Arne Ludwig

Leibniz Institute for Zoo and Wildlife Research & Humboldt University Berlin

Most European rewilding initiatives are based on the recovery of large herbivores, particularly European bison Bison bonasus, aiming at restoring ecosystem processes and increase trophic complexity. The growing support for the release of bison as a wild species, and change its legal status, in Spain, as an ecological analogue of the extinct steppe...

Most European rewilding initiatives are based on the recovery of large herbivores, particularly European bison Bison bonasus, aiming at restoring ecosystem processes and increase trophic complexity. The growing support for the release of bison as a wild species, and change its legal status, in Spain, as an ecological analogue of the extinct steppe...

Four dominant coat color phenotypes are found in fallow deer (Dama dama). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals (772 brown, 62 black, 126 menil, and 38 white) were examined for mutations in the ASIP, MC...

Horses revolutionized human history with fast mobility¹. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2–4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that re...

Current state of knowledge of the sterlet (Acipenser ruthenus Linnaeus, 1758) in Austria. Part 1: Population size Sturgeon populations worldwide have collapsed due to various anthropogen-ic impacts but knowledge gaps in habitat requirements and population dynamics still exist. In the Austrian Danube, habitat loss and the blocking of migration route...

Background Reindeer (Rangifer tarandus) are iconic mammals that inhabit the Arctic and sub-Arctic regions. In these areas, reindeer not only play a vital ecological role, but they also hold cultural and economic significance for indigenous communities. In order to thrive in the harsh conditions of the northernmost areas of the world, reindeer have...

A market study on sturgeon products in the Lower Danube countries (Bulgaria, Romania, Serbia and Ukraine) resulted in a total of 149 samples of caviar and meat, which we subjected to genetic-isotope analyses. The samples comprised 31 samples (21%) of illegal wild-caught origin, 17 samples (11.4%) sold in violation of CITES and EU regulations, and 4...

While the potamodromous sterlet was common in the past throughout the Upper Danube in Germany and Austria, it nearly vanished in the second half of the 20th century. Until recently, only one small and isolated reproductive sub-population is known from the German-Austrian border. However, isolated remnants in another section downstream of Vienna, ne...

Naked mole-rats form colonies with a single reproductively active female surrounded by subordinate workers. Workers perform offspring care, construction and defense of the burrow system, and food supply. Such division of labor, called “cooperative breeding,” is strongly associated with the evolution of monogamous mating behavior, as seen in several...

Girgentana is a charismatic breed of domestic goat (Capra hircus) characterised by unique corkscrew-shaped horns. They are commonly kept as livestock in Sicily, where they are indigenous, but are also shown in many European zoos because of their interesting morphology. Although the bezoar, or wild goat (Capra aegagrus), is commonly accepted as the...

Domestication of horses fundamentally transformed long-range mobility and warfare¹. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2–4 at Botai, Central Asia around 3500 bc³. Other longstanding candidate regions for horse domestic...

Environmental DNA (eDNA) techniques refer to utilizing the organisms’ DNA extracted from environment samples to genetically identify target species without capturing actual organisms. eDNA metabarcoding via high‐throughput sequencing can simultaneously detect multiple fish species from a single water sample, which is a powerful tool for the qualita...

The subpopulation of the Irrawaddy dolphin (Orcaella brevirostris) living in the Mekong River, Cambodia, is considered to be critically endangered. The aim of the investigation was to gain information about the genetic variation, health status and exposure to toxic compounds of these dolphins. Tissue samples from 27 Irrawaddy river dolphins found d...

Background The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentia...

Although the European roe deer (Capreolus capreolus) population of North-West Germany has a remarkable number of melanistic specimens between 10% and 25%, the underlying genetic mutation-causing melanism is still unknown. We used a gene targeting approach focusing on MC1R and ASIP as important genes of coat coloration. Overall, 1384 bp of MC1R and...

Although the European roe deer (Capreolus capreolus) population of NorthWest Germany has a remarkable number of melanistic specimens between 10% and 25%, the underlying genetic mutation-causing melanism is still unknown. We used a gene targeting approach focusing on MC1R and ASIP as important genes of coat coloration. Overall, 1384 bp of MC1R and 2...

Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7x coverage (mammoth) in 2008 to more than 50x coverage (Neand...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organi...

The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cr...

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to...

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 uti...

The analysis of single-nucleotide polymorphisms (SNPs) has proven to be advantageous for addressing variation within samples of highly degraded or low-quality DNA samples. This is because only short fragments need to be amplified to analyze SNPs, and this can be achieved by multiplex PCR. Here, we present a sensitive method for the targeted sequenc...

