@article{GaubertPatelVeronetal.2016,
  author    = {Gaubert, Philippe and Patel, Riddhi P. and Veron, Geraldine and Goodman, Steven M. and Willsch, Maraike and Vasconcelos, Raquel and Lourenco, Andre and Sigaud, Marie and Justy, Fabienne and Joshi, Bheem Dutt and Fickel, J{\"o}rns and Wilting, Andreas},
  title     = {Phylogeography of the Small Indian Civet and Origin of Introductions to Western Indian Ocean Islands},
  series = {The journal of heredity : official journal of the American Genetic Association},
  volume    = {108},
  journal   = {The journal of heredity : official journal of the American Genetic Association},
  publisher = {Oxford Univ. Press},
  address   = {Cary},
  issn      = {0022-1503},
  doi       = {10.1093/jhered/esw085},
  pages     = {270 -- 279},
  year      = {2016},
  abstract  = {The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (1) establish a time-calibrated phylogeography across the species' native range and (2) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified 3 geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3.2-2.3 million years ago (Mya), with no clear signature of past demographic expansion. Within Southeast Asia, Balinese populations separated from the rest 2.6-1.3 Mya. Western Indian Ocean populations were assigned to the Indian subcontinent + northern Indochina lineage and had the lowest mitochondrial diversity. Approximate Bayesian computation did not distinguish between single versus multiple introduction scenarios. The early diversification of the small Indian civet was likely shaped by humid periods in the Late Pliocene-Early Pleistocene that created evergreen rainforest barriers, generating areas of intra-specific endemism in the Indian subcontinent, East, and Southeast Asia. Later, Pleistocene dispersals through drier conditions in South and Southeast Asia were likely, giving rise to the species' current natural distribution. Our molecular data supported the delineation of only 4 subspecies in V. indica, including an endemic Balinese lineage. Our study also highlighted the influence of prefirst millennium AD introductions to western Indian Ocean islands, with Indian and/or Arab traders probably introducing the species for its civet oil.},
  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}
}
@article{KobelHoellerGleyJochinkeetal.2018,
  author    = {Kobel-H{\"o}ller, Konstanze and Gley, Kevin and Jochinke, Janina and Heider, Kristina and Fritsch, Verena Nadin and Ha Viet Duc Nguyen, and Lischke, Timo and Radek, Renate and Baumgrass, Ria and Mutzel, Rupert and Thewes, Sascha},
  title     = {Calcineurin Silencing in Dictyostelium discoideum Leads to Cellular Alterations Affecting Mitochondria, Gene Expression, and Oxidative Stress Response},
  series = {Protist},
  volume    = {169},
  journal   = {Protist},
  number    = {4},
  publisher = {Elsevier GMBH},
  address   = {M{\"u}nchen},
  issn      = {1434-4610},
  doi       = {10.1016/j.protis.2018.04.004},
  pages     = {584 -- 602},
  year      = {2018},
  abstract  = {Calcineurin is involved in development and cell differentiation of the social amoeba Dictyostelium discoideum. However, since knockouts of the calcineurin-encoding genes are not possible in D. discoideum it is assumed that the phosphatase also plays a crucial role during vegetative growth of the amoebae. Therefore, we investigated the role of calcineurin during vegetative growth in D. discoideum. RNAi-silenced calcineurin mutants showed cellular alterations with an abnormal morphology of mitochondria and had increased content of mitochondrial DNA (mtDNA). In contrast, mitochondria showed no substantial functional impairment. Calcineurin-silencing led to altered expression of calcium-regulated genes as well as mitochondrially-encoded genes. Furthermore, genes related to oxidative stress were higher expressed in the mutants, which correlated to an increased resistance towards reactive oxygen species (ROS). Most of the changes observed during vegetative growth were not seen after starvation of the calcineurin mutants. We show that impairment of calcineurin led to many subtle, but in the sum crucial cellular alterations in vegetative D. discoideum cells. As these alterations were not observed after starvation we propose a dual role for calcineurin during growth and development. Our results imply that calcineurin is one player in the mutual interplay between mitochondria and ROS during vegetative growth.},
  language  = {en}
}
@misc{PaijmansBarlowFoersteretal.2019,
  author    = {Paijmans, Johanna L. A. and Barlow, Axel and F{\"o}rster, Daniel W. and Henneberger, Kirstin and Meyer, Matthias and Nickel, Birgit and Nagel, Doris and Wors{\o}e Havm{\o}ller, Rasmus and Baryshnikov, Gennady F. and Joger, Ulrich and Rosendahl, Wilfried and Hofreiter, Michael},
