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Highly improved dating of primate ERV integrations

Hugo Martins, Palle Villesen
2009 Retrovirology  
</note> <url>http://www.biomedcentral.com/content/pdf/1742-4690-6-S2-info.pdf</url> </supplement> This abstract is available from: http://www.retrovirology.com/content/6/S2/P54 © 2009 Martins and Villesen  ... 
doi:10.1186/1742-4690-6-s2-p54 pmcid:PMC2767039 fatcat:j3jshskrg5eqtm6ubf45xs3tje

Profiling of cocaine using ratios of GC-MS peaks

Palle Villesen, Louise Stride Nielsen
2017 Scientific Reports  
Illicit cocaine seizures are often compared to each other by using gas chromatography-mass spectrometry (GC-MS) data from cocaine alkaloid compounds to determine whether two specimens originate from the same production batch or not. This can provide intelligence or investigative information at the early stages of an investigation or evidence in court. Traditional classification methods assume high stability of all alkaloids, use all of them to calculate the correlation between two profiles and
more » ... se a threshold to classify samples. Unstable alkaloids will have a strong influence on the performance. We show that comparing each alkaloid target compound individually improves the classification. Unfortunately, it requires normalization and is also sensitive to the stability. Instead we suggest to use ratios of all possible pairwise combinations of the GC-MS peaks. These ratios are scale free and directly comparable between samples. The peaks can be given different weights in the comparison of profiles using appropriate classification methods and we show that randomForest classification using these ratios have a high and reproducible performance in comparison with other methods. The performance of this method is not affected by noise, transformation or normalization and should be considered for future comparison of chromatographic profiles in general.
doi:10.1038/s41598-017-12042-x pmid:28912606 pmcid:PMC5599637 fatcat:mjske75tqjg4ljhpt7ycix5g7u

A periodic pattern of SNPs in the human genome

Bo Eskerod Madsen, Bo Eskerod Madsen, Palle Villesen, Carsten Wiuf
2007 Nature Precedings  
doi:10.1038/npre.2007.435 fatcat:5vs2pswenvee3pzzp77d5eeofm

Identification of endogenous retroviral reading frames in the human genome

Palle Villesen, Lars Aagaard, Carsten Wiuf, Finn Skou Pedersen
2004 Retrovirology  
Although we were unable to detect any unambiguous EST matches to this gene (Table 3) , RT-PCR analysis indicates low RNA abundance in a few human tissues including placenta (Kjeldbjerg AL, Aagaard L, Villesen  ... 
doi:10.1186/1742-4690-1-32 pmid:15476554 pmcid:PMC524368 fatcat:76o2iuix45hazk5qjl5thrlucy

A periodic pattern of SNPs in the human genome

Bo Eskerod Madsen, Bo Eskerod Madsen, Palle Villesen, Carsten Wiuf
2007 Nature Precedings  
doi:10.1038/npre.2007.435.1 fatcat:ubwb6o6mqvgudnu27tj6y45d6m

Homicide in Denmark 1992–2016

Asser H. Thomsen, Peter M. Leth, Hans Petter Hougen, Palle Villesen, Ole Brink
2019 Forensic Science International: Synergy  
We present the findings for homicides in Denmark for 1992-2016. There were 1417 homicide victims (62.2% males, 37.8% females) that were killed in 1321 homicide events. The most common methods were sharp force trauma (33.2%), gunshot (22.2%), blunt force trauma (21.9%) and asphyxia (17.6%), and all methods exhibited a reduction during the study period. The homicide rate was 1.05 per 100,000, 1.32 per 100,000 for males, and 0.78 per 100,000 for females. Domestic homicides were the largest main
more » ... up of homicides (76.5% of all female victims vs. 23.6% of male victims). Of the non-domestic homicides, 84.2% of victims were male, the largest group being in the setting of nightlife and/or intoxication. Most female victims (76.9%) were killed by someone in their family, while the largest share of male victims (34.5%) were killed by a friend or acquaintance. The offenders were males in 87.9% of all homicides.
doi:10.1016/j.fsisyn.2019.07.001 pmid:32411980 pmcid:PMC7219188 fatcat:mzk35whk75do7c2mpm5fypem2m

