Thomas Lehmann

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Verified

Thomas verified their affiliation via an institutional email.

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• PhD
• Head of Section Palaeomammalogy at Senckenberg Society for Nature Research

Cutting-edge analytical instrumentation is increasingly being developed and applied to the analysis of fossils. X-ray fluorescence (XRF) imaging spectroscopy is a powerful tool to resolve the elemental chemistry of fossil specimens. Most of the XRF application to study fossils is carried out at dedicated synchrotron radiation XRF beamlines. Recent...

The Messel Pit is a Konservat-Lagerstätte in Germany, representing the deposits of a latest early to earliest middle Eocene maar lake, and one of the first palaeontological sites to be included on the list of UNESCO World Heritage Sites. One aspect of Messel that makes it so extraordinary is that its sediments are rich in different fossilised organ...

Deep-time (=pre-Quaternary) maar lakes and certain other, hydrologically deep volcanogenic lakes, are often excellent Konservat-Lagerstätten representing unique windows into past biota and ecosystems. Many deposits from such lakes contain animal and plant remains in extraordinary preservation, often with soft tissues or fine morphological and anato...

Vocal production learning is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical and neurophysiological data from the Egyptian fruit-bat with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more s...

Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome...

Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low seque...

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a d...

Human accelerated regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep learning with chromatin capture experiments in human an...

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores...

The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral...

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion...

Conserved genomic sequences disrupted in humans may underlie uniquely human phenotypic traits. We identified and characterized 10,032 human-specific conserved deletions (hCONDELs). These short (average 2.56 base pairs) deletions are enriched for human brain functions across genetic, epigenomic, and transcriptomic datasets. Using massively parallel...

We reconstruct the phenotype of Balto, the heroic sled dog renowned for transporting diphtheria antitoxin to Nome, Alaska, in 1925, using evolutionary constraint estimates from the Zoonomia alignment of 240 mammals and 682 genomes from dogs and wolves of the 21st century. Balto shares just part of his diverse ancestry with the eponymous Siberian hu...

Species persistence can be influenced by the amount, type, and distribution of diversity across the genome, suggesting a potential relationship between historical demography and resilience. In this study, we surveyed genetic variation across single genomes of 240 mammals that compose the Zoonomia alignment to evaluate how historical effective popul...

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to ne...

Understanding the regulatory landscape of the human genome is a long-standing objective of modern biology. Using the reference-free alignment across 241 mammalian genomes produced by the Zoonomia Consortium, we charted evolutionary trajectories for 0.92 million human candidate cis-regulatory elements (cCREs) and 15.6 million human transcription fac...

The assembly of Africa's iconic C4 grassland ecosystems is central to evolutionary interpretations of many mammal lineages, including hominins. C4 grasses are thought to have become ecologically dominant in Africa only after 10 million years ago (Ma). However, paleobotanical records older than 10 Ma are sparse, limiting assessment of the timing and...

We describe two new osteolaemine crocodylids from the Early and early Middle Miocene of Kenya: Kinyang mabokoensis tax. nov. (Maboko, 15 Ma) and Kinyang tchernovi tax. nov. (Karungu and Loperot, 18 Ma). Additional material referable to Kinyang is known from Chianda and Moruorot. The skull was broad and dorsoventrally deep, and the genus can be diag...

A new and uniquely structured matrix of mammalian phenotypes, MaTrics ( Ma mmalian Tr aits for Comparative Genom ics ) in a digital form is presented. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics. MaTrics was developed within a project aimed to...

The inactivation of ancestral protein‐coding genes (gene loss) can be associated with phenotypic modifications. Within placental mammals, repeated losses of PNLIPRP1 (gene inhibiting fat digestion) occurred preferentially in strictly herbivorous species, while repeated NR1I3 losses (gene involved in detoxification) occurred preferentially in strict...

In mammals, the caudal vertebrae are certainly among the least studied elements of their skeleton. However, the tail plays an important role in locomotion (e.g., balance, prehensility) and behavior (e.g., signaling). Previous studies largely focused on prehensile tails in Primates and Carnivora, in which certain osteological features were selected...

