Publications by authors named "Olaf Thalmann"

15 Publications

  • Page 1 of 1

A refined proposal for the origin of dogs: the case study of Gnirshöhle, a Magdalenian cave site.

Sci Rep 2021 Mar 4;11(1):5137. Epub 2021 Mar 4.

Institute for Archaeological Sciences, University of Tübingen, Rümelinstraße 23, 72070, Tübingen, Germany.

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 Jura region (Southwestern Germany and Switzerland). By combining morphology, genetics, and isotopes, our multidisciplinary approach helps to evaluate alternate processes driving the early phases of domestication. The isotope analysis uncovered a restricted, low δN protein diet for all analyzed Gnirshöhle specimens, while morphological examinations and phylogenetic relationships did not unequivocally assign them to one or the other canid lineage. Intriguingly, the newly generated mitochondrial canid genomes span the entire genetic diversity of modern dogs and wolves. Such high mitochondrial diversity could imply that Magdalenian people tamed and reared animals originating from different wolf lineages. We discuss our results in light of three ecological hypotheses and conclude that both domestication and the existence of a specialized wolf ecomorph are highly probable. However, due to their proximity to humans and a restricted diet, we propose domestication as the most likely scenario explaining the patterns observed herein.
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http://dx.doi.org/10.1038/s41598-021-83719-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7933181PMC
March 2021

Leukocyte Telomere Length Is Not Reduced in Children and Adults with Cystic Fibrosis but Associates with Clinical Characteristics-A Cross-Sectional Study.

J Clin Med 2021 Feb 4;10(4). Epub 2021 Feb 4.

Department of Paediatric Gastroenterology and Metabolic Diseases, Poznań University of Medical Sciences, 60-572 Poznań, Poland.

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 length was similar in CF and HS (median (interquartile range): 0.799 (0.686-0.950) vs. 0.831 (0.707-0.986); = 0.5283) both in children and adults. In adults, women had longer telomeres than men (0.805 (0.715-0.931) vs. 0.703 (0.574-0.790); = 0.0002). Patients treated with inhaled corticosteroids had a shorter RTL compared to those without steroid therapy (0.765 (0.664-0.910) vs. 0.943 (0.813-1.191); = 0.0007) and this finding remained significant after adjusting for gender, age, BMI, and child/adult status ( = 0.0003). Shorter telomeres were independently associated with the presence of comorbidities (0.763 (0.643-0.905) vs. 0.950 (0.783-1.130); = 0.0006) and antibiotic treatment at the moment of blood sampling (0.762 (0.648-0.908) vs. 0.832 (0.748-1.129); = 0.0172). RTL correlated with number of multiple-day hospitalizations (rho = -0.251; = 0.0239), as well as number of hospitalization days (rho = -0.279; = 0.0113). Leukocyte RTL in children and adults with CF was not shorter than in healthy controls, and did not seem to have any potential as a predictor of CF survival. However, it inversely associated with the investigated clinical characteristics.
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http://dx.doi.org/10.3390/jcm10040590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7915028PMC
February 2021

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia.

Mol Ecol 2020 05 2;29(9):1596-1610. Epub 2020 Jan 2.

Department of Zoology, University of Cambridge, Cambridge, UK.

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 Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single Late Pleistocene population. Both the geographical origin of this ancestral population and how it became widespread remain unknown. Here, we used a spatially and temporally explicit modelling framework to analyse a data set of 90 modern and 45 ancient mitochondrial wolf genomes from across the Northern Hemisphere, spanning the last 50,000 years. Our results suggest that contemporary wolf populations trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum, and that this process was most likely driven by Late Pleistocene ecological fluctuations that occurred across the Northern Hemisphere. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore, and provides insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because Late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.
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http://dx.doi.org/10.1111/mec.15329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317801PMC
May 2020

Apolipoprotein E polymorphism determines vitamin K supplementation effectiveness in cystic fibrosis patients.

J Cyst Fibros 2018 07 4;17(4):e39-e40. Epub 2018 May 4.

Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland. Electronic address:

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http://dx.doi.org/10.1016/j.jcf.2018.04.007DOI Listing
July 2018

Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves.

