A "Copernican" reassessment of the human mitochondrial DNA tree from its root

Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This “Copernican” reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.     

A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

Several studies examined the fine-scale structure of human genetic variation in Europe. However, the European sets analyzed represent mainly northern, western, central, and southern Europe. Here, we report an analysis of approximately 166,000 single nucleotide polymorphisms in populations from eastern (northeastern) Europe: four Russian populations from European Russia, and three populations from the northernmost Finno-Ugric ethnicities (Veps and two contrast groups of Komi people). These were compared with several reference European samples, including Finns, Estonians, Latvians, Poles, Czechs, Germans, and Italians. The results obtained demonstrated genetic heterogeneity of populations living in the region studied. Russians from the central part of European Russia (Tver, Murom, and Kursk) exhibited similarities with populations from central–eastern Europe, and were distant from Russian sample from the northern Russia (Mezen district, Archangelsk region). Komi samples, especially Izhemski Komi, were significantly different from all other populations studied. These can be considered as a second pole of genetic diversity in northern Europe (in addition to the pole, occupied by Finns), as they had a distinct ancestry component. Russians from Mezen and the Finnic-speaking Veps were positioned between the two poles, but differed from each other in the proportions of Komi and Finnic ancestries. In general, our data provides a more complete genetic map of Europe accounting for the diversity in its most eastern (northeastern) populations.     

Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families

DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.     

Factors affecting cold hardiness in the small striped flea beetle, Phyllotreta undulata

The striped flea beetle, Phyllotreta undulata Kutschera (Coleoptera: Chrysomelidae), is a pest of cruciferous crops. It overwinters as an adult. During winter in northern European countries, such as Estonia, it is subject to sometimes severe temperatures that may fluctuate daily, over the season, and between seasons. The objective of this study was to investigate factors that affect its cold hardiness. In a series of five experiments, the effects of food plant, starvation, and acclimatization on the beetles’ ability to supercool and survive exposure to sub‐zero temperatures was investigated. The supercooling points (SCP) of overwintered beetles field‐collected from white mustard and Indian mustard differed from those caught from white cabbage and oilseed rape, but these differences disappeared after a 4‐day period of starvation at room temperature, indicating that gut content probably influences the potential to supercool. The duration and temperature of acclimation affected SCP in overwintered beetles. The decrease in SCP was more rapid at 22 °C than at 0 °C, probably because of faster dehydration and gut evacuation at the higher temperature. Acclimation at 0 °C for a week increased the ability of overwintered beetles to survive sub‐zero temperatures, lowering both SCP and lower lethal temperature (LLT₅₀). Some pre‐freeze mortality occurred; SCP and LLT₅₀ were correlated but the latter was a constant 3 °C higher than the former. The SCP of field‐collected pre‐winter beetles decreased gradually during the autumn. It also decreased when field‐collected pre‐winter beetles were acclimated at 0 °C in the laboratory, attaining its lowest level after 18 days. Phyllotreta undulata is well‐adapted to unstable and sometimes severe winter conditions; its high potential to supercool enhances its cold hardiness and ability to survive short periods at sub‐zero temperatures although it cannot survive freezing of its body fluids.     

Effective generation of transgenic mice by Bovine papillomavirus type 1 based self-replicating plasmid that is maintained as extrachromosomal genetic element in three generations of animals

The objective of our study was to analyze the efficiency and the properties of the inheritance of the Bovine papillomavirus type 1 (BPV1) replicator-based plasmid used as vector system for generation of transgenic animals. Previously, we have characterized a series of self-replicating plasmid vectors containing all viral factors necessary and sufficient for stable extrachromosomal replication of the BPV1 genome in the tissue culture system. We also demonstrated that the designed replicating vector system has a considerable benefit in the transgene expression, if compared to the regular expression vector. The vector, which showed the highest stability and maintenance function in the tissue culture was chosen for generation of the transgenic mice by pronuclear injections of the circular supercoiled plasmid. This method resulted in successful production of transgenic animals. Transmission efficiency of the vectors into the F(1) generation of animals varied between 0 and 48%, whereas transmission into the F(2) generation was uniformly near 50%. The maintenance of the vector-plasmids in the F(2) generation of transgenic animals as extrachromosomal genetic element was demonstrated by rescue of the plasmid into the Escherichia coli.     

Estonian Genome Project--before the take-off and take-off

I will give an overview of the preparations of the EGP including all aspects of the project and current satus of the pilot phase, describe the informatics part of the project together with other aspects (legal, ethical, logistics, financial etc.) and where we stand in terms of population genetics and genotyping technology in order to start using the sample collection for case--control studies for revealing the genetic component of the common diseases.