Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude

Background

The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial.

Results

Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions.

Conclusions

Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.     

Aging bone score and climatic factors

Hand radiograms for osseographic assessment of bone aging status were taken from more than 7,500 individuals residing in 31 different localities and belonging to 20 ethnic groups. Multiple regression analysis was used to evaluate possible associations between bone aging parameters and several climatic factors, to wit: hours of daylight in January and July, average monthly humidity and partial vapor pressure in January and July, and one climatic index pertaining to comfort conditions in life, namely, the Bioclimatic Index of Severity of Climatic Regime. Multiple regression analysis clearly pointed to significant correlations between climatic characteristics and indices defining the relative rate of bone aging in humans; it also evinced an independent contribution of July's humidity and January's mean temperature to earliest age at which first signs of bone aging can be found. In sum, there are grounds for concluding that temperature and humidity are key factors in triggering initial bone changes in individuals within the human populations prone to environmental effects. The combination of humidity and temperature with other factors which reflect the sharpness of the interseasonal differences in climatic conditions predispose the populations to early onset of bone changes. Am J Phys Anthropol 106:349–359, 1998. © 1998 Wiley-Liss, Inc.     

The Classical Assortative Mating Process when more than one Continuous Characteristic is Considered

In this article we give a general proof for the existence of the equilibrium position for the joint phenotypic distribution of several continuous characteristics, in a population which reproduces assortatively, and wherein generations are overlapping. This model is a more realistic one for human populations, compared with models arising from consideration of a single characteristic. By placing realistic conditions on the assortation process in the equilibrium position it is found that the consequences are even less realistic and less satisfactory compared with conclusions from single (continuous) characteristic models involving assortative mating. This suggests that a different approach to modelling the assortation process may be required, and this is discussed alsewhere (WILSON, 1981).     

Rapid differentiation of experimental populations of wheat for heading time in response to local climatic conditions

BACKGROUND AND AIMS: Dynamic management (DM) of genetic resources aims at maintaining genetic variability between different populations evolving under natural selection in contrasting environments. In 1984, this strategy was applied in a pilot experiment on wheat (Triticum aestivum). Spatio-temporal evolution of earliness and its components (partial vernalization sensitivity, daylength sensitivity and earliness per se that determines flowering time independently of environmental stimuli) was investigated in this multisite and long-term experiment. METHODS: Heading time of six populations from the tenth generation was evaluated under different vernalization and photoperiodic conditions. KEY RESULTS: Although temporal evolution during ten generations was not significant, populations of generation 10 were genetically differentiated according to a north-south latitudinal trend for two components out of three: partial vernalization sensitivity and narrow-sense earliness. CONCLUSIONS: It is concluded that local climatic conditions greatly influenced the evolution of population earliness, thus being a major factor of differentiation in the DM system. Accordingly, a substantial proportion (approximately 25 %) of genetic variance was distributed among populations, suggesting that diversity was on average conserved during evolution but was differently distributed by natural selection (and possibly drift). Earliness is a complex trait and each genetic factor is controlled by multiple homeoalleles; the next step will be to look for spatial divergence in allele frequencies.     

ABO blood groups in Peruvian mummies. I. An evaluation of techniques.

Blood groups of Peruvian mummies of known origin were determined by three different methods: agglutination-inhibition, induction of antibody production and mixed cell agglutination. The three techniques gave identical results, but the last two were useful in establishing the presence of H (O) antigen, while the first technique would not. The results indicate the presence of A, B, AB and O blood groups in America prior to known European contact. This suggests the need for a revision of concepts of blood groups in the American Indian.     

Adaptation in isolated populations: when does it happen and when can we tell?

Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here, we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affect the ability of outlier scans for selection to identify adaptive alleles using both single‐site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur and yet the adaptive variants are most likely to derive from a single ancestor (a ‘hard’ selective sweep); in this zone, four commonly used statistics detect selection with high power. Real‐world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole‐genome sequencing of differentiated populations.     

Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12

Detailed population data were obtained on the distribution of novel biallelic markers that finely dissect the human Y-chromosome haplogroup E-M78. Among 6,501 Y chromosomes sampled in 81 human populations worldwide, we found 517 E-M78 chromosomes and assigned them to 10 subhaplogroups. Eleven microsatellite loci were used to further evaluate subhaplogroup internal diversification. The geographic and quantitative analyses of haplogroup and microsatellite diversity is strongly suggestive of a northeastern African origin of E-M78, with a corridor for bidirectional migrations between northeastern and eastern Africa (at least 2 episodes between 23.9-17.3 ky and 18.0-5.9 ky ago), trans-Mediterranean migrations directly from northern Africa to Europe (mainly in the last 13.0 ky), and flow from northeastern Africa to western Asia between 20.0 and 6.8 ky ago. A single clade within E-M78 (E-V13) highlights a range expansion in the Bronze Age of southeastern Europe, which is also detected by haplogroup J-M12. Phylogeography pattern of molecular radiation and coalescence estimates for both haplogroups are similar and reveal that the genetic landscape of this region is, to a large extent, the consequence of a recent population growth in situ rather than the result of a mere flow of western Asian migrants in the early Neolithic. Our results not only provide a refinement of previous evolutionary hypotheses but also well-defined time frames for past human movements both in northern/eastern Africa and western Eurasia.     

Human Molecular Genetics: Research in Medical Genomics and Ethnogenomics

The review covers selected research topics in the fields of medical and ethnic genomics conducted at the Department of Molecular Bases of Human Genetics, the Institute of Molecular Genetics. Primary concern is given to genetic causes of monogenic neurological disorders, among them hepatolenticular degeneration (Wilson disease), torsion dystonia, and myotonic dystrophy. Results of polymorphic DNA marker surveys in Russia and neighboring countries are also presented.