PubMed Health⌕ Search

Biomedical subjects

Michael Hofreiter

Publications and source records attributed to Michael Hofreiter.

10 recordsLinked to original sources
PubMed2026

Ancient DNA reveals early use of melons in China's Song dynasty.

Melon (Cucumis melo L.) domestication is thought to have occurred independently once in Northeast Africa and twice in India, but archaeobotanical seed remains point to a possible additional domestication event in China. Because Cucumis seeds are difficult to diagnose morphologically, genomic data from archaeological material are needed to evaluate these scenarios and reconstruct ancient melon traits. We sequenced two Song Dynasty (960-1279 CE) melon seeds from Shuomen Gugang (China), recovering 5.5× and 2.1× nuclear genome coverage. Nuclear and chloroplast analyses place both seeds within cultivated C. melo from China, within the "agrestis" East Asian gene pool. To assess whether these seeds carried traits associated with sweet dessert melons, we examined loci underlying fruit phenotypes. Neither seed carried alleles for orange flesh; one harbored an allele linked to yellow/orange peel, the other possessed alleles associated with green flesh and reduced acidity. Since wild melons are monoecious, the presence of the derived andromonoecy allele in one seed, associated with rounder fruit shape, suggests early selection on fruit morphology. Together, these findings indicate that Song Dynasty melons were likely consumed as fresh or culinary fruits rather than sweet dessert melons. Their flesh coloration resonates with Song-period aesthetic sensibilities, exemplified by jade-green celadon ceramics frequently crafted in melon-shaped forms. By anchoring East Asian archaeobotanical remains within modern melon genomic variation, this study provides a temporal framework for melon cultivation in China and shows how ancient genomics can illuminate past crop use.

China↗
PubMed2026

Paleogenomic sex inference of mammoth remains sheds light on the anthropogenic nature of bone accumulations.

Whether large accumulations of woolly mammoth (Mammuthus primigenius) bones reflect natural mortality or deliberate human resource exploitation has long been debated, with major implications for understanding Late Pleistocene human-megafaunal interactions.1,2,3,4,5 Here, we use ancient DNA to investigate site-formation hypotheses by comparing genetic sex ratios from mammoth remains recovered in putative anthropogenic bone accumulations and from geographically dispersed, non-anthropogenic contexts. We studied genome-wide data from 521 woolly mammoths-including 100 mammoths from bone accumulation sites and 421 mammoths from natural depositional settings across Eurasia and North America-of which 448 are newly generated. Genetic sex determination reveals a striking contrast between contexts: mammoths from dispersed sites show a male bias (∼66.5%), which is consistent with the heightened vulnerability of solitary males to hazards such as natural traps, where bones are more likely to be preserved, whereas mammoths from anthropogenic bone accumulations are predominantly female (∼70%). This female bias is pervasive across multiple sites, indicating an anthropogenic origin for these accumulations as a result of Upper Paleolithic hunters preferentially exploiting female mammoths, possibly derived from herd contexts. Together, these results provide population-scale genetic evidence that highlights the central role of mammoths in the subsistence and material economies of some Paleolithic communities.

Animals↗
PubMed2025

A Million Years of Mammoth Mitogenome Evolution.

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Animals↗
PubMed2004

Lack of phylogeography in European mammals before the last glaciation.

In many extant animal and plant species in Europe and North America a correlation exists between the geographical location of individuals and the genetic relatedness of the mitochondrial (mt) DNA sequences that they carry. Here, we analyze mtDNA sequences from cave bears, brown bears, cave hyenas, and Neandertals in Europe before the last glacial maximum and fail to detect any phylogeographic patterns similar to those observed in extant species. We suggest that at the beginning of the last glacial maximum, little phylogeographic patterns existed in European mammals over most of their geographical ranges and that current phylogeographic patterns are transient relics of the last glaciation. Cycles of retreat of species in refugia during glacial periods followed by incomplete dispersal from one refugium into other refugia during interglacial periods is likely to be responsible for the deep genetic divergences between phylogeographic clusters of mtDNA seen today.

Animals↗
PubMed2004

No evidence of Neandertal mtDNA contribution to early modern humans.

The retrieval of mitochondrial DNA (mtDNA) sequences from four Neandertal fossils from Germany, Russia, and Croatia has demonstrated that these individuals carried closely related mtDNAs that are not found among current humans. However, these results do not definitively resolve the question of a possible Neandertal contribution to the gene pool of modern humans since such a contribution might have been erased by genetic drift or by the continuous influx of modern human DNA into the Neandertal gene pool. A further concern is that if some Neandertals carried mtDNA sequences similar to contemporaneous humans, such sequences may be erroneously regarded as modern contaminations when retrieved from fossils. Here we address these issues by the analysis of 24 Neandertal and 40 early modern human remains. The biomolecular preservation of four Neandertals and of five early modern humans was good enough to suggest the preservation of DNA. All four Neandertals yielded mtDNA sequences similar to those previously determined from Neandertal individuals, whereas none of the five early modern humans contained such mtDNA sequences. In combination with current mtDNA data, this excludes any large genetic contribution by Neandertals to early modern humans, but does not rule out the possibility of a smaller contribution.