  title     = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {505},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-42255},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-422555},
  pages     = {12},
  year      = {2019},
  abstract  = {Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.},
  language  = {en}
}
@article{PaijmansBarlowFoersteretal.2018,
  author    = {Paijmans, Johanna L. A. and Barlow, Axel and F{\"o}rster, Daniel W. and Henneberger, Kirstin and Meyer, Matthias and Nickel, Birgit and Nagel, Doris and Wors{\o}e Havm{\o}ller, Rasmus and Baryshnikov, Gennady F. and Joger, Ulrich and Rosendahl, Wilfried and Hofreiter, Michael},
  title     = {Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations},
  series = {BMC Evolutionary Biology},
  volume    = {18},
  journal   = {BMC Evolutionary Biology},
  number    = {156},
  publisher = {BioMed Central und Springer},
  address   = {London, Berlin und Heidelberg},
  issn      = {1471-2148},
  doi       = {10.1186/s12862-018-1268-0},
  pages     = {12},
  year      = {2018},
  abstract  = {Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.},
  language  = {en}
}
@article{GeisslerPoyarkovGrismeretal.2015,
  author    = {Geissler, Peter and Poyarkov, Nikolay A. and Grismer, Lee and Nguyen, Truong Q. and An, Hang T. and Neang, Thy and Kupfer, Alexander and Ziegler, Thomas and B{\"o}hme, Wolfgang and M{\"u}ller, Hendrik},
  title     = {New Ichthyophis species from Indochina (Gymnophiona, Ichthyophiidae): 1. The unstriped forms with descriptions of three new species and the redescriptions of I-acuminatus Taylor, 1960, I-youngorum Taylor, 1960 and I-laosensis Taylor, 1969},
  series = {Organisms, diversity \& evolution : official journal of the Gesellschaft f{\"u}r Biologische Systematik},
  volume    = {15},
  journal   = {Organisms, diversity \& evolution : official journal of the Gesellschaft f{\"u}r Biologische Systematik},
  number    = {1},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1439-6092},
  doi       = {10.1007/s13127-014-0190-6},
  pages     = {143 -- 174},
  year      = {2015},
  abstract  = {Caecilians of the genus Ichthyophis Fitzinger, 1826 are among the most poorly known amphibian taxa within Southeast Asia. Populations of Ichthyophis from the Indochina region (comprising Cambodia, Laos, and Vietnam) have been assigned to five taxa: Ichthyophis acuminatus, Ichthyophis bannanicus, Ichthyophis kohtaoensis, Ichthyophis laosensis, and Ichthyophis nguyenorum. Barcoding of recently collected specimens indicates that Indochinese congeners form a clade that includes several morphologically and genetically distinct but yet undescribed species. Although body coloration is supported by the molecular analyses as a diagnostic character at species level, unstriped forms are paraphyletic with respect to striped Ichthyophis. Based on our morphological and molecular analyses, three distinct unstriped ichthyophiid species, Ichthyophis cardamomensis sp. nov. from western Cambodia, Ichthyophis catlocensis sp. nov. from southern Vietnam, and Ichthyophis chaloensis sp. nov. from central Vietnam are described as new herein, almost doubling the number of Ichthyophis species known from the Indochinese region. All three new species differ from their unstriped congeners in a combination of morphological and molecular traits. In addition, redescriptions of three unstriped Ichthyophis species (Ichthyophis acuminatus, I. laosensis, I. youngorum) from Indochina and adjacent Thailand are provided.},
  language  = {en}
}
@article{GrahnKurushimaBillingsetal.2011,
  author    = {Grahn, R. A. and Kurushima, J. D. and Billings, N. C. and Grahn, J. C. and Halverson, J. L. and Hammer, E. and Ho, C. K. and Kun, T. J. and Levy, J. K. and Lipinski, M. J. and Mwenda, J. M. and Ozpinar, H. and Schuster, R. K. and Shoorijeh, S. J. and Tarditi, C. R. and Waly, N. E. and Wictum, E. J. and Lyons, L. A.},
  title     = {Feline non-repetitive mitochondrial DNA control region database for forensic evidence},
  series = {Forensic science international : an international journal dedicated to the applications of genetics in the administration of justice ; Genetics},
  volume    = {5},
  journal   = {Forensic science international : an international journal dedicated to the applications of genetics in the administration of justice ; Genetics},
  number    = {1},
  publisher = {Elsevier},
  address   = {Clare},
  issn      = {1872-4973},
  doi       = {10.1016/j.fsigen.2010.01.013},
  pages     = {33 -- 42},
  year      = {2011},
  abstract  = {The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. The current study evaluates 402 bp of the mtDNA control region (CR) from 1394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0\% are clearly derived from the major mitotypes. Unique sequences are found in 7.5\% of the cats. The overall genetic diversity for this data set is 0.8813 +/- 0.0046 with a random match probability of 11.8\%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide.},
