TY - GEN A1 - Beermann, Jan A1 - Westbury, Michael V. A1 - Hofreiter, Michael A1 - Hilgers, Leon A1 - Deister, Fabian A1 - Neumann, Hermann A1 - Raupach, Michael J. T1 - Cryptic species in a well-known habitat BT - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida) T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1059 KW - multiple sequence alignment KW - Oxidase Subunit-I KW - mitochondrial genome KW - control region KW - Ribosomal-RNA KW - asellota crustacea KW - gammarus crustacea KW - deep-sea KW - DNA KW - evolution Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-460792 SN - 1866-8372 IS - 1059 ER - TY - JOUR A1 - Beermann, Jan A1 - Westbury, Michael V. A1 - Hofreiter, Michael A1 - Hilgers, Leon A1 - Deister, Fabian A1 - Neumann, Hermann A1 - Raupach, Michael J. T1 - Cryptic species in a well-known habitat BT - applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida) JF - Scientific reports N2 - Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-25225-x SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - THES A1 - Westbury, Michael V. T1 - Unraveling evolution through Next Generation Sequencing T1 - Entschlüsselung von Evolution durch Sequenzierung der nächsten Generation N2 - The sequencing of the human genome in the early 2000s led to an increased interest in cheap and fast sequencing technologies. This interest culminated in the advent of next generation sequencing (NGS). A number of different NGS platforms have arisen since then all promising to do the same thing, i.e. produce large amounts of genetic information for relatively low costs compared to more traditional methods such as Sanger sequencing. The capabilities of NGS meant that researchers were no longer bound to species for which a lot of previous work had already been done (e.g. model organisms and humans) enabling a shift in research towards more novel and diverse species of interest. This capability has greatly benefitted many fields within the biological sciences, one of which being the field of evolutionary biology. Researchers have begun to move away from the study of laboratory model organisms to wild, natural populations and species which has greatly expanded our knowledge of evolution. NGS boasts a number of benefits over more traditional sequencing approaches. The main benefit comes from the capability to generate information for drastically more loci for a fraction of the cost. This is hugely beneficial to the study of wild animals as, even when large numbers of individuals are unobtainable, the amount of data produced still allows for accurate, reliable population and species level results from a small selection of individuals. The use of NGS to study species for which little to no previous research has been carried out on and the production of novel evolutionary information and reference datasets for the greater scientific community were the focuses of this thesis. Two studies in this thesis focused on producing novel mitochondrial genomes from shotgun sequencing data through iterative mapping, bypassing the need for a close relative to serve as a reference sequence. These mitochondrial genomes were then used to infer species level relationships through phylogenetic analyses. The first of these studies involved reconstructing a complete mitochondrial genome of the bat eared fox (Otocyon megalotis). Phylogenetic analyses of the mitochondrial genome confidently placed the bat eared fox as sister to the clade consisting of the raccoon dog and true foxes within the canidae family. The next study also involved reconstructing a mitochondrial genome but in this case from the extinct Macrauchenia of South America. As this study utilised ancient DNA, it involved a lot of parameter testing, quality controls and strict thresholds to obtain a near complete mitochondrial genome devoid of contamination known to plague ancient DNA studies. Phylogenetic analyses confidently placed Macrauchenia as sister to all living representatives of Perissodactyla with a divergence time of ~66 million years ago. The third and final study of this thesis involved de novo assemblies of both nuclear and mitochondrial genomes from brown and striped hyena