Short Tandem Repeats in Human Exons: A Target for Disease Mutations

Bo Madsen, Palle Villesen, Carsten Wiuf
2008 BMC Genomics  
In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions), are common throughout the genome, but the implications of structural variations are still not clearly understood. Long tandem repeats (e.g. microsatellites or simple repeats) are known to be hypermutable (indel-rich), but are rare in exons and only occasionally associated with diseases. Here we focus on short (imperfect) tandem repeats (STRs) which fall below the radar of conventional
more » ... tandem repeat detection, and investigate whether STRs are targets for disease-related mutations in human exons. In particular, we test whether they share the hypermutability of the longer tandem repeats and whether disease-related genes have a higher STR content than non-disease-related genes. Results: We show that validated human indels are extremely common in STR regions compared to non-STR regions. In contrast to longer tandem repeats, our definition of STRs found them to be present in exons of most known human genes (92%), 99% of all STR sequences in exons are shorter than 33 base pairs and 62% of all STR sequences are imperfect repeats. We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. Conclusion: Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. In addition, STRs constitute an obvious target when screening for rare mutations, because of the relatively low amount of STRs in exons (1,973,844 bp) and the limited length of STR regions.
doi:10.1186/1471-2164-9-410 pmid:18789129 pmcid:PMC2543027 fatcat:hx663g6gojdvhmsqexvgaz2heu

Improved Integration Time Estimation of Endogenous Retroviruses with Phylogenetic Data

Hugo Martins, Palle Villesen, Darren P. Martin
2011 PLoS ONE  
Endogenous retroviruses (ERVs) are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and
more » ... tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 59 and 39 Long Terminal Repeats (LTRs) sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches. Results: We show that there are strong advantages in using multiple species data and state-of-the-art phylogenetic analysis. We incorporate both simple phylogenetic information and Monte Carlo Markov Chain (MCMC) methods to date the integrations of these viruses based on a relaxed molecular clock approach over a Bayesian phylogeny model and applied them to several selected ERV sequences in primates. These methods treat each ERV locus as having a distinct evolutionary rate for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks. Conclusions: The use of a fixed rate produces results that vary considerably with ERV family and the actual evolutionary rate of the sequence, and should be avoided whenever multi-species phylogenetic data are available. For genome-wide studies, the simple phylogenetic approach constitutes a better alternative, while still being computationally feasible.
doi:10.1371/journal.pone.0014745 pmid:21394200 pmcid:PMC3048862 fatcat:yp5i6f6efzgclexhv2vjl52yku

Variation in chemical profiles within large seizures of cocaine bricks

Louise Stride Nielsen, Palle Villesen, Christian Lindholst
2017 Forensic Science International  
Cocaine is usually trafficked from South America throughout the world in packages of approximately one kilogram shaped as bricks and imprinted with a logo. Seizures consisting of multiple cocaine bricks gives the opportunity to examine the variation in the chemical profile within cocaine bricks assumed to originate from the same manufacturer and maybe even the same production batch. This knowledge may be important to the forensic investigator when chemical profiles from cocaine samples of
more » ... n origin are compared. In the present study, the alkaloid and residual solvent profiles from three large cocaine seizures each containing identical cocaine bricks was examined. The three cases consisted of 36, 84 and 100 cocaine bricks, respectively. Each cocaine brick was profiled according to its cocaine alkaloid and residual solvent content using gas chromatography-mass spectrometry (GC-MS) and headspace GC-MS. The study showed that each of the three identical looking seizures consisted of up to four groups of cocaine bricks displaying the same cocaine alkaloid and residual solvent profile. The size of the groups varied from 2.4 to 63.3 kg cocaine. The study also showed that the residual solvent profile within each of the three large seizures exhibited very little variation whereas the alkaloid profile varied considerably more. This finding suggest that the same organic solvent is used for the production of several batches of cocaine HCl. Therefore, the residual solvent profile may be a tool to link different production batches from the same manufacturer even though the alkaloid profile are different.
doi:10.1016/j.forsciint.2017.10.007 pmid:29078162 fatcat:ww2yc7e7zvfbnjclcf6fke3j2e

