Michael Hofreiter

Michael Hofreiter
Universität Potsdam · Institute of Biochemistry and Biology

PhD

About

718
Publications
334,386
Reads
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30,399
Citations
Introduction
I am an evolutionary biologist using genomic approaches, especially on extinct species. I do a lot of collaborative work, which is shown by the wide range of topics (currently beetles, wolves, extinct dwarf elephants, ancient Egyptian date palms and museum specimens) found in my featured research.
Additional affiliations
April 2009 - March 2014
University of York
Position
  • Professor (Full)
May 1999 - March 2010
Max Planck Institute for Evolutionary Anthropology
Position
  • Group Leader
October 2013 - present
Universität Potsdam
Position
  • Professor (Full)

Publications

Publications (718)
Article
Full-text available
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied anci...
Article
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The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from...
Article
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The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be i) the result of long‐term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or ii) due to rapid population decline caused by human persecution...
Article
Evolution on islands, together with the often extreme phenotypic changes associated with it, has attracted much interest from evolutionary biologists. However, measuring the rate of change of phenotypic traits of extinct animals can be challenging, in part due to the incompleteness of the fossil record. Here, we use combined molecular and fossil ev...
Article
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The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancie...
Article
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Invading species along with increased anthropogenization may lead to hybridization events between wild species and closely related domesticates. As a consequence, wild species may carry introgressed alleles from domestic species, which is generally assumed to yield adverse effects in wild populations. The opposite evolutionary consequence, adaptive...
Article
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Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam’s famous Ha Long Bay and with l...
Preprint
Full-text available
Studying the behavioural ecology of long-extinct species is challenging due to the difficulty in measuring the behavioural phenotype and correlating this with genetic and environmental factors. However, a multidisciplinary approach integrating isotope analysis of diet and ancient DNA analysis of genetic relationships offers a potential framework to...
Article
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Sengis (Macroscelidea) are members of the Afroinsectivora, a group of mammals belonging to the supercohort Afrotheria. Sengis’ low population densities and their distribution, which includes politically unstable regions with ongoing armed conflicts, hinder contemporary sampling of comprehensive datasets. We overcome this obstacle for the species Pe...
Article
Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of e...
Article
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Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 71 species representing the main phylogenetic lineages, life-h...
Article
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Evidence for divergent selection and adaptive variation across the landscape can provide insight into a species' ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect the footprints of climate‐mediated selection in natural populations. Here, we analysed ddRAD sequencing data (21,892...
Preprint
Learning plays an important role in the ecology and evolution of species. Although learning has been extensively studied in extant populations, studying learning in long extinct species represents a much greater challenge because individuals and thei behaviour cannot be directly observed, and their individual relatedness is more challenging to stud...
Article
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Background Modern integrative taxonomy-based annelid species descriptions are detailed combining morphological data and, since the last decades, also molecular information. Historic species descriptions are often comparatively brief lacking such detail. Adoptions of species names from western literature in the past led to the assumption of cosmopol...
Article
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Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species’ gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data...
Preprint
Full-text available
Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 66 species representing the main phylogenetic lineages, life-h...
Article
Full-text available
The gray wolf (Canis lupus) population on the Iberian Peninsula was the largest in western and central Europe during most of the 20th century, with its size apparently never under a few hundred individuals. After partial legal protection in the 1970s in Spain, the northwest Iberian population increased to about 300-350 packs and then stabilized. In...
Article
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Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degrad...
Poster
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Fossil mammals and birds from caves are the only biological tools for the reconstruction of the Alpine climate before the last great glaciation, since all other archives such as lake sediments or bogs were destroyed by the glacial advance about 20,000 years ago. There are some species that are adapted to a certain climate and tolerate only very sma...
Article
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We undertook a phylogenetic analysis of genetic and anatomical data focusing on golden moles (Chrysochloridae) and tenrecs (Tenrecidae). Our results support the now well-resolved topology for extant tenrecids, in addition to the paraphyly of ‘Chrysochlorinae’ and the genera Chrysochloris and Chlorotalpa as traditionally used. Carpitalpa arendsi is...
Conference Paper
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Sengis or elephant shrews (Macroscelidea) are small African mammals, with most species inhabiting arid regions. The four-toed sengi (Petrodromus tetradactylus), however, roams diverse habitats from coastal and Afromontane forest, to Zambezian woodlands and savannahs, to Congolian lowland forest. It has one of the largest geographic ranges of all se...
Article
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The blue antelope or bluebuck ( Hippotragus leucophaeus ) is an extinct species of antelope that lived in South Africa until ca. 1799–1800. Disappearing only 34 years after it was described, it was the first large African mammal species to have become extinct in recent times. Therefore, current scientific knowledge of the blue antelope is limited t...
Article
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Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus...
Preprint
Evidence for spatially varying selection and adaptive variation can provide insight into a species’ ability to adapt to different environments. However, despite recent advances in genomics, it remains difficult to detect footprints of spatially varying selection in natural populations. Here we analysed ddRAD sequencing data (21,892 SNPs) in conjunc...
Article
Full-text available
The fossil fauna of the Schottloch was excavated and described 140 years ago. A modern analysis of the extensive material has now been carried out for the first time. The taxonomic position of the cave bear remains, the degree of mountain adaptation compared to other high alpine cave faunas and the geological period during which the cave bears used...
Article
