Olaf Thalmann

Ludwig-Maximilians-University of Munich | LMU · Department of Veterinary Sciences

Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we...

Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 cap...

The question, whether a dog is a dog or rather a wolf, is highly debated in the field of zooarchaeology, paleogenetic, and stable isotopes. Recent evidence points towards an onset of wolf domestication in south-western Germany and northern Switzerland at around 16 to 15,000 years ago. Regarding diet of wolves and potential dogs, both groups fed on...

Investigations into the mechanisms regulating obesity are frantic and novel translational approaches are needed. The raccoon dog (Nyctereutes procyonoides) is a canid species representing a promising model to study metabolic regulation in a species undergoing cycles of seasonal obesity and fasting. To understand the molecular mechanisms of metaboli...

The question, whether a dog is a dog or rather a wolf, became recently highly debated. Recent evidence points towards an onset of domestication at around 16 to 15,000 years ago including an intriguing example of the Kesslerloch cave (CH), where beside wolf remains, one large canid has been morphologically and genetically confirmed as dog. Regarding...

Dogs are known to be the oldest animals domesticated by humans. Although many studies have examined wolf domestication, the geographic and temporal origin of this process is still being debated. To address this issue, our study sheds new light on the early stages of wolf domestication during the Magdalenian period (16–14 ka cal BP) in the Hegau Jur...

We hypothezied that telomere length is considerably altered in cystic fibrosis (CF) patients compared to healthy subjects (HS), and that leukocyte telomere length variation reflects the severity of CF. Relative telomere length (RTL) was assessed by qPCR in 70 children aged 5–10 (34 CF; 36 HS) and 114 adults aged 18–45 (53 CF; 61 HS). Telomere lengt...

Humans are constantly exposed to health risks inherent to the environment in which they live, thereby including non-human fauna. Zoonoses are infectious diseases caused by agents such as bacteria, parasites, or viruses being transmitted to humans from wild animals and livestock. The close proximity of animals and humans facilitate the spread of zoo...

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographical distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the Late...

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that have maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pl...

Methylation patterns in ancient Scandinavians

Domestication is the result of a complex interplay of both biological and cultural processes. The mechanisms underlying today's variety of domesticates has long sparked the interest of researchers but has always been difficult to define. While dogs (Canis familiaris) are now firmly established as the earliest domesticated animal, most questions abo...

Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly i...

Domestication is the result of a complex interplay of both biological and cultural processes. The mechanism underlying today’s variety of domesticates has long sparked the interest of researchers but has always been difficult to define. While dogs (Canis familiaris) are now firmly established as the earliest domesticated animal, most questions abou...

Background Carnivores are re-establishing in many human-populated areas, where their presence is often contentious. Reaching consensus on management decisions is often hampered by a dispute over the size of the local carnivore population. Understanding the reproductive dynamics and individual movements of the carnivores can provide support for mana...

Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constrai...

Using next generation sequencing and high resolution melt analyses, we identified and typed 53 SNPs in Nazca boobies (Sula granti) from the Galápagos to build a pedigree.

The golden jackal of Africa (Canis aureus) has long been considered a conspecific of jackals distributed throughout Eurasia, with the nearest source populations in the Middle East. However, two recent reports found that mitochondrial haplotypes of some African golden jackals aligned more closely to gray wolves (Canis lupus) [1, 2], which is surpris...

Fossil-bearing asphalt deposits are an understudied and potentially significant source of ancient DNA. Previous attempts to extract DNA from skeletons preserved at the Rancho La Brea tar pits in Los Angeles, California, have proven unsuccessful, but it is unclear whether this is due to a lack of endogenous DNA, or if the problem is caused by asphal...

Data S1. Nucleotide alignment of partial proboscidean and human cytochrome b sequences, highlighting the primers designed.

Dog Domestication The precise details of the domestication and origins of domestic dogs are unclear. Thalmann et al. (p. 871 ; see the cover) analyzed complete mitochondrial genomes from present-day dogs and wolves, as well as 18 fossil canids dating from 1000 to 36,000 years ago from the Old and New Worlds. The data suggest that an ancient, now ex...

Unraveling the various mechanisms that facilitate adaptive processes in nature is a pivotal challenge uniting evolutionary biologists, physiologists, ecologists and scientists from many diverse fields. While over the past decades, we have acquired comprehensive knowledge about the physiological, immunological or morphological modifications that all...

The origin of domestic dogs remains controversial, with genetic data indicating a separation between modern dogs and wolves in the Late Pleistocene. However, only a few dog-like fossils are found prior to the Last Glacial Maximum, and it is widely accepted that the dog domestication predates the beginning of agriculture about 10,000 years ago. In o...

List of primers used in this study. (PDF)

Haplotype assignments for the network analysis. (PDF)

Neighbour Joining tree generated with complete mitochondrial genomes of 72 dogs and 30 wolves using 1,000 bootstrap steps. The shaded areas indicate the four well supported dog clusters and the arrows point at the support values for each clade. (PDF)

Neighbour Joining tree representing a fully annotated version of the tree shown in Figure 2 generated with 413 bp of the hypervariable region of the mitochondrial genome. Red values indicate the bootstrap support after 1,000 steps. The identifiers are explained in Table S2 with the exception of sequences labelled “JAL”. The latter nomenclature is a...

The scheme of Altai dog sequencing superimposed on the canine mitochondrial DNA sequence from GenBank (EU789784). Vertical dashed lines indicate the boundaries of 413 bp sequence used in this work. Small arrows indicate positions of all primers from Table S1. Bars 1–6 indicate independent PCR reactions with different primer combinations: (1) – D1F/...

