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Article: Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World’s Rarest Hyena Species, the Brown Hyena

Ludwig, Arne

Molecular biology and evolution, 35(5):1225-1237

2018

Abstract: 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 ... ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	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 ∼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.
Keywords	genomics ; diversity ; evolution ; hyena ; population genomics
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Decline of genetic diversity in ancient domestic stallions in Europe

Ludwig, Arne

Science advances, 4(4):eaap9691

2018

Abstract: Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in ... ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Present-day domestic horses are immensely diverse in their maternally inherited mitochondrial DNA, yet they show very little variation on their paternally inherited Y chromosome. Although it has recently been shown that Y chromosomal diversity in domestic horses was higher at least until the Iron Age, when and why this diversity disappeared remain controversial questions. We genotyped 16 recently discovered Y chromosomal single-nucleotide polymorphisms in 96 ancient Eurasian stallions spanning the early domestication stages (Copper and Bronze Age) to the Middle Ages. Using this Y chromosomal time series, which covers nearly the entire history of horse domestication, we reveal how Y chromosomal diversity changed over time. Our results also show that the lack of multiple stallion lineages in the extant domestic population is caused by neither a founder effect nor random demographic effects but instead is the result of artificial selection—initially during the Iron Age by nomadic people from the Eurasian steppes and later during the Roman period. Moreover, the modern domestic haplotype probably derived from another, already advantageous, haplotype, most likely after the beginning of the domestication. In line with recent findings indicating that the Przewalski and domestic horse lineages remained connected by gene flow after they diverged about 45,000 years ago, we present evidence for Y chromosomal introgression of Przewalski horses into the gene pool of European domestic horses at least until medieval times.
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Endogenous Retroviral Insertions Indicate a Secondary Introduction of Domestic Sheep Lineages to the Caucasus and Central Asia between the Bronze and Iron Age

Ludwig, Arne

Genes, 8(6):165

2017

Abstract: Sheep were one of the first livestock species domesticated by humans. After initial domestication in the Middle East they were spread across Eurasia. The modern distribution of endogenous Jaagsiekte sheep retrovirus insertions in domestic sheep breeds ... ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Sheep were one of the first livestock species domesticated by humans. After initial domestication in the Middle East they were spread across Eurasia. The modern distribution of endogenous Jaagsiekte sheep retrovirus insertions in domestic sheep breeds suggests that over the course of millennia, successive introductions of improved lineages and selection for wool quality occurred in the Mediterranean region and most of Asia. Here we present a novel ancient DNA approach using data of endogenous retroviral insertions in Bronze and Iron Age domestic sheep from the Caucasus and Pamir mountain areas. Our findings support a secondary introduction of wool sheep from the Middle East between the Late Bronze Age and Iron Age into most areas of Eurasia.
Keywords	ancient DNA ; archaeozoology ; endogenous retrovirus ; mitochondrial haplotype ; retrotype
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Expression Patterns of Atlantic Sturgeon (Acipenser oxyrinchus) During Embryonic Development

Ludwig, Arne

G3: Genes, genomes, genetics, 7(2):533-542

2017

Abstract: During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in ... ...

Institution	Leibniz-Institut für Gewässerökologie und Binnenfischerei Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	During teleost ontogeny the larval and embryonic stages are key stages, since failure during this period of tissue differentiation may cause malformations, developmental delays, poor growth, and massive mortalities. Despite the rapid advances in sequencing technologies, the molecular background of the development of economical important but endangered fish species like the Atlantic sturgeon (Acipenser oxyrinchus) has not yet been thoroughly investigated. The current study examines the differential expression of transcripts involved in embryonic development of the Atlantic sturgeon. Addressing this goal, a reference transcriptome comprising eight stages was generated using Illumina HiSeq 2500 platform. The constructed de novo assembly counted to 441,092 unfiltered and 179,564 filtered transcripts. Subsequently, the expression profile of four developmental stages ranging from early (gastrula) to late stages of pre-larval development (2 dph) were investigated applying Illumina MiSeq platform. Differential expression analysis revealed distinct expression patterns among stages, especially between the two early and the two later stages. Transcripts up-regulated at the two early stages were mainly enriched in transcripts linked to developmental processes while transcripts expressed at the last two stages were mainly enriched in transcripts important to muscle contraction. Furthermore important stage specific expression has been detected for the hatching stage with transcripts enriched in molecule transport and for the 2 dph stage with transcripts enriched in visual perception and lipid digestion. Our investigation represents a significant contribution to the understanding of Atlantic sturgeon embryonic development and transcript characterization along with the differential expression results will significantly contribute to sturgeon research and aquaculture.
Keywords	Acipenser ; Development ; Hatching ; RNA-seq ; embryogenesis
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

