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Detailed information on the Alu loci. The Microsoft Excel file contains detailed information abou... more Detailed information on the Alu loci. The Microsoft Excel file contains detailed information about the exact lengths of the amplicons for every genomic Alu locus investigated in this study. Additionally shown are the lengths of the A-tails and the Target Site Duplications (TSD), as well as the sequences of the TSDs. (XLS 36Â kb)
List of all STR-typing results for the prehistoric individuals. The Microsoft Excel file contains... more List of all STR-typing results for the prehistoric individuals. The Microsoft Excel file contains four sheets with all STR-typing results for all prehistoric individuals investigated in this study. Sheets 1-3 contain the results of all 13 STR systems that were used for kinship calculation. The fourth sheet contains the STR-typing results that were obtained to check the authenticity of the DNA extracts. (XLSX 23Â kb)
Genomic locations of all 30 Alu loci. This file contains precise locations of all 30 Alu loci inv... more Genomic locations of all 30 Alu loci. This file contains precise locations of all 30 Alu loci investigated. (XLS 37Â kb)
List of all Alu primers used. The Microsoft Excel file contains all primer sequences that were us... more List of all Alu primers used. The Microsoft Excel file contains all primer sequences that were used in this study. (XLSX 10Â kb)
Sequences of randomly selected loci. This file contains sequencing results of 3 randomly selected... more Sequences of randomly selected loci. This file contains sequencing results of 3 randomly selected loci with 5 sequences in total to check for authenticity. (PDF 18Â kb)
doi:10.1038/nature12326 Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga
Zoomorphology, 1998
Plagiostomum lemani possesses extremely specialized intraepidermal sensory cells. These obvious p... more Plagiostomum lemani possesses extremely specialized intraepidermal sensory cells. These obvious photoreceptors, which are not visible with the light microscope, are ciliary aggregations located in an intracellular cavity. The numerous spiralled cilia have the classic 9 × 2 + 2 arrangement at their base and a modified pattern of microtubules apically. The discovered differentiations do not show a connection to the surface. Neither mantle cells nor pigment cells have been found. The structural similarities with other epidermal photoreceptors of species among the different taxa of free-living Plathelminthes are outlined. Besides the larval stages of the taxon Polycladida known so far, the same kind of light-sensing photoreceptive cell has never been described in any other species of the Plathelminthes.& b d y :
ABSTRACT The western Amazonian treefrog Dendropsophus bifurcus (Andersson, 1945) is not as widesp... more ABSTRACT The western Amazonian treefrog Dendropsophus bifurcus (Andersson, 1945) is not as widespread as previously thought. Specimens from Bolivia and southern Peru, previously assigned to that species, are distinct and differ in calls, colouration and behaviour. The new species described here can be most easily distinguished from D. bifurcus from the northwestern part of the Amazon Basin in Colombia, Ecuador and northern Peru by its tibial colour pattern, and from the sympatric D. leucophyllatus by adult size and ventral colouration. Molecular data (12S and 16S rRNA) indicate that this Amazonian species is not even closely related to the Amazonian D. bifurcus, but has its closest relative, D. elegans, in the Atlantic Forest region of southeastern Brazil. Dendropsophus bifurcus appears to be only one of various species believed to be widespread in Amazonia, but actually consisting of groups of cryptic species that may not even, as in D. bifurcus and the new species, be closely related. We also discuss the inclusion of D. anceps in the D. leucophyllatus species group.
Genes, Jan 12, 2012
One of the most unexpected insights that followed from the completion of the human genome a decad... more One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.
Diversity, Oct 25, 2017
The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), h... more The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400-500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.
Journal of Molecular Evolution, Jun 29, 2005
Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic i... more Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-ntlong numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model-the nucleotide composition-is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the ''common ancestor'' of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.
Mobile DNA, 2016
Background: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for p... more Background: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter. Results: For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000 years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500 bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150 bp. Conclusions: Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome.