Mol Biol Evol 2018 05;35(5):1190-1209

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA.

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 inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.
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http://dx.doi.org/10.1093/molbev/msy031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6455901PMC
May 2018

Non-invasive genetic monitoring involving citizen science enables reconstruction of current pack dynamics in a re-establishing wolf population.

BMC Ecol 2017 12 19;17(1):44. Epub 2017 Dec 19.

Department of Biology, University of Turku, Turku, Finland.

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 management decisions, but individual-level information can be difficult to obtain from elusive, wide-ranging species. Non-invasive genetic sampling can yield such information, but makes subsequent reconstruction of population history challenging due to incomplete population coverage and error-prone data. Here, we combine a collaborative, volunteer-based sampling scheme with Bayesian pedigree reconstruction to describe the pack dynamics of an establishing grey wolf (Canis lupus) population in south-west Finland, where wolf breeding was recorded in 2006 for the first time in over a century.

Results: Using DNA extracted mainly from faeces collected since 2008, we identified 81 individual wolves and assigned credible full parentages to 70 of these and partial parentages to a further 9, revealing 7 breeding pairs. Individuals used a range of strategies to obtain breeding opportunities, including dispersal to established or new packs, long-distance migration and inheriting breeding roles. Gene flow occurred between all packs but inbreeding events were rare.

Conclusions: These findings demonstrate that characterizing ongoing pack dynamics can provide detailed, locally-relevant insight into the ecology of contentious species such as the wolf. Involving various stakeholders in data collection makes these results more likely to be accepted as unbiased and hence reliable grounds for management decisions.
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http://dx.doi.org/10.1186/s12898-017-0154-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5738207PMC
December 2017

Prediction of harmful variants on mitochondrial genes: Test of habitat-dependent and demographic effects in a euryhaline fish.

Ecol Evol 2017 06 18;7(11):3826-3835. Epub 2017 Apr 18.

Department of Biology University of Turku Turku Finland.

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 constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of collected from brackish and freshwater habitats. Based on inter- and intraspecific comparisons, we estimated that 84% and 68% of the nonsynonymous polymorphisms in the freshwater and brackish water populations, respectively, are weakly or moderately deleterious. Using in silico prediction tools (MutPred, SNAP2), we subsequently identified nonsynonymous polymorphisms with potentially harmful effect. Both prediction methods indicated that the functional effects of the fixed nonsynonymous substitutions between nine- and three-spined stickleback were weaker than for polymorphisms within species, indicating that harmful nonsynonymous polymorphisms within populations rarely become fixed between species. No significant differences in mean estimated functional effects were identified between freshwater and brackish water nine-spined stickleback to support the hypothesis that reduced osmoregulatory energy demand in the brackish water environment reduces the strength of purifying selection at OXPHOS genes. Instead, elevated frequency of nonsynonymous polymorphisms in the freshwater environment ( = 0.549 vs. 0.283; Fisher's exact test  = .032) suggested that purifying selection is less efficient in small freshwater populations. This study shows the utility of in silico functional prediction tools in population genetic and evolutionary research in a nonmammalian vertebrate and demonstrates that mitochondrial energy production genes represent a promising system to characterize the demographic, life history and potential habitat-dependent effects of segregating amino acid variants.
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http://dx.doi.org/10.1002/ece3.2989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5468147PMC
June 2017

Genome-wide Evidence Reveals that African and Eurasian Golden Jackals Are Distinct Species.

Curr Biol 2015 08 30;25(16):2158-65. Epub 2015 Jul 30.