Ludwig, Arne

PLOS ONE, 11(3):e0150780

2016

Abstract: A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative.
Keywords	Bats ; Gentic loci ; Forearms ; Mitochondria ; Sequence alignment ; Phylogenetic analysis ; Wings ; Taxonomy
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Highly resolved phylogenetic relationships within order acipenseriformes according to novel nuclear markers

Ludwig, Arne / Peng, Zuogang

Genes, 10(1):38

2019

Abstract: Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.
Keywords	Acipenseriformes ; molecular clock ; nuclear markers ; phylogeny
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Geographical differentiation of the Euchiloglanis fish complex (Teleostei: Siluriformes) in the Hengduan Mountain Region, China: Phylogeographic evidence of altered drainage patterns

Ludwig, Arne / Peng, Zuogang

Ecology and evolution, 7(3):928-940

2017

Abstract: The uplift of the Tibetan Plateau caused significant ecogeographical changes that had a major impact on the exchange and isolation of regional fauna and flora. Furthermore, Pleistocene glacial oscillations were linked to temporal large‐scale landmass and ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	The uplift of the Tibetan Plateau caused significant ecogeographical changes that had a major impact on the exchange and isolation of regional fauna and flora. Furthermore, Pleistocene glacial oscillations were linked to temporal large‐scale landmass and drainage system reconfigurations near the Hengduan Mountain Region and might have facilitated speciation and promoted biodiversity in southwestern China. However, strong biotic evidence supporting this role is lacking. Here, we use the Euchiloglanis fish species complex as a model to demonstrate the compound effects of the Tibetan Plateau uplift and Pleistocene glacial oscillations on species formation in this region. The genetic structure and geographical differentiation of the Euchiloglanis complex in four river systems within the Hengduan Mountain Region were deduced using the cytochrome b (cyt b) gene and 10 microsatellite loci from 360 to 192 individuals, respectively. The results indicated that the populations were divided into four independently evolving lineages, in which the populations from the Qingyi River and Jinsha River formed two sub‐lineages. Phylogenetic relationships were structured by geographical isolation, especially near drainage systems. Divergence time estimation analyses showed that the Euchiloglanis complex diverged from its sister clade Pareuchiloglanis sinensis at around 1.3 Million years ago (Ma). Within the Euchiloglanis complex, the divergence time between the Dadu–Yalong and Jinsha–Qingyi River populations occurred at 1.0 Ma. This divergence time was in concordance with recent geological events, including the Kun‐Huang Movement (1.2–0.6 Ma) and the lag time (<2.0 Ma) of river incision in the Hengduan Mountain Region. Population expansion signals were detected from mismatched distribution analyses, and the expansion times were concurrent with Pleistocene glacier fluctuations. Therefore, current phylogeographic patterns of the Euchiloglanis fish complex in the Hengduan Mountain Region were influenced by the uplift event of the Tibetan Plateau and were subsequently altered by paleo‐river transitions during the late Pleistocene glacial oscillations.
Keywords	Euchiloglanis ; Hengduan Mountain Region ; Pleistocene glacial oscillations ; genetic structure ; phylogeny ; phylogeography
Language	English
Document type	Article
Database	Repository for Life Sciences

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Article: Adaptive Evolution of the Eda Gene and Scales Loss in Schizothoracine Fishes in Response to Uplift of the Tibetan Plateau

Zhang, Cunfang / Tong, Chao / Ludwig, Arne / Peng, Zuogang

International journal of molecular sciences, 19(10):2953

2018

Abstract: Schizothoracine is the predominant wild fish subfamily of the Tibetan plateau (TP). Their scales, pharyngeal teeth and barbels have gradually regressed with increasing altitude. Schizothoracine have been divided into three groups: primitive, specialized ... ...