This manual has been developed in the framework of the project ‘Identifying genomic loci underlying mammalian phenotypic variability using Forward Genomics’ which was funded by the Leibniz Gemeinschaft (SAW-2016-SGN-2). The project brought together an interdisciplinary scientific network covering the fields of morphology (Work Modules M1/M2, ‘Pheno...

We describe three new hyaenodonts from the late Ypresian locality of Prémontré (Aisne, France; close to MP 10 reference level). The new species – Lesmesodon gunnelli nov. sp., Cynohyaenodon smithae nov. sp., and Eurotherium mapplethorpei nov. sp. – represent the oldest occurrences of these three European genera. Lesmesodon gunnelli is also reported...

A new and uniquely structured matrix of mammalian phenotypes, MaTrics ( Ma mmalian Tr aits for Comparative Genom ics ) is presented in a digital form. By focussing on mammalian species for which genome assemblies are available, MaTrics provides an interface between mammalogy and comparative genomics. MaTrics was developed as part of a project to li...

The assembly of Africa’s iconic C4 grassland and savanna ecosystems is central to evolutionary interpretations of many mammals, including hominins. Based largely on pollen, biomarkers, and isotopic data, C4 grasses are thought to have become ecologically dominant in Africa only after 10 Ma. However, paleobotanical records older than 10 Ma are spars...

The aardvark is the last living Tubulidentata, an order of afrotherian mammals. Afrotheria is supported strongly by molecular analyses, yet sparingly by morphological characters. Moreover, the biology of the aardvark remains incompletely known. The inner ear, and its ontogeny in particular, has not been studied in details yet, though it bears key e...

Obituary of Gerhard Storch

Palaeontological deposits on Rusinga Island, Lake Victoria, Kenya, provide a rich record of floral and faunal evolution in the early Neogene of East Africa. Yet, despite a wealth of available fossil material, previous palaeoenvironmental reconstructions from Rusinga have resulted in widely divergent results, ranging from closed forest to open woodl...

We here present the first detailed study of the specimen KNM-RU 18340 from Rusinga Island (Kenya), the only known complete early Miocene chameleon skull, using micro-CT. This specimen represents one of the oldest chameleon fossils ever recovered. For the first time, the skull bone internal surfaces, their sutures, and elements contained inside the...

Obituary of Gerhard Storch (II) DOI: 10.37520/fi.2020.001

Paleontological deposits on Rusinga Island, Lake Victoria, Kenya, provide a rich record of floral and faunal evolution in the early Neogene of East Africa. Yet, despite a wealth of available fossil material, previous paleoenvironmental reconstructions from Rusinga have resulted in widely divergent results, ranging from closed forest to open woodlan...

The Paleocene is an important epoch in the development of the flora and fauna in the Cenozoic,but relatively few terrestrial fossil sites of this age are known in Europe. For many groups, like plants and mammals, the catastrophic events at the Cretaceous–Paleogene (K/Pg, formerly K/T) boundary had ushered in significant changes, and our understandi...

Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phyloge...

RXFP2 C-terminal length variations are common in mammals. Visualization of the last coding exon of RXFP2 and the encoded final transmembrane domain, which is highly conserved among species. The sequence alignment shows that the length of the cytoplasmic domain varies between species, with several species having shorter or longer C-termini than huma...

Sequence divergence patterns in the promoter region of RXFP2 and INSL3. We analyzed sequence divergence in the promoter region of both genes. The y-axis shows the percent sequence identity between the reconstructed sequence of the placental mammal ancestor and the sequence of every extant mammal on a scale from 0 to 100. Testicond afrotherian mamma...

Relaxed or intensified selection on RXFP2 in placental mammals. We used RELAX [52] to test individually for each mammal if RXFP2 evolves under relaxed or intensified selection. Red: species for which relaxed selection at a raw P value < 0.05 was found. Blue: species for which an intensification of selection at a raw P value < 0.05 was detected. Bol...

Uncertainty about the position of the aardvark within Afrotheria and the phylogeny of the hyrax-elephant-manatee clade. (A) Topology according to [32]. This placement of the aardvark in a clade together with tenrec, golden mole, and elephant shrew is supported by [30] and [33]; however, these studies obtained a different phylogeny for the hyrax-ele...