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles Young Drive East, Los Angeles, CA 90095-1606, USA. Electronic address:

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), which is surprising given the absence of gray wolves in Africa and the phenotypic divergence between the two species. Moreover, these results imply the existence of a previously unrecognized phylogenetically distinct species despite a long history of taxonomic work on African canids. To test the distinct-species hypothesis and understand the evolutionary history that would account for this puzzling result, we analyzed extensive genomic data including mitochondrial genome sequences, sequences from 20 autosomal loci (17 introns and 3 exon segments), microsatellite loci, X- and Y-linked zinc-finger protein gene (ZFX and ZFY) sequences, and whole-genome nuclear sequences in African and Eurasian golden jackals and gray wolves. Our results provide consistent and robust evidence that populations of golden jackals from Africa and Eurasia represent distinct monophyletic lineages separated for more than one million years, sufficient to merit formal recognition as different species: C. anthus (African golden wolf) and C. aureus (Eurasian golden jackal). Using morphologic data, we demonstrate a striking morphologic similarity between East African and Eurasian golden jackals, suggesting parallelism, which may have misled taxonomists and likely reflects uniquely intense interspecific competition in the East African carnivore guild. Our study shows how ecology can confound taxonomy if interspecific competition constrains size diversification.
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http://dx.doi.org/10.1016/j.cub.2015.06.060DOI Listing
August 2015

Attempted DNA extraction from a Rancho La Brea Columbian mammoth (Mammuthus columbi): prospects for ancient DNA from asphalt deposits.

Ecol Evol 2014 Feb 11;4(4):329-36. Epub 2014 Jan 11.

Department of Ecology and Evolutionary Biology, University of California Los Angeles, California 90095.

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 asphalt-mediated inhibition. In an attempt to test these hypotheses, a recently recovered Columbian mammoth (Mammuthus columbi) skeleton with an unusual pattern of asphalt impregnation was studied. Ultimately, none of the bone samples tested successfully amplified M. columbi DNA. Our work suggests that reagents typically used to remove asphalt from ancient samples also inhibit DNA extraction. Ultimately, we conclude that the probability of recovering ancient DNA from fossils in asphalt deposits is strongly (perhaps fatally) hindered by the organic compounds that permeate the bones and that at the Rancho La Brea tar pits, environmental conditions might not have been ideal for the general preservation of genetic material.
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http://dx.doi.org/10.1002/ece3.928DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936381PMC
February 2014

Ancient DNA analysis affirms the canid from Altai as a primitive dog.

PLoS One 2013 6;8(3):e57754. Epub 2013 Mar 6.

Department of Genomic Diversity and Evolution, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.

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 order to evaluate the genetic relationship of one of the oldest dogs, we have isolated ancient DNA from the recently described putative 33,000-year old Pleistocene dog from Altai and analysed 413 nucleotides of the mitochondrial control region. Our analyses reveal that the unique haplotype of the Altai dog is more closely related to modern dogs and prehistoric New World canids than it is to contemporary wolves. Further genetic analyses of ancient canids may reveal a more exact date and centre of domestication.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3590291PMC
September 2013

A comparison of brain gene expression levels in domesticated and wild animals.

PLoS Genet 2012 Sep 27;8(9):e1002962. Epub 2012 Sep 27.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

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 species (dogs and wolves, pigs and wild boars, and domesticated and wild rabbits). We compared the expression differences with those between domesticated guinea pigs and a distant wild relative (Cavia aperea) as well as between two lines of rats selected for tameness or aggression towards humans. There were few gene expression differences between domesticated and wild dogs, pigs, and rabbits (30-75 genes (less than 1%) of expressed genes were differentially expressed), while guinea pigs and C. aperea differed more strongly. Almost no overlap was found between the genes with differential expression in the different domestication events. In addition, joint analyses of all domesticated and wild samples provided only suggestive evidence for the existence of a small group of genes that changed their expression in a similar fashion in different domesticated species. The most extreme of these shared expression changes include up-regulation in domesticates of SOX6 and PROM1, two modulators of brain development. There was almost no overlap between gene expression in domesticated animals and the tame and aggressive rats. However, two of the genes with the strongest expression differences between the rats (DLL3 and DHDH) were located in a genomic region associated with tameness and aggression, suggesting a role in influencing tameness. In summary, the majority of brain gene expression changes in domesticated animals are specific to the given domestication event, suggesting that the causative variants of behavioral domestication traits may likewise be different.
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http://dx.doi.org/10.1371/journal.pgen.1002962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459979PMC
September 2012

Efficient recovery of whole blood RNA--a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species.

BMC Biotechnol 2012 Jun 27;12:33. Epub 2012 Jun 27.

Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA.

