@article{MartinsFickelMinhLeetal.2017,
  author    = {Martins, Renata F. and Fickel, J{\"o}rns and Minh Le, and Thanh Van Nguyen, and Nguyen, Ha M. and Timmins, Robert and Gan, Han Ming and Rovie-Ryan, Jeffrine J. and Lenz, Dorina and F{\"o}rster, Daniel W. and Wilting, Andreas},
  title     = {Phylogeography of red muntjacs reveals three distinct mitochondrial lineages},
  series = {BMC evolutionary biology},
  volume    = {17},
  journal   = {BMC evolutionary biology},
  number    = {34},
  publisher = {BioMed Central},
  address   = {London},
  issn      = {1471-2148},
  doi       = {10.1186/s12862-017-0888-0},
  pages     = {12},
  year      = {2017},
  abstract  = {Background: The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia. Results: We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. Interestingly, we found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum. Conclusions: Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac.},
  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{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{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}
}
@phdthesis{RibeiroMartins2017,
  author    = {Ribeiro Martins, Renata Filipa},
  title     = {Deciphering evolutionary histories of Southeast Asian Ungulates},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-404669},
  school      = {Universit{\"a}t Potsdam},
  pages     = {vii, 115},
  year      = {2017},
  abstract  = {Im Verlauf von Jahrmillionen gestalteten evolution{\"a}re Kr{\"a}fte die Verbreitung und genetische Variabilit{\"a}t von Arten, indem sie die Anpassungsf{\"a}higkeit und {\"U}berlebenswahrscheinlichkeit dieser Arten beeinflussten. Da S{\"u}dostasien eine außerordentlich artenreiche Region darstellt, eignet sie sich besonders, um den Einfluss dieser Kr{\"a}fte zu untersuchen. Historische Klimaver{\"a}nderungen hatten dramatische Auswirkungen auf die Verf{\"u}gbarkeit sowie die Verbreitung von Habitaten in S{\"u}dostasien, weil hierdurch wiederholt das Festland mit sonst isolierten Inseln verbunden wurde. Dies beeinflusste nicht nur, wie Arten in dieser Region verbreitet sind, sondern erm{\"o}glichte auch eine zunehmende genetische Variabilit{\"a}t. Zwar ist es bekannt, dass Arten mit {\"a}hnlicher Evolutionsgeschichte unterschiedliche phylogeographische Muster aufweisen k{\"o}nnen. Die zugrundeliegenden Mechanismen sind jedoch nur gering verstanden. Diese Dissertation behandelt die Phylogeographie von drei Gruppen von Huftieren, welche im S{\"u}den und S{\"u}dosten Asiens vorkommen. Dabei war das vornehmliche Ziel, zu verstehen, wie es zur Ausbildung verschiedener Arten sowie zu einer regionalen Verteilung von genetischer Variabilit{\"a}t kam. Hierf{\"u}r untersuchte ich die mitochondrialen Genome alter Proben. Dadurch war es m{\"o}glich, Populationen des gesamten Verbreitungsgebietes der jeweiligen Arten zu untersuchen - auch solche Populationen, die heutzutage nicht mehr existieren. Entsprechend der einzelnen Huftiergruppen ist diese Arbeit in drei Kapitel unterteilt: Muntjaks (Muntiacus sp.), Hirsche der Gattung Rusa und asiatische Nash{\"o}rner. Alle drei Gruppen weisen eine Aufteilung in unterschiedliche Linien auf, was jeweils direkt auf Ereignisse des Pleistoz{\"a}ns zur{\"u}ckgef{\"u}hrt werden kann. Muntjaks sind eine weit verbreitete Art, die in verschiedensten Habitaten vorkommen kann. Ich wies nach, dass es in der Vergangenheit zu genetischem Austausch zwischen Populationen von verschiedenen Inseln des Sundalandes kam. Dies deutet auf die F{\"a}higkeit von Muntjaks hin, sich an die ehemaligen Landbr{\"u}cken anzupassen. Jedoch zeige ich auch, dass mindestens zwei Hindernisse bei ihrer Verbreitung existierten, wodurch es zu einer Differenzierung von Populationen kam: eine Barriere trennte Populationen des asiatischen Festlands von denen der Sundainseln, die andere isolierte sri-lankische von restlichen Muntjaks. Die zwei untersuchten Rusa-Arten weisen ein anderes Muster auf, was wiederum eine weitere Folge der pleistoz{\"a}nen Landbr{\"u}cken darstellt. Beide Arten sind ausschließlich monophyletisch. Allerdings gibt es Anzeichen f{\"u}r die Hybridisierung dieser Arten auf Java, was durch eine fr{\"u}here Ausbreitung des sambar (R. unicolor) gef{\"o}rdert wurde. Aufgrund dessen fand ich zudem, dass all jene Individuen der anderen Art, R. timorensis, die durch den Menschen auf die {\"o}stlichen Sundainseln gebracht wurden, in Wahrheit Hybride sind. F{\"u}r den dritten Teil war es mir m{\"o}glich, Proben von Vertretern ausgestorbener Populationen vom asiatischen Festland des Sumatra- und des Java-Nashorns (Dicerorhinus sumatrensis und Rhinoceros sondaicus) zu analysieren. Die Ergebnisse meiner Arbeit belegen, dass die genetische Vielfalt dieser historischen Populationen bedeutend gr{\"o}ßer war als die der heutigen Nachkommen. Ihre jeweilige Evolutionsgeschichte korreliert stark mit pleistoz{\"a}nen Prozessen. Außerdem betonen meine Ergebnisse das enorme Ausmaß von verlorener genetischer Diversit{\"a}t dieser stark bedrohten Arten. Jede Art besitzt eine individuelle phylogeographische Geschichte. Ebenso fand ich aber auch allgemeing{\"u}ltige Muster von genetischer Differenzierung in allen Gruppen, welche direkt mit Ereignissen des Pleistoz{\"a}ns assoziiert werden k{\"o}nnen. Vergleicht man jedoch die einzelnen Ergebnisse der Arten, wird deutlich, dass die gleichen geologischen Prozesse nicht zwangsl{\"a}ufig in gleiche evolutive Ergebnisse resultieren. Einer der Gr{\"u}nde hierf{\"u}r k{\"o}nnte zum Beispiel die unterschiedliche Durchl{\"a}ssigkeit der entstandenen Landkorridore des Sundaschelfs sein. Die M{\"o}glichkeit diese neuen Habitate zu nutzen und somit auch zu passieren steht im direkten Bezug zu den spezifischen {\"o}kologischen Bed{\"u}rfnissen der Arten.Zusammenfassend leisten meine Erkenntnisse einen wichtigen Beitrag, die Evolution und geographische Aufteilung der genetischen Vielfalt in diesem Hotspot an Biodiversit{\"a}t zu verstehen. Obendrein k{\"o}nnen sie aber auch Auswirkungen auf die Erhaltung und systematische Klassifikation der untersuchten Arten haben.},
  language  = {en}
}