Michael Hofreiter

Michael Hofreiter
Universität Potsdam · Institute of Biochemistry and Biology

PhD

About

682
Publications
239,799
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24,332
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
October 2013 - present
Universität Potsdam
Position
  • Professor (Full)
April 2009 - March 2014
The University of York
Position
  • Professor (Full)
May 1999 - March 2010
Max Planck Institute for Evolutionary Anthropology
Position
  • Group Leader

Publications

Publications (682)
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
Full-text available
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
Full-text available
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
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
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Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species. Many species are described from few individuals, and recollection 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 co...
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
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(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
IN PRESS: 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 h...
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
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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...
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
Objective Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Made...
Article
Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data fr...
Article
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Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale¹, the oldest genomic...
Article
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During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four species; the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous studies investigated the evolutionary histories of the spotted and brown hyenas, but little is known about the remaini...
Article
Background The forelimb-specific gene tbx5 is highly conserved and essential for the development of forelimbs in zebrafish, mice, and humans. Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures. Results To determine the sequence of...
Article
The Torrener Bärenhöhle (Cave of Torren) is an alpine bear cave in the limestone Alps near Salzburg (Austria). The entrance of this cave is located in the riverbed of a periodically flowing stream that floods the caverns during snowmelt or after heavy rainfall. Due to these flooding events, the fossiliferous layers were repeatedly destroyed and the...
Article
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.¹ • Hofreiter M. • Paijmans J.L.A. • Goodchild H. • Speller C.F. • Barlow A. • Fortes G.G. • Thomas J.A. • Ludwig A. • Collins M.J. The future of ancient DNA: Technical adva...
Article
Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eur...
Article
Full-text available
Native to southern Africa, the blue antelope (Hippotragus leucophaeus) is the only large African mammal species known to have become extinct in historical times. However, it was poorly documented prior to its extinction ~ 1800 AD, and many of the small number of museum specimens attributed to it are taxonomically contentious. This places limitation...
Article
Full-text available
The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of t...
Article
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,...
Article
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A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequen...
Article
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Background Numerous megafauna species from northern latitudes went extinct during the Pleistocene/Holocene transition as a result of climate-induced habitat changes. However, several ungulate species managed to successfully track their habitats during this period to eventually flourish and recolonise the holarctic regions. So far, the genomic impac...
Preprint
Full-text available
The date palm ( Phoenix dactylifera ) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild re...
Article
There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E...
Article
Full-text available
Trachypithecus, which currently contains 20 species divided into four groups, is the most speciose and geographically dispersed genus among Asian colobines. Despite several morphological and molecular studies, however, its evolutionary history and phylogeography remain poorly understood. Phayre's langur (Trachypithecus phayrei) is one of the most w...
Article
Full-text available
Taxonomic progress is often hindered by intrinsic factors, such as morphologically cryptic species that require a broad suite of methods to distinguish, and extrinsic factors, such as uncertainties in the allocation of scientific names to species. These uncertainties can be due to a wide variety of factors, including old and poorly preserved type s...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for...
Preprint
Full-text available
During the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four extant genera, each of which contains only a single species. These species include the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous genome studies have analysed the evolutionar...
Article
Full-text available
Objective: Plant carnivory is distributed across the tree of life and has evolved at least six times independently, but sequenced and annotated nuclear genomes of carnivorous plants are currently lacking. We have sequenced and structurally annotated the nuclear genome of the carnivorous Roridula gorgonias and that of a non-carnivorous relative, Ma...
Article
Full-text available
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion ind...
Article
Full-text available
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a via...
Chapter
Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtain...
Article
The two species of the Bokermannohyla claresignata species group (Anura: Hylidae) have not been collected for the last four decades. It is the only species group of the hyline tribe Cophomantini that has not yet been analysed genetically. Its phylogenetic position is thus uncertain, and it has a combination of adult and larval character states that...
Article
The two species of the Bokermannohyla claresignata species group (Anura: Hylidae) have not been collected for the last four decades. It is the only species group of the hyline tribe Cophomantini that has not yet been analysed genetically. Its phylogenetic position is thus uncertain, and it has a combination of adult and larval character states that...