Background: 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, care must be taken in RNA preparation as factors like DNA contamination, RNA integrity or transcript abundance can affect downstream applications. Here, we evaluated five commonly used RNA extraction methods using whole blood sampled under varying conditions from 20 wild carnivores.

Results: Despite the use of minute starting volumes, all methods produced quantifiable RNA extracts (1.4 - 18.4 μg) with varying integrity (RIN 4.6 - 7.7), the latter being significantly affected by the storage and extraction method used. We observed a significant overall effect of the extraction method on DNA contamination. One particular extraction method, the LeukoLOCK™ filter system, yielded high RNA integrity along with low DNA contamination and efficient depletion of hemoglobin transcripts highly abundant in whole blood. In a proof of concept sequencing experiment, we found globin RNA transcripts to occupy up to ¼ of all sequencing reads if libraries were not depleted of hemoglobin prior to sequencing.

Conclusion: By carefully choosing the appropriate RNA extraction method, whole blood can become a valuable source for high-throughput applications like expression arrays or transcriptome sequencing from natural populations. Additionally, candidate genes showing signs of selection could subsequently be genotyped in large population samples using whole blood as a source for RNA without harming individuals from rare or endangered species.
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http://dx.doi.org/10.1186/1472-6750-12-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406948PMC
June 2012

Historical sampling reveals dramatic demographic changes in western gorilla populations.

BMC Evol Biol 2011 Apr 1;11:85. Epub 2011 Apr 1.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

Background: 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 in the past. In order to better understand the dynamics associated with the divergences of great ape populations, these analytical approaches were applied to western gorillas (Gorilla gorilla) and in particular to the isolated and Critically Endangered Cross River gorilla subspecies (G. g. diehli).

Results: We used microsatellite genotypes from museum specimens and contemporary samples of Cross River gorillas to infer both the long-term and recent population history. We find that Cross River gorillas diverged from the ancestral western gorilla population ~17,800 years ago (95% HDI: 760, 63,245 years). However, gene flow ceased only ~420 years ago (95% HDI: 200, 16,256 years), followed by a bottleneck beginning ~320 years ago (95% HDI: 200, 2,825 years) that caused a 60-fold decrease in the effective population size of Cross River gorillas. Direct comparison of heterozygosity estimates from museum and contemporary samples suggests a loss of genetic variation over the last 100 years.

Conclusions: The composite history of western gorillas could plausibly be explained by climatic oscillations inducing environmental changes in western equatorial Africa that would have allowed gorilla populations to expand over time but ultimately isolate the Cross River gorillas, which thereafter exhibited a dramatic population size reduction. The recent decrease in the Cross River population is accordingly most likely attributable to increasing anthropogenic pressure over the last several hundred years. Isolation of diverging populations with prolonged concomitant gene flow, but not secondary admixture, appears to be a typical characteristic of the population histories of African great apes, including gorillas, chimpanzees and bonobos.
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http://dx.doi.org/10.1186/1471-2148-11-85DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078889PMC
April 2011

Evolutionary history of the Falklands wolf.

Curr Biol 2009 Nov;19(20):R937-8

Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 90095-1606, USA.

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http://dx.doi.org/10.1016/j.cub.2009.09.018DOI Listing
November 2009

Demographic history and genetic differentiation in apes.

Curr Biol 2006 Jun;16(11):1133-8

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

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 may guide conservation efforts. We sequenced multiple intergenic autosomal regions totaling 22,400 base pairs (bp) in ten individuals each from western, central, and eastern chimpanzee groups and in nine bonobos, and 16,000 bp in ten Bornean and six Sumatran orangutans. These regions are analyzed together with homologous information from three human populations and gorillas. We find that whereas orangutans have the highest diversity, western chimpanzees have the lowest, and that the demographic histories of most groups differ drastically. Special attention should therefore be paid to sampling strategies and the statistics chosen when comparing levels of variation within and among groups. Finally, we find that the extent of genetic differentiation among "subspecies" of chimpanzees and orangutans is comparable to that seen among human populations, calling the validity of the "subspecies" concept in apes into question.
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http://dx.doi.org/10.1016/j.cub.2006.04.033DOI Listing
June 2006