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 contribut...

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...

Revisiting the origins of modern horses The domestication of horses was very important in the history of humankind. However, the ancestry of modern horses and the location and timing of their emergence remain unclear. Gaunitz et al. generated 42 ancient-horse genomes. Their source samples included the Botai archaeological site in Central Asia, cons...

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 less than 10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near...

Microsatellite genotype data and mitochondrial DNA haoplotypes.

In threatened wildlife populations, it is important to determine whether observed low genetic diversity may be due to recent anthropogenic pressure or the consequence of historic events. Historical size of the Irrawaddy dolphin (Orcaella brevirostris) population inhabiting the Mekong River is unknown and there is significant concern for long-term s...

Permission to publish Fig 1 under a CC BY license. (XLSX)

China has recently become the leader country for sturgeon aquaculture and caviar production, deeply changing the traditional geography of this market in few years. As a consequence, some species originating from the Far East Asia increased their economic relevance, joining the ones traditionally harvested for caviar. In this context, the possibilit...

Wild horses unexpectedly survived terminal Pleistocene megafaunal extinctions until eventual European extirpation in the twentieth century. This survival is tied to either their occurrence in cryptic open habitats or their adaptation to forests. Our niche modelling inferred an increasing presence of horses in post-glacial forests, and our analysis...

With an estimated population size of less than 10,000 individuals worldwide, the brown hyena ( Parahyaena brunnea ) has been listed as ‘near threatened’ by the IUCN. Despite this rank, studies involving DNA analyses of the brown hyena are limited. Little consideration has been focussed towards population structure within the brown hyena, which coul...

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 sele...

Ancient genomics of horse domestication The domestication of the horse was a seminal event in human cultural evolution. Librado et al. obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestica...

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 s...

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 endange...

Horses have been valued for their diversity of coat colour since prehistoric times; this is especially the case since their domestication in the Caspian steppe in ~3,500 BC. Although we can assume that human preferences were not constant, we have only anecdotal information about how domestic horses were influenced by humans. Our results from genoty...

Sturgeons are well known for the delicacy of their eggs, the caviar, one of the most valuable products on the food market. The high price of caviar led in the past to a severe overharvest of wild sturgeon species and to an increase in trade of counterfeit products sold with impunity in spite of the strict trade limitations. A priority in the effort...

Horseback riding is the most fundamental use of domestic horses and has had a huge influence on the development of human societies for millennia. Over time, riding techniques and the style of riding improved. Therefore, horses with the ability to perform comfortable gaits (e.g. ambling or pacing), so-called 'gaited' horses, have been highly valued...

High throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best-suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture-enrichment methods represent cost-effective alternatives that increase t...

European mouflons (Ovis orientalis musimon) are Mediterranean sheep that were introduced worldwide as park and game animals during the last few centuries. Today, European mouflons are endangered in their natural refuge areas. Mouflons are able to interbreed with domestic breeds to form fertile hybrids of an intermediate phenotype. As some introduce...

Considering the hidden mode of inheritance of some coat-color-associated alleles, we investigated the presence/absence of coat-color-associated alleles in 1093 domestic horses of 55 breeds and 20 specimens of Przewalski’s horse. For coat-color genotyping, allele specific PCR, pyrosequencing and Li-Cor analyses were conducted on 12 coat-color-associ...

The arid climate of many regions within Central Asia often leads to excellent archaeological preservation, especially in sealed funerary contexts, allowing for ancient DNA analyses. While geneticists have looked at human remains, clothes, tools, and other burial objects are often neglected. In this paper, we present the results of an ancient DNA st...

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...

The Red Mountain Cattle (RHV) is an important native ancient breed from the lower mountain ranges of Central Europe, which was originally raised for milk and meat production and as draught animal. In the 1980s, the RHV was close to extinction and only the sperm of a single purebreed bull and a few cows were available for breed formation. In this st...

Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter...

A market survey was performed on caviar from Romania and Bulgaria, two of the last range states of critically endangered sturgeons threatened by poaching and illegal trade. Twenty-seven samples were collected between April 2011 and February 2012, including two samples of Bulgarian farm caviar bought in an Austrian fish shop. Mitochondrial sequences...

Divergent selection among environments affects species distributions and can lead to speciation. In this article, we investigated the transcriptomes of two ecotypes of scaleless carp (Gymnocypris przewalskii przewalskii and G. p. ganzihonensis) from the Tibetan Plateau. We used a transcriptome sequencing approach to screen approximately 250,000 exp...