and focussed on demographic, genetic diversity and population genomic analyses within the brown hyena. Previous studies of the brown hyena hinted at very low levels of genomic diversity and, perhaps due to this, were unable to find any notable population structure across its range. By incorporating a large number of genetic loci, in the form of complete nuclear genomes, population structure within the brown hyena was uncovered. On top of this, genomic diversity levels were compared to a number of other species. Results showed the brown hyena to have the lowest genomic diversity out of all species included in the study which was perhaps caused by a continuous and ongoing decline in effective population size that started about one million years ago and dramatically accelerated towards the end of the Pleistocene. The studies within this thesis show the power NGS sequencing has and its utility within evolutionary biology. The most notable capabilities outlined in this thesis involve the study of species for which no reference data is available and in the production of large amounts of data, providing evolutionary answers at the species and population level that data produced using more traditional techniques simply could not. N2 - Die Sequenzierung des ersten menschlichen Genoms Anfang der 2000er Jahre förderte das Interesse an kostengünstigen und gleichzeitig schnelleren Sequenziertechniken. Dieses Interesse erreichte seinen derzeitigen Höhepunkt in der Einführung des sogenannten Next Generation Sequencings (NGS). Seitdem wurden zahlreiche NGS-Plattformen entwickelt, die alle dem gleichen Prinzip folgen, nämlich das Erzeugen großer Mengen genetischer Information zu relativ geringen Preisen verglichen mit herkömmlichen Methoden wie der Sanger-Sequenzierung. Die neue Leistungsfähigkeit von NGS bedeutete, dass Forscher nicht mehr länger an Organismen gebunden waren an denen bereits seit Jahren geforscht wurde (bspw. Modellorganismen oder der Mensch), sondern ermöglichte eine Verschiebung in Richtung neuerer und unterschiedlicher Arten von Interesse. Dieses Potential hat viele Wissenschaftsfelder positiv beeinflusst innerhalb der Biowissenschaften, u.a. das Feld der Evolutionsbiologie. Forscher haben angefangen sich zunehmend von Modellorganismen in Laboratorien wegzubewegen hinzu wildlebenden, natürlich vorkommenden Populationen und Arten, was unser Verständnis von Evolution maßgeblich erweitert hat. NGS hat mehrere Vorteile aufzuweisen gegenüber den herkömmlichen Sequenziermethoden. Der wohl größte Vorteil ist die Gewinnung genetischer Daten für mehrere Genorte (Loci) gleichzeitig zu einem Bruchteil der bisherigen Kosten. Das ist besonders nützlich für die Untersuchung wildlebender Tiere da, selbst wenn nicht ausreichend viele Individuen vorliegen, die gewonnene Menge an Daten genaue und verlässliche Ergebnisse auf Populations- sowie Artebene für eine kleine Auswahl an Individuen liefert. Die Verwendung von NGS zur Untersuchung von Arten, für die bisher wenig oder gar keine vorherigen Forschungsergebnisse vorliegen sowie die Gewinnung neuartiger Informationen im Bereich Evolution ebenso wie die Erstellung eines Referenzdatensatzes, der der wissenschaftlichen Gemeinschaft zur Verfügung gestellt werden kann, waren der Fokus dieser Arbeit. Zwei Studien in dieser Arbeit setzten ihren Fokus in der Gewinnung noch nicht publizierter, mitochondrialer Genome, die mittels iterative mapping erstellt wurden und so das Vorhandensein einer Referenzsequenz eines nahen Verwandten der untersuchten Art unnötig machten. In beiden Fällen wurden Shotgun Sequenzierungsdaten verwendet. Die so gewonnenen mitochondrialen Genome wurden dann genutzt, um innerartliche Verwandtschaftsverhältnisse mit hilfe von phylogenetischen Analysen zu klären. Die erste Studie befasste sich mit der Rekonstruktion des kompletten mitochondrialen Genoms des Löffelhundes (Otocyon megalotis). Die phylogenetische Analyse des mitochondrialen Genoms positionierten den Löffelhund sicher als Schwestergruppe der Klade bestehend aus Marderhund und echten Füchsen innerhalb der Familie Canidae. Die zweite Studie hat sich ebenfalls mit der Rekonstruktion eines mitochondrialen Genoms