Institution	Leibniz-Institut für Zoo- und Wildtierforschung (Berlin)
Abstract	Schizothoracine is the predominant wild fish subfamily of the Tibetan plateau (TP). Their scales, pharyngeal teeth and barbels have gradually regressed with increasing altitude. Schizothoracine have been divided into three groups: primitive, specialized and highly specialized. Ectodysplasin-A (Eda) has been considered as a major gene that contributes to the development of skin appendages. The present study cloned the Eda genes of 51 Schizothoracine fish species which represent the three groups and five Barbinae species. Phylogenetic analyses indicated that Eda may have acted as the genetic trigger for scale loss in the Schizothoracine. Furthermore, 14 single nucleotide polymorphisms (SNPs) and two deletions (18 bp and 6 bp in size), were also detected in the Eda coding sequence of the highly specialized group compared to the primitive group. The same SNPs and two indels result in four non-synonymous and two G-X-Y and 1 XY motif indels, which possibly contribute to significant structure changes in the Eda gene. The domain including (G-X-Y)n motif in the Eda gene is relatively conserved amongst teleosts. Based on the above results, we hypothesize that the evolution of Eda gene might be associated with the scale loss in Schizothoracine fishes in response to the phased uplift of the TP.
Keywords	Eda gene ; Schizothoracine ; Tibetan plateau ; adaptive evolution ; scale loss
Language	English
Document type	Article
Database	Repository for Life Sciences

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Book ; Thesis: Abstammung der europäischen Hausschafe und Phylogenie der eurasischen Wildschafe

Ludwig, Arne

(Schriften zu genetischen Ressourcen ; 9)

1998

Author's details	von Arne Ludwig
Series title	Schriften zu genetischen Ressourcen ; 9
Collection
Keywords	Schaf ; Systematik ; Phylogenie ; Domestikation ; Schafrasse
Subject	Schaf ; Abstammung ; Entwicklung ; Entwicklungsgeschichte ; Phylogenese ; Stammesentwicklung ; Stammesgeschichte ; Ovis ; Domestizierung ; Haustierwerdung ; Hausschaf ; Ovis ammon aries ; Ovis aries ; Klassifikation ; Taxonomie ; Biosystematik
Size	VI, 122 S. : Ill., graph. Darst.
Publisher	Zentralstelle für Agrardokumentation und -information (ZADI), Informationszentrum für Genetische Ressourcen (IGR)
Publishing place	Bonn
Document type	Book ; Thesis
Thesis / German Habilitation thesis	Berlin, Humboldt-Univ., Diss., 1997
Note	Zsfassung in engl. Sprache
HBZ-ID	HT008495086
Database	Catalogue ZB MED Nutrition, Environment, Agriculture

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988/2085	available for loan (reading room)	Freihandmagazin (U1)

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Article ; Online: Accelerated Adiabatic Passage of a Single Electron Spin Qubit in Quantum Dots.

Liu, Xiao-Fei / Matsumoto, Yuta / Fujita, Takafumi / Ludwig, Arne / Wieck, Andreas D / Oiwa, Akira

Physical review letters

2024 Volume 132, Issue 2, Page(s) 27002

Abstract: Adiabatic processes can keep the quantum system in its instantaneous eigenstate, which is robust to noises and dissipation. However, it is limited by sufficiently slow evolution. Here, we experimentally demonstrate the transitionless quantum driving ( ... ...

Abstract	Adiabatic processes can keep the quantum system in its instantaneous eigenstate, which is robust to noises and dissipation. However, it is limited by sufficiently slow evolution. Here, we experimentally demonstrate the transitionless quantum driving (TLQD) of the shortcuts to adiabaticity in gate-defined semiconductor quantum dots (QDs) to greatly accelerate the conventional adiabatic passage for the first time. For a given efficiency of quantum state transfer, the acceleration can be more than twofold. The dynamic properties also prove that the TLQD can guarantee fast and high-fidelity quantum state transfer. In order to compensate for the diabatic errors caused by dephasing noises, the modified TLQD is proposed and demonstrated in experiment by enlarging the width of the counterdiabatic drivings. The benchmarking shows that the state transfer fidelity of 97.8% can be achieved. This work will greatly promote researches and applications about quantum simulations and adiabatic quantum computation based on the gate-defined QDs.
Language	English
Publishing date	2024-01-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.132.027002
Database	MEDical Literature Analysis and Retrieval System OnLINE

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