Animals↗
PubMed2004

Evidence for reproductive isolation between cave bear populations.

The European cave bear (Ursus spelaeus), which became extinct around 15,000 years ago, had several morphologically different forms. Most conspicuous of these were small Alpine cave bears found at elevations of 1,600 to 2,800 m. Whereas some paleontologists have considered these bears a distinct form, or even a distinct species, others have disputed this. By a combination of morphological and genetic methods, we have analyzed a population of small cave bears from Ramesch Cave (2,000 m altitude) and one of larger cave bears from Gamssulzen Cave (1,300 m), situated approximately 10 km apart in the Austrian Alps (Figure 1A). We find no evidence of mitochondrial gene flow between these caves during the 15,000 years when they were both occupied by cave bears, although mitochondrial DNA sequences identical to those from Gamssulzen Cave could be recovered from a site located about 200 km to the south in Croatia. We also find no evidence that the morphology of the bears in the two caves changed to become more similar over time. We suggest that the two cave bear forms may have represented two reproductively isolated subspecies or species.

Animals↗
PubMed2004

Nondestructive DNA extraction method for mitochondrial DNA analyses of museum specimens.

Museum specimens have provided the material for a large proportion of ancient DNA studies conducted during the last 20 years. However, a major drawback of the genetic analyses is that the specimens investigated are usually damaged, as parts of skin, bone, or a tooth have to be removed for DNA extraction. To get around these limitations, we have developed a nondestructive extraction method for bone, tooth, and skin samples. We found that it is possible to amplify mitochondrial DNA (mtDNA) sequences up to at least 414 bp long from samples up to 164 years old. Using this method, almost 90% (35 of 40) of the investigated samples yielded amplifiable mtDNA. Moreover, we found that repeated extractions of the same samples allowed amplifications of the expected length for all samples at least three times and for some samples up to at least five times. Thus this method opens up the possibility to repeatedly use museum collections for mtDNA analyses without damaging the specimens and thus without reducing the value of irreplaceable collections for morphological analyses.

Animals↗
PubMed2003

Mitochondrial DNA sequence from an enigmatic gorilla population (Gorilla gorilla uellensis).

Although today gorillas are found in only two widely separate, discontinuous western and eastern African populations, rumors of the existence of an additional gorilla population in central Africa have inspired recent unsuccessful field expeditions in search of the "mystery ape" termed Gorilla gorilla uellensis. Such a gorilla population would have considerable conservation and scientific interest, and would presumably have descended from a population of gorillas that was thought to exist until the end of the 19th century on the Uele River in the current-day Democratic Republic of Congo. However, the sole evidence for the existence of these gorillas is three skulls and one mandible brought to the Royal Museum for Central Africa (Tervuren, Belgium) in 1898. We determined a mitochondrial DNA sequence from one of these specimens and compared it to sequences from other gorillas. Contrary to expectations, the sequence obtained did not exhibit the phylogenetic distinctiveness typical of a representative of a peripheral isolated population. Rather, the results suggest a scenario in which the museum specimens did not originally derive from the northern Congo, but were brought from the area of current distribution of western gorillas to that location; the subsequent discovery and collection of the specimens there gave rise to the false inference of a local gorilla population.

Africa, Central↗
PubMed2002

Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears.

Cave bears (Ursus spelaeus) existed in Europe and western Asia until the end of the last glaciation some 10,000 years ago. To investigate the genetic diversity, population history, and relationship among different cave bear populations, we have determined mitochondrial DNA sequences from 12 cave bears that range in age from about 26,500 to at least 49,000 years and originate from nine caves. The samples include one individual from the type specimen population, as well as two small-sized high-Alpine bears. The results show that about 49,000 years ago, the mtDNA diversity among cave bears was about 1.8-fold lower than the current species-wide diversity of brown bears (Ursus arctos). However, the current brown bear mtDNA gene pool consists of three clades, and cave bear mtDNA diversity is similar to the diversity observed within each of these clades. The results also show that geographically separated populations of the high-Alpine cave bear form were polyphyletic with respect to their mtDNA. This suggests that small size may have been an ancestral trait in cave bears and that large size evolved at least twice independently.

Animals↗