CESAR reveals an intact exon alignment for the sixth exon of the RXFP2 gene in the blind mole rat genome. (A) The genome alignment between human and the blind mole rat shows a 200-bp insertion in the middle of RXFP2 coding exon 6. This “mutation” would inactivate the gene by disrupting the reading frame. (B) In contrast to the genome alignment, CES...

List of primers and annealing temperatures used for PCR analysis of inactivating mutations in RFPX2. RXFP2, relaxin/insulin-like family peptide receptor. (DOCX)

Ultra-sensitive genome alignments exclude the possibility of undetected functional copies of RXFP2 or INSL3. We computed genome alignments between human and the seven afrotherians using alignment parameters that are much more sensitive than the standard parameters typically used for genome alignment (Materials and methods). These alignments reveal...

Assembly errors in RXFP2 and INSL3 exons in Chinese hamster and panda. (A) Exon 15 of RXFP2 exhibits a 1-bp insertion in the Chinese hamster genome (obtained by sequencing the ovary cell line CHO-K1). However, there is not a single sequencing read from the SRA that confirms this insertion, showing that it is an assembly error. (B) Exon 1 of INSL3 e...

RXFP2 of human, chimpanzee, bonobo, and gorilla exhibit a 17-amino acid N-terminal elongation. UCSC browser screenshot of the human genome showing the beginning of the RXFP2 coding region and aligning sequence of placental mammals (dot represents a base or amino acid that is identical to human). The start codon that is annotated for the human RXFP2...

Dating the loss of RXFP2. The table shows the Ka/Ks value of the terminal branch leading to the four Afrotheria that lost RXFP2 (referred to as “K”) and the Ka/Ks value for all other mammals (referred to as “Ks”) that have an intact RXFP2 gene. The lower and upper bound of the divergence time between these species and their closest sister species (...

Lineage divergence time estimates from individual studies listed in TimeTree [57]. We added the estimates from [32]. (XLSX)

Illustration of the process of testicular descent and the position of testes in different mammals. (A) Illustration of the developmental process that results in testicular descent. The gubernaculum is shown in green. (B) Simplified representation of the position of the testes (orange) and kidneys (blue) illustrating the three conditions discussed h...

Three conflicting hypotheses for the basal split of placental mammals. All three phylogenies receive substantial support from morphological and molecular characters [23, 24, 26]. Kleisner and colleagues [3] concluded that testicondy is the ancestral state for placental mammals by considering both Exafroplacentalia (A) and Atlantogenata (C). The phy...

The remnants of RXFP2 and INSL3 in Afrotheria are found in the context of conserved gene order. Gene order is conserved in the RXFP2 (A) and INSL3 (B) genomic locus across Afrotheria, Boreoeutheria, Xenarthra, and marsupials. Filled boxes represent genes. An open box indicates the remnants of RXFP2 and INSL3 in Afrotheria that lost these genes. ZAR...

PCR and Sanger sequencing experiments confirm inactivating mutations in RXFP2 in the lesser hedgehog tenrec and show that RXFP2 is also lost in the greater hedgehog tenrec and the dugong. (A) The frameshifting deletion in exon 4 in the lesser hedgehog tenrec genome is confirmed in a different individual of the same species. (B) The frameshifting in...

Assembly gaps should not be mistaken for exon deletions. UCSC genome browser screenshot shows the human INSL3 locus and alignment chains to two gorilla genome assemblies (blocks in the alignment chain indicate aligning regions, double lines indicate unaligning sequence). While exon 2 does not align in the gorGor3 assembly, presumably indicating the...

Species and their genome assemblies for which we analyzed the RXFP2 and INSL3 coding sequence. INSL3, insulin-like 3; RXFP2, relaxin/insulin-like family peptide receptor. (XLSX)

The Konservat-Lagerstatte Menat (Puy-de-Dome, France) is an outstanding archive of a Paleocene ecosystem, which was deposited in a former maar lake. Excavations during the last century have yielded an extensive flora and fauna record, therefore an overview of the current state of paleontological investigations is given in this paper. Additionally,...

Early Miocene outcrops near Karungu, Western Kenya, preserve a range of fluvio-lacustrine, lowland landscapes that contain abundant fossils of terrestrial and aquatic vertebrates. Primates are notably rare among these remains, although nearby early Miocene strata on Rusinga Island contain a rich assemblage of fossilized catarrhines and strepsirrhin...