Conservation of ancient full-length open reading frames in vertebrate endogenous retroviruses

Hugo Martins, Palle Villesen
2011 Retrovirology  
least 1000 uninterrupted nucleotides) for all three major retroviral genes:gag,pol and env,grouped by their locus'LTR divergence percentage <80 % 80-85% 85-90% 90-95% >95 % total © 2011 Martins and Villesen  ... 
doi:10.1186/1742-4690-8-s2-p47 pmcid:PMC3236936 fatcat:4mrljvhirzgjdhgkhtoa34u47y

Fast and non-invasive PCR sexing of primates: apes, Old World monkeys, New World monkeys and Strepsirrhines

Palle Villesen, Tina Fredsted
2006 BMC Ecology  
One of the key tools for determining the social structure of wild and endangered primates is the ability to sex DNA from small amounts of non-invasive samples that are likely to include highly degraded DNA. Traditional markers for molecular sex determination of primates are developed on the basis of the human sequence and are often non-functional in distantly related primate species. Hence, it is highly desirable to develop markers that simultaneously detect Y- and X-chromosome specific
more » ... s and also work across many species. A novel method for sex identification in primates is described using a triple primer PCR reaction and agarose gel electrophoresis of the sex-chromosomal isoforms of the ubiquitously transcribed tetratricopeptide repeat protein gene (UTX/UTY). By comparing genomic data from several mammals we identified the UTX/UTY locus as the best candidate for a universal primate sexing marker. Using data from several species we identified a XY-conserved region, a Y conserved region and an X conserved region. This enabled the design of a triple primer PCR setup that amplifies X and Y products of different length in a single PCR reaction. This simple PCR amplification of X and Y fragments is useful for sexing DNA samples from all species of primates. Furthermore, since the amplified fragments are very short the method can be applied to fragmented DNA extracted from non-invasive samples.
doi:10.1186/1472-6785-6-8 pmid:16762053 pmcid:PMC1524723 fatcat:rs3kpqqoljfmhfrm5udttot7p4

Introgression of mountain hare (Lepus timidus) mitochondrial DNA into wild brown hares (Lepus europaeus) in Denmark

Tina Fredsted, Trine Wincentz, Palle Villesen
2006 BMC Ecology  
In Europe the mountain hare (Lepus timidus) exists in Great Britain, Norway, Sweden, Finland, parts of the Alps and in Eastern Europe, but not in Denmark. Interspecific hybridization has been demonstrated between native Swedish mountain hares and introduced brown hares (Lepus europaeus). During the data collection in a study concerning Danish brown hares we identified 16 hares with a single very divergent haplotype. Phylogenetic analysis shows that the divergent Danish haplotype is most closely
more » ... related to the Swedish mountain hare. The frequency of Lepus timidus mtDNA haplotype in the Eastern Danish hare populations is estimated to 6%. In contrast to what is known, the Danish hare populations are not pure L. europaeus populations but include introgressed brown hares with Swedish L. timidus mtDNA. The most probable explanation of this is natural migration or translocation of introgressed brown hares from Sweden. The impurity of hare populations has implications for conservation and population genetics.
doi:10.1186/1472-6785-6-17 pmid:17105672 pmcid:PMC1654140 fatcat:wtgbv53fovadrifjqyspmt6qa4