Detailed information on the Alu loci. The Microsoft Excel file contains detailed information abou... more Detailed information on the Alu loci. The Microsoft Excel file contains detailed information about the exact lengths of the amplicons for every genomic Alu locus investigated in this study. Additionally shown are the lengths of the A-tails and the Target Site Duplications (TSD), as well as the sequences of the TSDs. (XLS 36Â kb)
List of all STR-typing results for the prehistoric individuals. The Microsoft Excel file contains... more List of all STR-typing results for the prehistoric individuals. The Microsoft Excel file contains four sheets with all STR-typing results for all prehistoric individuals investigated in this study. Sheets 1-3 contain the results of all 13 STR systems that were used for kinship calculation. The fourth sheet contains the STR-typing results that were obtained to check the authenticity of the DNA extracts. (XLSX 23Â kb)
Genomic locations of all 30 Alu loci. This file contains precise locations of all 30 Alu loci inv... more Genomic locations of all 30 Alu loci. This file contains precise locations of all 30 Alu loci investigated. (XLS 37Â kb)
List of all Alu primers used. The Microsoft Excel file contains all primer sequences that were us... more List of all Alu primers used. The Microsoft Excel file contains all primer sequences that were used in this study. (XLSX 10Â kb)
Sequences of randomly selected loci. This file contains sequencing results of 3 randomly selected... more Sequences of randomly selected loci. This file contains sequencing results of 3 randomly selected loci with 5 sequences in total to check for authenticity. (PDF 18Â kb)
doi:10.1038/nature12326 Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga
Zoomorphology, 1998
Plagiostomum lemani possesses extremely specialized intraepidermal sensory cells. These obvious p... more Plagiostomum lemani possesses extremely specialized intraepidermal sensory cells. These obvious photoreceptors, which are not visible with the light microscope, are ciliary aggregations located in an intracellular cavity. The numerous spiralled cilia have the classic 9 × 2 + 2 arrangement at their base and a modified pattern of microtubules apically. The discovered differentiations do not show a connection to the surface. Neither mantle cells nor pigment cells have been found. The structural similarities with other epidermal photoreceptors of species among the different taxa of free-living Plathelminthes are outlined. Besides the larval stages of the taxon Polycladida known so far, the same kind of light-sensing photoreceptive cell has never been described in any other species of the Plathelminthes.& b d y :
ABSTRACT The western Amazonian treefrog Dendropsophus bifurcus (Andersson, 1945) is not as widesp... more ABSTRACT The western Amazonian treefrog Dendropsophus bifurcus (Andersson, 1945) is not as widespread as previously thought. Specimens from Bolivia and southern Peru, previously assigned to that species, are distinct and differ in calls, colouration and behaviour. The new species described here can be most easily distinguished from D. bifurcus from the northwestern part of the Amazon Basin in Colombia, Ecuador and northern Peru by its tibial colour pattern, and from the sympatric D. leucophyllatus by adult size and ventral colouration. Molecular data (12S and 16S rRNA) indicate that this Amazonian species is not even closely related to the Amazonian D. bifurcus, but has its closest relative, D. elegans, in the Atlantic Forest region of southeastern Brazil. Dendropsophus bifurcus appears to be only one of various species believed to be widespread in Amazonia, but actually consisting of groups of cryptic species that may not even, as in D. bifurcus and the new species, be closely related. We also discuss the inclusion of D. anceps in the D. leucophyllatus species group.
Genes, Jan 12, 2012
One of the most unexpected insights that followed from the completion of the human genome a decad... more One of the most unexpected insights that followed from the completion of the human genome a decade ago was that more than half of our DNA is derived from transposable elements (TEs). Due to advances in high throughput sequencing technologies it is now clear that TEs comprise the largest molecular class within most metazoan genomes. TEs, once categorised as "junk DNA", are now known to influence genomic structure and function by increasing the coding and non-coding genetic repertoire of the host. In this way TEs are key elements that stimulate the evolution of metazoan genomes. This review highlights several lines of TE research including the horizontal transfer of TEs through host-parasite interactions, the vertical maintenance of TEs over long periods of evolutionary time, and the direct role that TEs have played in generating morphological novelty.
Diversity, Oct 25, 2017
The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), h... more The human-specific Alu elements, belonging to the class of Short INterspersed Elements (SINEs), have been shown to be a powerful tool for population genetic studies. An earlier study in this department showed that it was possible to analyze Alu presence/absence in 3000-year-old skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. We developed duplex Alu screening PCRs with flanking primers for two Alu elements, each combined with a single internal Alu primer. By adding an internal primer, the approximately 400-500 bp presence signals of Alu elements can be detected within a range of less than 200 bp. Thus, our PCR approach is suited for highly fragmented ancient DNA samples, whereas NGS analyses frequently are unable to handle repetitive elements. With this analysis system, we examined remains of 12 individuals from the Lichtenstein cave with different degrees of DNA degradation. The duplex PCRs showed fully informative amplification results for all of the chosen Alu loci in eight of the 12 samples. Our analysis system showed that Alu presence/absence analysis is possible in samples with different degrees of DNA degradation and it reduces the amount of valuable skeletal material needed by a factor of four, as compared with a singleplex approach.
Journal of Molecular Evolution, Jun 29, 2005
Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic i... more Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-ntlong numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model-the nucleotide composition-is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the ''common ancestor'' of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.
Mobile DNA, 2016
Background: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for p... more Background: As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter. Results: For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000 years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500 bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150 bp. Conclusions: Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome.