late Pleistocene/Early Holocene. Species distribution projections, the reconstruction of the demographic history, a genetic isolation-by-distance pattern and a gradual variation of pelage pattern support the hypothesis of a post-Toba population expansion of the Asian golden cat from south China/Indochina to PeninsularMalaysia and Sumatra. Our findings reject the current classification of five subspecies for the Asian golden cat, but instead support either a monotypic species or one comprising two subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese golden cats, occurring north of the Isthmus: C. t. moormensis.},
  language  = {en}
}