EVOLUTION OF ANT-CULTIVAR SPECIALIZATION AND CULTIVAR SWITCHING IN APTEROSTIGMA FUNGUS-GROWING ANTS

Palle Villesen, Ulrich G. Mueller, Ted R. Schultz, Rachelle M. M. Adams, Amy C. Bouck
2004 Evolution  
Almost all of the more than 200 species of fungus-growing ants (Formicidae: Attini) cultivate litterdecomposing fungi in the family Lepiotaceae (Basidiomycota: Agaricales). The single exception to this rule is a subgroup of ant species within the lower attine genus Apterostigma, which cultivate pterulaceous fungi distantly related to the Lepiotaceae. Comparison of cultivar and ant phylogenies suggests that a switch from lepiotaceous to pterulaceous fungiculture occurred only once in the history
more » ... of the fungus-growing ants. This unique switch occurred after the origin of the genus Apterostigma, such that the basal Apterostigma lineages retained the ancestral attine condition of lepiotaceous fungiculture, and none oí the Apterostigma lineages in the monophyletic group of pterulaceous fungiculturists are known to have reverted back to lepiotaceous fungiculture. The origin of pterulaceous fungiculture in attine ants may have involved a unique transition from the ancestral cultivation of litter-decomposing lepiotaceous fungi to the cultivation of wood-decomposing pterulaceous fungi. Phylogenetic analyses further indicate that distantly related Apterostigma ant species sometimes cultivate the same cultivar lineage, indicating evolutionarily frequent, and possibly ongoing, exchanges of fungal cultivars between Apterostigma ant species. The pterulaceous cultivars form two sister clades, and different Apterostigma ant lineages are invariably associated with, and thus specialized on, only one of the two cultivar clades. However, within clades Apterostigma ant species are able to switch between fungi. This pattern of broad specialization by attine ants on defined cultivar clades, coupled with flexible switching between fungi within cultivar clades, is also found in other attine lineages and appears to be a general phenomenon of fungicultural evolution in all fungus-growing ants. Fungus-growing ants (Formicidae, tribe Attini) are well In contrast, the lower attine ants (eight genera, including the known for their habit of cultivating fungi for food, a behavior genus Apterostigma) cultivate morphologically unspecialized that originated in the common ancestor of attine ants about fungi (called G3 fungi) from which the Gl fungi arose (S.A. 50-60 million years ago (Wilson 1971; Schultz and Meier Rehner, pers. comm.; P. Abbott, N. Gerardo, and U. Mueller, 1995; Mueller et al. 2001 ). Since then, attine ants have un-unpubl. data), and which are therefore evolutionarily pledergone an adaptive radiation that has resulted in 13 extant siomorphic with respect to the G1 group (Chapela et al. 1994 ; genera containing more than 210 described species, all ob-Mueller et al. 1998). There is only one known exception to ligately dependent on the farming of mutualistic fungi, usu-this lepiotaceous cultivation of Gl and G3 fungi: some but ally in nests excavated in the soil (Schultz and Meier 1995; not all ant species in the genus Apterostigma cultivate fungi Weiterer et al. 1998; Brandâo and Mayhé-Nunes 2001). Do-that are distantly related to the Lepiotaceae (Fig. 1) . These mestication of fungi from free-living populations, as well as so-called G2 fungi are characterized by a unique micromorcultivar exchanges between ant species in the same and in phology (Chapela et al. 1994) and are cultivated by their different genera, have occurred multiple times during the Apterostigma hosts in hanging "veiled gardens" in which evolutionary history of the attine ants (Chapela et al. 1994 ; the cultivated fungus also forms a thin mycelial envelope that Mueller et al. 1998; Mueller 2002; Mueller and Gerardo surrounds the garden proper. G2 fungi were grouped into the 2002). family Tricholomataceae (Basidiomycota: Agaricales) in two Distinct modes of fungal cultivation characterize different previous phylogenetic analyses (Chapela et al. 1994 ; Monattine ant lineages. The great majority of species cultivate calvo et al. 2000), but recent work suggests a close affinity lepiotaceous fungi (Basidiomycota: Agaricales: Lepiotaceae) with the family Pterulaceae (Basidiomycota: Agaricales) from one of two distinct groups, termed Gl and G3 fungi by (Munkacsi et al. 2004) . Chapela et al. (1994) . The fungi of the higher attine ants This study elucidates the origin and evolution of the cul-(calledGl fungi, zcultivated by the ant genera Sencomyrmex, tivation of pterulaceous fungi by ants in the genus Apter-Trachymyrmex, and the leafcutter ants Atta and Acromyrmex) ostigma. Phylogenetic analyses of both fungi and ants support possess several derived morphological features that probably a single origin of pterulaceous fungal cultivation. Our analarose during a long history of coevolution with attine ants, y sis divides the pterulaceous cultivars into two distinct 2252
doi:10.1554/03-203 fatcat:fap6wthwz5gehbeuu5xw6vzoci