auseinandergesetzt, diesmal von einer bereits ausgestorbenen Art Südamerikas, dem Macrauchenia. Da diese Studie auf sehr alter DNA (ancient DNA) basiert, schließt sie viele Parametertests, Qualitätskontrollen sowie strenge Filterkriterien ein um ein fast vollständiges mitochondriales Genom erhalten zu können, frei von den für ancient DNA typischen Kontaminationen. Phylogenetische Analysen positionieren Macrauchenia als Schwestergruppe zu allen anderen lebenden Vertretern der Perissodactyla mit einer Abspaltung vor ~66 Millionen Jahren. Die dritte und letzte Studie dieser Arbeit beinhaltet die de novo Konstruktionen von nukleären und mitochondrialen Genomen der Schabracken- und Streifenhyäne mit Fokus auf demographische, genetische Diversität sowie Populationsgenomische Analysen innerhalb der Schabrackenhyänen. Vorausgehende Studien an der Schabrackenhyäne gaben Hinweise für einen geringen Grad an genomischer Diversität und, waren vielleicht deshalb, bisher nicht in der Lage eine nennenswerte Populationsstruktur der Schabrackenhyäne aufzudecken. Zusätzlich wurde die genomische Diversität mit der von einer Reihe anderer Arten verglichen. Die Ergebnisse zeigen, dass die Schabrackenhyäne die niedrigste genomische Diversität aufweist im Vergleich zu den in dieser Studie verwendeten Arten, was vielleicht mit einem kontinuierlichen und fortschreitenden Rückgang der effektiven Populationsgröße dieser Spezies zu erklären ist, der vor ca. einer Million Jahre eingesetzt hat und dramatisch zugenommen hat zum Ende des Pleistozän. Die Studien dieser Arbeit zeigen das Potential von NGS Sequenzierung und ihren Nutzen innerhalb der Evolutionsbiologie. Die nennenswertesten Anwendungen von NGS, die in dieser Arbeit hervorgehoben wurden, sind zum Einen der Nutzen für Organismen bzw. Arten für die es keine verfügbaren Referenzdaten gibt sowie zum Anderen die Gewinnung von großen Datenmengen, die die Grundlage bilden zur Beantwortung evolutionsbiologischer Fragestellungen auf Art- und Populationsebene, was vorhergegangene, traditionelle Methoden bisher nicht leisten konnten. KW - Next generation sequencing KW - Evolution KW - Hyena KW - Evolution KW - Hyäne KW - Sequenzierung der nächsten Generation Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-409981 ER - TY - GEN A1 - Folkertsma, Remco A1 - Westbury, Michael V. A1 - Eccard, Jana A1 - Hofreiter, Michael T1 - The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 481 KW - Microtus arvalis KW - Arvicolinae KW - mitochondrial genome KW - common vole KW - phylogeny Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412994 SN - 1866-8372 IS - 481 ER - TY - GEN A1 - Westbury, Michael V. A1 - Hartmann, Stefanie A1 - Barlow, Axel A1 - Wiesel, Ingrid A1 - Leo, Viyanna A1 - Welch, Rebecca A1 - Parker, Daniel M. A1 - Sicks, Florian A1 - Ludwig, Arne A1 - Dalen, Love A1 - Hofreiter, Michael T1 - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 589 KW - evolution KW - hyena KW - genomics KW - population genomics KW - diversity Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-414132 SN - 1866-8372 IS - 589 ER - TY - JOUR A1 - Westbury, Michael V. A1 - Hartmann, Stefanie A1 - Barlow, Axel A1 - Wiesel, Ingrid A1 - Leo, Viyanna A1 - Welch, Rebecca A1 - Parker, Daniel M. A1 - Sicks, Florian A1 - Ludwig, Arne A1 - Dalen, Love A1 - Hofreiter, Michael T1 - Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena JF - Molecular biology and evolution N2 - Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species. KW - evolution KW - hyena KW - genomics KW - population genomics KW - diversity Y1 - 2018 U6 - https://doi.org/10.1093/molbev/msy037 SN - 0737-4038 SN - 1537-1719 VL - 35 IS - 5 SP - 1225 EP - 1237 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Folkertsma, Remco A1 - Westbury, Michael V. A1 - Eccard, Jana A1 - Hofreiter, Michael T1 - The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae) JF - Mitochondrial DNA Part B N2 - The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus. KW - Microtus arvalis KW - Arvicolinae KW - mitochondrial genome KW - common vole KW - phylogeny Y1 - 2018 U6 - https://doi.org/10.1080/23802359.2018.1457994 SN - 2380-2359 VL - 3 IS - 1 SP - 446 EP - 447 ER -