  language  = {en}
}
@article{SilvaIturrizaKetmaierTiedemann2012,
  author    = {Silva-Iturriza, Adriana and Ketmaier, Valerio and Tiedemann, Ralph},
  title     = {Profound population structure in the Philippine Bulbul Hypsipetes philippinus (Pycnonotidae, Ayes) is not reflected in its Haemoproteus haemosporidian parasite},
  series = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics and infectious diseases (MEEGID)},
  volume    = {12},
  journal   = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics and infectious diseases (MEEGID)},
  number    = {1},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1567-1348},
  doi       = {10.1016/j.meegid.2011.10.024},
  pages     = {127 -- 136},
  year      = {2012},
  abstract  = {In this study we used molecular markers to screen for the occurrence and prevalence of the three most common haemosporidian genera (Haemoproteus, Plasmodium, and Leucocytozoon) in blood samples of the Philippine Bulbul (Hypsipetes philippinus), a thrush-size passerine bird endemic to the Philippine Archipelago. We then used molecular data to ask whether the phylogeographic patterns in this insular host-parasite system might follow similar evolutionary trajectories or not. We took advantage of a previous study describing the pattern of genetic structuring in the Philippine Bulbul across the Central Philippine Archipelago (6 islands, 7 populations and 58 individuals; three mitochondrial DNA genes). The very same birds were here screened for the occurrence of parasites by species-specific PCR assays of the mitochondrial cytochrome b gene (471 base pairs). Twenty-eight out of the 58 analysed birds had Haemoproteus (48\%) infections while just 2\% of the birds were infected with either Leucocytozoon or Plasmodium. Sixteen of the 28 birds carrying Haemoproteus had multiple infections. The phylogeography of the Philippine Bulbul mostly reflects the geographical origin of samples and it is consistent with the occurrence of two different subspecies on (1) Semirara and (2) Carabao, Boracay, North Gigante, Panay, and Negros, respectively. Haemoproteus phylogeography shows very little geographical structure, suggesting extensive gene flow among locations. While movements of birds among islands seem very sporadic, we found co-occurring evolutionary divergent parasite lineages. We conclude that historical processes have played a major role in shaping the host phylogeography, while they have left no signature in that of the parasites. Here ongoing population processes, possibly multiple reinvasions mediated by other hosts, are predominant.},
  language  = {en}
}
@article{PavesiDeidunDeMatthaeisetal.2012,
  author    = {Pavesi, Laura and Deidun, Alan and De Matthaeis, Elvira and Tiedemann, Ralph and Ketmaier, Valerio},
  title     = {Mitochondrial DNA and microsatellites reveal significant divergence in the beachflea Orchestia montagui (Talitridae: Amphipoda)},
  series = {Aquatic sciences : research across boundaries},
  volume    = {74},
  journal   = {Aquatic sciences : research across boundaries},
  number    = {3},
  publisher = {Springer},
  address   = {Basel},
  issn      = {1015-1621},
  doi       = {10.1007/s00027-012-0250-y},
  pages     = {587 -- 596},
  year      = {2012},
  abstract  = {Talitrids are semiterrestrial crustacean amphipods inhabiting sandy and rocky beaches; they generally show limited active dispersal over long distances. In this study we assessed levels of population genetic structure and variability in the talitrid amphipod Orchestia montagui, a species strictly associated to stranded decaying heaps of the seagrass Posidonia oceanica. The study is based on six populations (153 individuals) and covers five basins of the Mediterranean Sea (Tyrrhenian, Ionian, Adriatic, Western and Eastern basins). Samples were screened for polymorphisms at a fragment of the mitochondrial DNA (mtDNA) coding for the cytochrome oxidase subunit I gene (COI; 571 base pairs) and at eight microsatellite loci. MtDNA revealed a relatively homogeneous haplogroup, which clustered together the populations from the Western, Tyrrhenian and Eastern basins, but not the populations from the Adriatic and Ionian ones; microsatellites detected two clusters, one including the Adriatic and Ionian populations, the second grouping all the others. We found a weak geographic pattern in the genetic structuring of the species, with a lack of isolation by distance at either class of markers. Results are discussed in terms of probability of passive dispersal over long distances through heaps of seagrass.},
  language  = {en}
}