EVOLUTION OF ANT-CULTIVAR SPECIALIZATION AND CULTIVAR SWITCHING IN APTEROSTIGMA FUNGUS-GROWING ANTS

Palle Villesen, Ulrich G. Mueller, Ted R. Schultz, Rachelle M. M. Adams, Amy C. Bouck
2004 Evolution  
Almost all of the more than 200 species of fungus-growing ants (Formicidae: Attini) cultivate litterdecomposing fungi in the family Lepiotaceae (Basidiomycota: Agaricales). The single exception to this rule is a subgroup of ant species within the lower attine genus Apterostigma, which cultivate pterulaceous fungi distantly related to the Lepiotaceae. Comparison of cultivar and ant phylogenies suggests that a switch from lepiotaceous to pterulaceous fungiculture occurred only once in the history
more » ... of the fungus-growing ants. This unique switch occurred after the origin of the genus Apterostigma, such that the basal Apterostigma lineages retained the ancestral attine condition of lepiotaceous fungiculture, and none oí the Apterostigma lineages in the monophyletic group of pterulaceous fungiculturists are known to have reverted back to lepiotaceous fungiculture. The origin of pterulaceous fungiculture in attine ants may have involved a unique transition from the ancestral cultivation of litter-decomposing lepiotaceous fungi to the cultivation of wood-decomposing pterulaceous fungi. Phylogenetic analyses further indicate that distantly related Apterostigma ant species sometimes cultivate the same cultivar lineage, indicating evolutionarily frequent, and possibly ongoing, exchanges of fungal cultivars between Apterostigma ant species. The pterulaceous cultivars form two sister clades, and different Apterostigma ant lineages are invariably associated with, and thus specialized on, only one of the two cultivar clades. However, within clades Apterostigma ant species are able to switch between fungi. This pattern of broad specialization by attine ants on defined cultivar clades, coupled with flexible switching between fungi within cultivar clades, is also found in other attine lineages and appears to be a general phenomenon of fungicultural evolution in all fungus-growing ants. Fungus-growing ants (Formicidae, tribe Attini) are well In contrast, the lower attine ants (eight genera, including the known for their habit of cultivating fungi for food, a behavior genus Apterostigma) cultivate morphologically unspecialized that originated in the common ancestor of attine ants about fungi (called G3 fungi) from which the Gl fungi arose (S.A. 50-60 million years ago (Wilson 1971; Schultz and Meier Rehner, pers. comm.; P. Abbott, N. Gerardo, and U. Mueller, 1995; Mueller et al. 2001 ). Since then, attine ants have un-unpubl. data), and which are therefore evolutionarily pledergone an adaptive radiation that has resulted in 13 extant siomorphic with respect to the G1 group (Chapela et al. 1994 ; genera containing more than 210 described species, all ob-Mueller et al. 1998). There is only one known exception to ligately dependent on the farming of mutualistic fungi, usu-this lepiotaceous cultivation of Gl and G3 fungi: some but ally in nests excavated in the soil (Schultz and Meier 1995; not all ant species in the genus Apterostigma cultivate fungi Weiterer et al. 1998; Brandâo and Mayhé-Nunes 2001). Do-that are distantly related to the Lepiotaceae (Fig. 1) . These mestication of fungi from free-living populations, as well as so-called G2 fungi are characterized by a unique micromorcultivar exchanges between ant species in the same and in phology (Chapela et al. 1994) and are cultivated by their different genera, have occurred multiple times during the Apterostigma hosts in hanging "veiled gardens" in which evolutionary history of the attine ants (Chapela et al. 1994 ; the cultivated fungus also forms a thin mycelial envelope that Mueller et al. 1998; Mueller 2002; Mueller and Gerardo surrounds the garden proper. G2 fungi were grouped into the 2002). family Tricholomataceae (Basidiomycota: Agaricales) in two Distinct modes of fungal cultivation characterize different previous phylogenetic analyses (Chapela et al. 1994 ; Monattine ant lineages. The great majority of species cultivate calvo et al. 2000), but recent work suggests a close affinity lepiotaceous fungi (Basidiomycota: Agaricales: Lepiotaceae) with the family Pterulaceae (Basidiomycota: Agaricales) from one of two distinct groups, termed Gl and G3 fungi by (Munkacsi et al. 2004) . Chapela et al. (1994) . The fungi of the higher attine ants This study elucidates the origin and evolution of the cul-(calledGl fungi, zcultivated by the ant genera Sencomyrmex, tivation of pterulaceous fungi by ants in the genus Apter-Trachymyrmex, and the leafcutter ants Atta and Acromyrmex) ostigma. Phylogenetic analyses of both fungi and ants support possess several derived morphological features that probably a single origin of pterulaceous fungal cultivation. Our analarose during a long history of coevolution with attine ants, y sis divides the pterulaceous cultivars into two distinct 2252
doi:10.1111/j.0014-3820.2004.tb01601.x pmid:15562688 fatcat:74lcyfywrrcy3fq7wszvnxouze