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...

This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).

Discovering the Genomic Basis of Morphological and Physiological Differences between Mammalian Species with Forward Genomics Michael Hiller1,2, Hermann Ansorge3, Triantafyllos Chavakis4, Jörns Fickel5, Peter Giere6, Peter Grobe7, Jochen Hampe8, Thomas Lehmann3, Sylvia Ortmann5, Irina Ruf3, Clara Stefen3, Elly Tanaka4, Lars Vogt9, Heiko Stuckas3 1...

We describe new material of Rhinocerotidae recently collected in western Kenya. A skull from Karungu is one of the best-preserved Miocene skulls in Africa. It differs substantially from that of Rusingaceros leakeyi, the only other relatively well-known rhino from this region and age, in its degree of brachycephaly, possession of a deep nasal notch,...

Leptictida are basal Paleocene to Oligocene eutherians from Europe and North America comprising species with highly specialized postcranial features including elongated hind limbs. Among them, the European Leptictidium was probably a bipedal runner or jumper. Because the semicircular canals of the inner ear are involved in detecting angular acceler...

A 50 m thick stratigraphic section at Ngira, near Karungu on the shore of Lake Victoria in western Kenya, documents the early Miocene paleoenvironments of the area. The basal Ngira paleosol is a 7.6 m thick, oxisolic Vertisol that formed during a prolonged period of pedogenesis; it began as a smectite-dominated Vertisol that was later overprinted t...

This contribution contains the 3D model described and figured in the following publication: Crochet, J.-Y., Hautier, L., Lehmann, T., 2015. A pangolin (Manidae, Pholidota, Mammalia) from the French Quercy phosphorites (Pech du Fraysse, Saint-Projet, Tarn-et-Garonne, late Oligocene, MP 28). Palaeovertebrata 39(2)-e4. doi:10.18563/pv.39.2.e4

Pangolins have never shown a high taxic diversity and their fossil record is scarce. We report here the first discovery of a partial humerus from late Oligocene deposits in Pech du Fraysse (MP28, France). The new specimen from Pech du Fraysse is described and compared to various extant and extinct species of pangolins. It shows a suite of morpholog...

Plesiorycteropus (Malagasy aardvarks) is the sole genus belonging to an extinct mammalian order, the Bibymalagasia, that lived in Madagascar in the Quaternary. Its systematic and phylogenetic position is controversial because Plesiorycteropus morphologically resembles aardvarks (Tubulidentata), whereas a recent molecular analysis proposed that it b...

The Aardvark (Orycteropus afer) is a very unique, but relatively widespread African mammal. Although some morphological variation has been observed between forest and savannah populations and among different African regions, they are all considered as a single species. However, no modern taxonomic revision is available. All captive aardvarks in Eur...

The lineage of apes and humans (Hominoidea) evolved and radiated across Afro-Arabia in the early Neogene during a time of global climatic changes and ongoing tectonic processes that formed the East African Rift. These changes probably created highly variable environments and introduced selective pressures influencing the diversification of early ap...

‘Crocodylus’ pigotti is a relatively small crocodylid from the Miocene of Rusinga Island in Lake Victoria, Kenya. Known only from one relatively complete skull and limited, fragmentary, referred material, ‘Crocodylus’ pigotti lacks a detailed description. Moreover, recent analyses have shown ‘Crocodylus’ pigotti to be an osteolaemine crocodylid, mo...

Environmental reconstructions of early Miocene sites are important for understanding the remarkable diversity and abundance of African mammals today. These provide essential context for the faunal interchange that occurred with the appearance of land bridges between Afro-Arabia and Eurasia. Tragulids, for example, were ecological precursors of some...

Zoological institutions are important players in conservation, education, and research. Numerous zoos, for instance, have developed breeding programmes for species that are threatened or endangered, sometimes leading to their reintroduction in the wild (Frankham et al. 2002). Most of these institutions have also developed scientific facilities and...

Most of us have seen movies where, with the single beam of a gunlike device, a mad scientist in a white lab coat shrinks large-bodied animals to the size of an ant. Were elephants and elephant shrews victims of such a fantastic fate? From the time of their first description in 1800, elephant shrews (Macroscelidea) were considered related to shrews...