Likelihood mapping analysis of all 142 canids without further partitioning of the data. Upper panel shows the distribution pattern of all quartets and the lower panel depicts the fraction of each occupied region. (PDF)

Haplotype Network summarizing the phylogenetic relationships of unique haplotypes. Identical haplotypes are collapsed and the sizes of the circles indicate the frequencies. Different haplotypes are labelled with H_XX (yellow circles) and hypothesized median vectors with mvXX (red circles). The length of the links between nodes is proportional to mu...

Nomenclature, accession number and breed/geographical origin of the individual dog/wolf haplotypes. (PDF)

Differentially expressed genes. (XLSX)

GO enrichment results. (XLS)

PCA of gene expression variation. Blue: domesticated/tame rat, red: wild/aggressive rat; circles: females, squares: males. (PDF)

Domestication-related genes. (XLSX)

Full details on samples and sequencing runs performed for this study. (XLS)

Gene expression values used in the analyses, stored as R objects. (ZIP)

PCA of SNV data. Blue: domesticated/tame rat, red: wild/aggressive rat; circles: females, squares: males. (PDF)

Transcript sequence differences to the reference genome in genes with common expression in domesticated animals. For each gene, the median fold change of expression in domesticated vs. wild animals is plotted as a function of the difference between wild and domesticated mean sequence difference to the reference genome. The p-values are from Wilcoxo...

PCA of expression data in all 12 rabbit samples. Note the large distance separating A115 from all other samples. Blue: domesticated, red: wild, circles: females, squares: males. (PDF)

“Extreme” and random permutations when testing for shared gene expression across domestication events. (DOCX)

Shown is the number of genes that are 1∶1 orthologues in the given comparison and that are “expressed” in both pairs (i.e. have >0 counts in at least half the samples in both species pairs that are compared). (DOCX)

Extreme and random permutations when searching for genes with shared expression in domesticated animals. A detailed step-by-step description of this Figure is provided in Note S1. A. Expression levels of a hypothetical gene in three pairs (circles, squares, triangles) of domesticated (blue) and wild (red) animals. The dotted line is the overall mea...

Q-Q plots comparing the p-value distribution of the un-permuted data to all possible extreme permutations for the analyses without guinea pigs. p-values are for the effect of domestication in the ANOVA analyses of dogs, pigs and rabbits, and were −log10 transformed. The real, un-permuted data is shown on the y-axis compared to each of the respectiv...

Q-Q plots comparing the p-value distribution of the un-permuted data to all possible extreme permutations for the analyses including guinea pigs. p-values are for the effect of domestication in the ANOVA analyses of dogs, pigs, rabbits and guinea pigs, and were −log10 transformed. The real, un-permuted data is shown on the respective y-axis compare...

Sequence polymorphism in genes with common expression in domesticated animals. (DOCX)

Domestication has led to similar changes in morphology and behavior in several animal species, raising the question whether similarities between different domestication events also exist at the molecular level. We used mRNA sequencing to analyze genome-wide gene expression patterns in brain frontal cortex in three pairs of domesticated and wild spe...

Since the emergence of next generation sequencing platforms, unprecedented opportunities have arisen in the study of natural vertebrate populations. In particular, insights into the genetic and epigenetic mechanisms of adaptation can be revealed through study of the expression profiles of genes. However, as a pre-requisite to expression profiling,...

Supplementary Information. The accompanied pdf-file provides in depth information regarding the sample preparation for 454 sequencing, two additional tables and a figure that depicts the sampling set up [56-58].

Owing to their high abundance in eukaryotic genomes, bisexual mode of inheritance and hyper-mutability, microsatellites have quickly developed into an invaluable tool in molecular and wildlife genetics. Despite their widespread application, microsatellites have only marginally been used in studies utilising ancient/historical materials. This is pri...

Supplementary Information. Here we provide additional information regarding laboratory methods and data analyses.

Today many large mammals live in small, fragmented populations, but it is often unclear whether this subdivision is the result of long-term or recent events. Demographic modeling using genetic data can estimate changes in long-term population sizes while temporal sampling provides a way to compare genetic variation present today with that sampled i...

After visiting the Falkland Islands during the voyage of the Beagle, Charles Darwin remarked on the surprising presence of a wolf-like canid unique to the islands [1 • Darwin C. The zoology of the voyage of H.M.S. Beagle, under the command of Captain Fitzroy, R.N., during the years 1832 to 1836. Smith, Elder and Co, London, London1838 • Google Sc...

Many studies in molecular ecology rely upon the genotyping of large numbers of low-quantity DNA extracts derived from noninvasive or museum specimens. To overcome low amplification success rates and avoid genotyping errors such as allelic dropout and false alleles, multiple polymerase chain reaction (PCR) replicates for each sample are typically us...

Relatively little is known about the evolutionary and demographic histories of gorillas, one of our closest living relatives. In this study, we used samples from both western (Gorilla gorilla) and eastern (Gorilla beringei) gorillas to infer the timing of the split between these geographically disjunct populations and to elaborate the demographic h...

Comparisons of genetic variation between humans and great apes are hampered by the fact that we still know little about the demographics and evolutionary history of the latter species. In addition, characterizing ape genetic variation is important because they are threatened with extinction, and knowledge about genetic differentiation among groups...

Numts are fragments of mitochondrial DNA (mtDNA) that have been translocated to the nucleus, where they can persist while their mitochondrial counterparts continue to rapidly evolve. Thus, numts represent 'molecular fossils' useful for comparison with mitochondrial variation, and are particularly suited for studies of the fast-evolving hypervariabl...

Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic 'barcode' for an objective species classification sch...

Analysis of mitochondrial DNA sequence variation has been used extensively to study the evolutionary relationships of individuals and populations, both within and across species. So ubiquitous and easily acquired are mtDNA data that it has been suggested that such data could serve as a taxonomic ‘barcode’ for an objective species classification sch...