Patterns Of DNA Variation Research Articles

Patterns of DNA variation between the autosomes, the X chromosome and the Y chromosome in Bos taurus genome

The new ARS-UCD1.2 assembly of the bovine genome has considerable improvements over the previous assembly and thus more accurate identification of patterns of genetic variation can be achieved with it. We explored differences in genetic variation between autosomes, the X chromosome, and the Y chromosome. In particular, variant densities, annotations, lengths (only for InDels), nucleotide divergence, and Tajima’s D statistics between chromosomes were considered. Whole-genome DNA sequences of 217 individuals representing different cattle breeds were examined. The analysis included the alignment to the new reference genome and variant identification. 23,655,295 SNPs and 3,758,781 InDels were detected. In contrast to autosomes, both sex chromosomes had negative values of Tajima’s D and lower nucleotide divergence. That implies a correlation between nucleotide diversity and recombination rate, which is obviously reduced for sex chromosomes. Moreover, the accumulation of nonsynonymous mutations on the Y chromosome could be associated with loss of recombination. Also, the relatively lower effective population size for sex chromosomes leads to a lower expected density of variants.

Phylogenetic relationships and taxonomic issues in Gastridium (Poaceae) inferred from plastid and nuclear DNA sequence analysis

Gastridium P. Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, whose species number and diversity are still imperfectly known. We examined patterns of DNA diversity at two plastid (trnH-psbA, trnL-F) and one nuclear (ITS) DNA markers in 44 individuals of the four taxa (Gastridium lainzii, G. phleoides, G. scabrum, G. ventricosum) recently recognised by different authors, based on morpho-ecological descriptors. Diversity data were explored with multiple statistical and phylogenetic tools, and integrated with available GenBank sequences of Gastridium and closely related genera. Despite the limited variability detected, evidence of within-taxon genetic cohesion and estimates of molecular divergence comparable with those of species in the same subtribal lineage (Agrostidinae) were recovered. The identified plastid genealogies are congruent with a subdivision of the genus into four distinct species, coherently with collected morphological descriptors. Phylogenetic reconstructions with ITS were less corresponding to the four taxa, possibly due to reticulation and polyploidization. The broader plastid and nuclear tree topologies were consistent with previous assessments, highlighting the overall little resolution of species and genera within Agrostidinae, and the close relationships shared by Gastridium and Triplachne. The hypothesis of closely related, but separately evolving, lineages within Gastridium is discussed, suggesting a re-evaluation of its current taxonomy.

Footprints of divergent evolution in two Na+/H+ type antiporter gene families (NHX and SOS1) in the genus Populus.

Populus, a deciduous tree species of major economic and ecological value, grows across the range in which trees are distributed in the Northern Hemisphere. Patterns of DNA variation are often used to identify the evolutionary forces shaping the genotypes of distinctive species lineages. Sodium/hydrogen (Na+/H+) antiporter genes have been shown to play a central role in plant salt tolerance. Here, we analyzed DNA nucleotide polymorphisms in the Na+/H+ antiporter (NHX and SOS1) gene families across 30 different Populus species using several methods of phylogenetic analysis and functional verification. NHX and SOS1 gene families in the genus Populus have expanded from the state in their common ancestors by duplication events, and their distinct lineages have been retained. Signals of positive selection at certain amino acid sites in different members of the Na/H antiporter gene families show that the dynamics that drive the evolution of each gene vary. SOS1 has undergone duplication in Populus euphratica and been subjected to adaptive evolution in section Turanga; the paralog of PeSOS1 (PeSOS1.2) can complement the Escherichia coli mutant EP432; and the expression pattern of PeSOS1.2 is different from that of PeSOS1, a fact which may have been beneficial for P. euphratica, conferring a fitness advantage in saline habitats. The divergent evolution of the individual members of the NHX and SOS1 gene families is likely to have been influenced by the varied ecological and environmental niches occupied by the different poplar species, giving rise to evolutionary footprints that reflect the specific functions and subcellular localizations of the proteins encoded by these genes.

Massive parallel sequencing of human whole mitochondrial genomes with Ion Torrent technology: an optimized workflow for Anthropological and Population Genetics studies

Investigation of human mitochondrial DNA variation patterns and phylogeny has been extensively used in Anthropological and Population Genetics studies and sequencing the whole mitochondrial genome is progressively becoming the gold standard. Among the currently available massive parallel sequencing technologies, Ion Torrent™ semiconductor sequencing represents a promising approach for such studies. Nevertheless, an experimental protocol conceived to enable the achievement of both as high as possible yield and of the most homogeneous sequence coverage through the whole mitochondrial genome is still not available. The present work was thus aimed at improving the overall performance of whole mitochondrial genomes Ion Torrent™ sequencing, with special focus on the capability to obtain robust coverage and highly reliable variants calling. For this purpose, a series of cost-effective modifications in standard laboratory workflows was fine-tuned to optimize them for medium- and large-scale population studies. A total of 54 human samples were thus subjected to sequencing of the whole mitochondrial genome with the Ion Personal Genome Machine™ System in four distinct experiments and using Ion 314 chips. Seven of the selected samples were also characterized by means of conventional Sanger sequencing for the sake of comparison. Obtained results demonstrated that the implemented optimizations had definitely improved sequencing outputs in terms of both variants calling efficiency and coverage uniformity, enabling to setup an effective and accurate protocol for whole mitochondrial genome sequencing and a considerable reduction in experimental time consumption and sequencing costs.

Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life.

DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function. Overall, patterns of amino acid variation suggest convergent or parallel evolution at the protein level connected to the transition into a parasitic life style. Denser sampling of two diverse insect taxa revealed that the beetles (Coleoptera) show more amino acid variation than the butterflies and moths (Lepidoptera), indicating fundamental difference in patterns of molecular evolution in COI. Several amino acid sites were found to be under notably strong purifying selection in Lepidoptera as compared to Coleoptera. Overall, these findings demonstrate the utility of the global DNA barcode library to extend far beyond identification and taxonomy, and will hopefully be followed by a multitude of work.

Corrigendum: Levels and patterns of DNA variation in two sympatric mangrove species, Rhizophora apiculata and R. mucronata from Thailand [Genes Genet. Syst. (2009) 84, p. 277-286

The last sentence on p. 286 In both R. apiculata and R. mucronata pollen release is very limited (Kusmana, personal communication), which could cause increased levels of inbreeding. should be deleted.

Assessing Human Variation Data for Signatures of Natural Selection

In this article, we highlight some of the different types of natural selection, their effects on patterns of DNA variation, and some of the statistical tests that are commonly used to detect such effects. We also explain some of the relative strengths and weaknesses of different strategies that can be used to detect signatures of natural selection at individual loci. These strategies are illustrated by their application to empirical data from gene variants that are often associated with differences in disease susceptibility. We briefly outline some of the methods proposed to scan the genome for evidence of selection. Finally, we discuss some of the problems associated with identifying signatures of selection and with making inferences about the nature of the selective process.

Levels and patterns of DNA variation in two sympatric mangrove species, Rhizophora apiculata and R. mucronata from Thailand

In mangrove species the past geomorphic changes in coastal regions and reproductive systems are important factors of their distribution and genetic structure of populations. However, very little is known about the levels of genetic variation of Rhiozophora species in Southeast Asia. In this study, we surveyed levels and patterns of genetic variation as well as population structure of two sympatric mangrove species, Rhizophora apiculata and R. mucronata in Thailand, using five nuclear genes and two cpDNA regions. In all investigated DNA regions, nucleotide variation within species was low, while nucleotide divergence between the two species was considerable. The nuclear genes evolved 10 times faster than the cpDNA regions. In both R. apiculata and R. mucronata, significant positive F(IS) values were found, indicating deviation from Hardy-Weinberg proportions and a deficiency of heterozygotes. In both species, we found significant genetic differentiation between populations. However, the pattern of population differentiation (F(ST)) of R. apiculata differed from that of R. mucronata. Our results suggest that the two investigated species have different demographic history, even though they are sympatric and have similar reproductive systems.

Homo in the middle pleistocene: Hypodigms, variation, and species recognition

AbstractIt is generally accepted that modern humans evolved in Africa. This consensus has emerged in the last two decades, as molecular evidence has been coupled with findings from paleontology and prehistory. Patterns of DNA variation in living populations, morphology of fossils, and archeological traces can all be read to show that our species has deep roots in Africa and began to disperse into other regions only late in the Pleistocene. There are still questions about the timing of these dispersals and the extent to which modern people replaced or exchanged genes with other, more archaic groups, but new problems are now coming more clearly into focus. These relate to the ancestry of Homo sapiens in the Middle Pleistocene. In this essay, I emphasize the evidence available from Middle Pleistocene localities in Africa and Europe, exploring variation among individuals, composition of hypodigms, species‐level taxonomy, and evolutionary relationships of the hominin populations. One obvious difficulty is that the fossils are scarce. For the most part, only incomplete crania are available from African localities. The record is more comprehensive for the Sima de los Huesos in Spain, but principally crania and jaws are known from other European sites. This means that skull traits and measurements must provide the basis for sorting individuals to groups and building differential diagnoses. For much of the material, dating is still poorly controlled, although a few of the most important assemblages can now be placed more securely within a Middle Pleistocene chronological framework. Despite these constraints, it is possible to point toward tentative solutions.

Polymorphism in the activity of human crossover hotspots independent of local DNA sequence variation

Meiotic crossovers in the human genome cluster into highly localized hotspots identifiable indirectly from patterns of DNA diversity and directly by high-resolution sperm typing. Little is known about factors that control hotspot activity and the apparently rapid turnover of hotspots during recent evolution. Clues can, however, be gained by characterizing variation in sperm crossover activity between men. Previous studies have identified single nucleotide polymorphisms within hotspots that appear to suppress crossover activity and which may be involved in hotspot attenuation/extinction. We now analyse a closely spaced pair of hotspots (MSTM1a, MSTM1b) on chromosome 1q42.3, the former being a candidate for a young hotspot that has failed to leave a significant mark on haplotype diversity. Extensive surveys of different men revealed substantial polymorphism in sperm crossover frequencies at both hotspots, but with very different patterns of variation. Hotspot MSTM1b was active in all men tested but with widely differing crossover frequencies. In contrast, MSTM1a was active in only a few men and appeared to be recombinationally inert in the remainder, providing the first example of presence/absence polymorphism of a human hotspot. Haplotype analysis around both hotspots identified active and suppressed men sharing identical haplotypes, establishing that these major variations in the presence/absence of a hotspot and in quantitative activity are not caused by local DNA sequence variation. These findings suggest a role for distal regulators or epigenetic factors in hotspot activity and provide the first direct evidence for the rapid evolution of recombination hotspots in humans.

The Coalescent and Infinite-Site Model of a Small Multigene Family

The infinite-site model of a small multigene family with two duplicated genes is studied. The expectations of the amounts of nucleotide variation within and between two genes and linkage disequilibrium are obtained, and a coalescent-based method for simulating patterns of polymorphism in a small multigene family is developed. The pattern of DNA variation is much more complicated than that in a single-copy gene, which can be simulated by the standard coalescent. Using the coalescent simulation of duplicated genes, the applicability of statistical tests of neutrality to multigene families is considered.