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Sengis (order Macroscelidea) are small mammals endemic to Africa. The taxonomy and phylogeny of sengis has been difficult to resolve due to a lack of clear morphological apomorphies. Molecular phylogenies have already significantly revised sengi systematics, but until now no molecular phylogeny has included all 20 extant species. In addition, the a...
Article
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A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collectio...
Article
Full-text available
Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers...
Article
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Malagasy frogs of the subgenus Brygoomantis in the mantellid frog genus Mantidactylus currently comprise 14 described species of mostly brown, riparian frogs. Data from DNA barcoding suggested that the diversity of this subgenus is dramatically underestimated by current taxonomy. We here provide a comprehensive revision of this subgenus. We use hyb...
Article
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The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the pos...
Article
Full-text available
Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial...
Article
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Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely al...
Conference Paper
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Afrotheria are one of the four major clades of placental mammals that have been defined based on molecular data. It unites morphologically diverse lineages with a common ancient origin in Africa: elephants, sea cows, hyraxes, aardvarks, sengis, golden moles and tenrecs. Under the current systematic consensus, afrotherians are divided into an ungula...
Article
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The fossils of the Grotta dell’Orso, recovered by Ludwig Moser (in the years 1876 to 1914), are stored in the collections of the Natural History Museum in Vienna. The cave bear remains dominating the fossil fauna were subjects to a revision. The morphological data of the dentition and the metapodials as well as the result of a DNA analysis are cont...
Article
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African otter shrews (Potamogalidae) are Afrotherian mammals adapted to a semi-aquatic lifestyle. Given their rareness, genetic data on otter shrews are limited. By applying laboratory methods tuned for the recovery of archival DNA and an iterative mapping approach, we reconstructed whole mitochondrial genomes of the Giant (Potamogale velox) and Ru...
Article
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Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-yr-old seeds from Libya...
Preprint
Full-text available
The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the pos...
Article
Full-text available
The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day do...
Article
Full-text available
Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites. For taxonomic studies, comparative morphological analysis of type specimens housed in natural history c...
Article
Full-text available
A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collectio...
Article
Full-text available
(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula...
Article
The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of...
Article
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The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the...
Article
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Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental cond...
Preprint
Full-text available
The blue antelope ( Hippotragus leucophaeus ) is the only large African mammal to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan ( H. equinus ) or sable ( H. niger ) antelopes, further reducing the possi...
Conference Paper
Macroscelidea or sengis are small mammals endemic to Africa and consists of 20 extant species only. Together with aardvarks, hyraxes, elephants, sea cows and afrosoricidans, they form the Afrotheria, the major clade of placental mammals with ancient African origin. Due to mostly cryptic morphological traits, biologist had a hard time disentangling...
Article
Birds-of-paradise represent a textbook example for geographical speciation and sexual selection. Perhaps the most iconic genus is Paradisaea, which is restricted to New Guinea and a few surrounding islands. Although several species concepts have been applied in the past to disentangle the different entities within this genus, no attempt has been ma...
Article
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Steller’s sea cow, an extinct sirenian and one of the largest Quaternary mammals, was described by Georg Steller in 1741 and eradicated by humans within 27 years. Here, we complement Steller’s descriptions with paleogenomic data from 12 individuals. We identified convergent evolution between Steller’s sea cow and cetaceans but not extant sirenians,...
Article
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Mantellid frogs of the Madagascar-endemic Gephyromantis plicifer complex consist of three nominal species (G. luteus, G. plicifer and G. sculpturatus) as well as several genetically divergent lineages (candidate species), but uncertainties surround the identity of the name-bearing types of all three established nomina. We applied laboratory techniq...
Article
Full-text available
The extinct ‘Gomphotheriidae’ is the only proboscidean family that colonised South America. The phylogenetic position of the endemic taxa has been through several revisions using morphological comparisons. Morphological studies are enhanced by palaeogenetic analyses, a powerful tool to resolve phylogenetic relationships; however, aDNA preservation...
Article
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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...
Article
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Both molecular data and archaeological evidence strongly support an African origin for the domestic donkey. Recent genetic studies further suggest that there were two distinct maternal lineages involved in its initial domestication. However, the exact introduction time and the dispersal process of domestic donkeys into ancient China are still unres...
Article
Full-text available
Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitoch...
Article
Full-text available
Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental cond...
Article
Full-text available
After initial detection of target archival DNA of a 116-year-old syntype specimen of the smooth lantern shark, Etmopterus pusillus , in a single-stranded DNA library, we shotgun-sequenced additional 9 million reads from this same DNA library. Sequencing reads were used for extracting mitochondrial sequence information for analyses of mitochondrial...
Conference Paper
Sengis are small African mammals with an odd character combination and a long independent evolution. They have traditionally been divided into four morphologically well-defined genera: Macroscelides, Petrodromus, and Elephantulus (Macroscelidinae, soft-furred sengis) as well as Rhynchocyon (Rhynchocyoninae, giant sengis). Molecular analyses, howeve...
Article
Full-text available
Since the 19th century, the addax (Addax nasomaculatus) has lost approximately 99% of its former range. Along with its close relatives, the blue antelope (Hippotragus leucophaeus) and the scimitar-horned oryx (Oryx dammah), the addax may be the third large African mammal species to go extinct in the wild in recent times. Despite this, the evolution...
Article
Full-text available
Accurate information on name-bearing types, including corresponding type localities, is essential for proper taxonomy. However, such geographic information is often missing or unreliable. The localities of type specimens collected 100–200 years ago can be difficult to trace due to changes in local names or simple inaccuracies. Such a case can be fo...
Article
Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal mate...