From genotype to phenotype: maintenance of a chemical polymorphism in the context of high geneflow [article]

Bodil K Ehlers, Gauthier Perrine, Palle Villesen, Sylvain Santoni, John D Thompson, Thomas Bataillon
2020 bioRxiv   pre-print
A major question in evolution is how to maintain many adaptive phenotypes within a species. In Mediterranean wild thyme, a staggering number of discrete chemical phenotypes (chemotypes) coexist in close geographic proximity. Plant chemotypes are defined by the dominant monoterpene produced in their essential oil. We study the genetics of six distinct chemotypes nested within two well established ecotypes. Ecotypes, and chemotypes within ecotypes, are spatially segregated, and their distribution
more » ... tracks local differences in the abiotic environment. The ecotypes have undergone a rapid shift in distribution associated with current climate change. Here, combining genomic, phenotypic, and environmental data, we show how the genetics of ecotype determination can allow for such rapid evolutionary response despite high gene flow among ecotypes. Variation in three terpene-synthase loci explains almost all variation in ecotype identity, with one single locus accounting for as much as 78% of it. Phenotypic selection on ecotypes combined with low segregating genotypic redundancy and tight genetic determination leaves a clear footprint at the genomic level: alleles associated with ecotype identity track environmental variation despite extensive gene flow. Different chemotypes, nested within each ecotype, also track environmental variation. However, in contrast to ecotypes, chemotype identity is determined by more loci and show a wider range of genotypic redundancy, which dilutes the impact of phenotypic selection on alleles associated with different chemotypes. Identifying the genetics behind this polymorphism in thyme is a crucial step towards understanding the maintenance of this widespread chemical polymorphism found in many aromatic Lamiaceae.
doi:10.1101/2020.09.24.299651 fatcat:spi3hhsh6zcwbg3svpvwwx4ci4
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