Levels Of DNA Sequence Variation Research Articles

How Can We Resolve Lewontin's Paradox?

We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone—Lewontin’s Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.

Genetic connectivity among populations of two congeneric direct-developing whelks varies across spatial scales

ABSTRACTWe examined the phylogeographic structure of two congeneric, direct-developing, intertidal whelks endemic to New Zealand, Cominella virgata and C. maculosa. A total of 855 specimens were collected from 23 rocky shore locations and we used them to determine the level of DNA sequence variation at the mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I gene. Cominella virgata and C. maculosa have relatively high levels of haplotype diversity but low levels of nucleotide diversity. Sample sites formed regional groups that were composed of genetically differentiated populations, a finding consistent with their limited dispersal abilities. Cominella virgata showed higher levels of regional differentiation than C. maculosa, and there were also species-specific differences in genetic patterns within some regions. Both species exhibited genetic homogenisation among proximate sites within groups, suggesting some dispersal does occur between areas that are not connected by contiguous rocky shore habitat.

Within‐river genetic connectivity patterns reflect contrasting geomorphology

AbstractAimTo test the hypothesis that geomorphological features, shaped by underlying geology, can influence within‐river connectivity patterns in freshwater‐limited fishes.LocationRivers draining the eastern flanks of the Southern Alps in South Island, New Zealand.MethodsWe analyse up to 1624 bp of mtDNA from 499 ‘flathead’ Galaxias specimens from 145 localities across 14 different river systems. Variation among sampling sites within systems is characterized using ϕ statistics.ResultsAlthough similar levels of DNA sequence variation were detected in all rivers sampled, spatial partitioning of this variation was significantly greater within schist (n = 5; mean ϕST = 0.696) than within greywacke (n = 10; mean ϕST = 0.268) rivers.Main conclusionsPopulation connectivity can be strongly influenced by underlying geology, leading to profound differences in the connectivity, phylogeography and diversity of riverine species.

Scanning electron microscopy of the leaf epidermis in Arundinarieae (Poaceae: Bambusoideae): evolutionary implications of selected micromorphological features

Arundinarieae (temperate woody bamboos) is a taxonomically challenging group and the taxa in this tribe show a low level of DNA sequence variation, especially for plastid markers. As a result of the scarcity of flowering collections, species identification mainly depends on vegetative features, and leaf epidermal micromorphology has proven to be useful in bamboo taxonomy. In this study, we used scanning electron microscopy to investigate the abaxial leaf epidermal micromorphology of 94 species in 24 genera of Arundinarieae and three species of Bambuseae. Leaf epidermal characteristics differed mainly in the number and distribution pattern of papillae. Seven papilla forms were assigned, which had little taxonomic value at the generic and subtribal levels. However, the papilla patterns combined with other leaf epidermal features were useful in the discrimination of several species. Most papilla types were shared between tribes Arundinarieae and Bambuseae. We assessed the phylogenetic implications of the leaf epidermal micromorphology based on recently published molecular phylogenetic analyses. With one exception, none of the papilla types corresponded to a particular clade in the plastid or nuclear phylogenetic trees. Based on these results, the papilla patterns have limited phylogenetic value. (C) 2014 The Linnean Society of London

Evolutionary dynamics across discontinuous freshwater systems: Rapid expansions and repeated allopolyploid origins in the Palearctic white water–lilies (Nymphaea)

AbstractWhite water–lilies (Nymphaea) provide an excellent model for studying evolutionary diversification in a discontinuous habitat system, which has experienced dramatic differences in connectivity during different climatic periods. Here we explore cytogenetic and molecular variation and phylogenetic relationships in the Eurasian clade of this genus based on relative nuclear DNA contents, AFLP fingerprints, and nuclear (ITS) and cpDNA sequences. In line with some recent taxonomic treatments, our results support that the Eurasian clade consists of three species. We show that the Eurosiberian N. candida is an allopolyploid that originated at least twice by hybridization in the wide overlap zone between the mainly European N. alba lineage and the mainly Asian N. tetragona lineage. The N. alba lineage served as the chloroplast donor except for the Karelian N. candida, but the ITS region of the allopolyploid was homogenized in the direction of N. alba in all cases. The southern, widespread lineage of N. candida probably originated first, whereas the northwestern lineage, restricted to a small, previously glaciated area in Karelia, may have originated as late as in the current interglacial. We observed only low levels of DNA sequence variation within N. alba and N. tetragona, indicating rapid range expansions possibly preceeded by strong bottlenecks in glacial refugia. Our results suggest that populations of freshwater organisms found now in disjunct aquatic habitats across Eurasia were connected during previous climatic periods. These connections promoted rapid expansions of divergent lineages and repeated formation of evolutionary novelty via hybridization and polyploidization.

DNA barcoding of a large genus, Aspalathus L. (Fabaceae)

AbstractThe DNA barcode potential of three regions (the nuclear ribosomal ITS and the plastid psbA‐trnH and trnT‐trnL intergenic spacers) was investigated for the plant genus Aspalathus L. (Fabaceae: Crotalarieae). Aspalathus is a large genus (278 species) that revealed low levels of DNA sequence variation in phylogenetic studies. In a 51‐species dataset for the psbA‐trnH and ITS regions, 45% and 16% of sequences respectively were identical to the sequence of at least one other species, with two species undiscriminated even when the two regions were combined. In contrast, trnT‐trnL discriminated between all species in this dataset. In a larger ITS and trnT‐trnL dataset, including a further 82 species, 7 species in five pairwise comparisons remained undiscriminated when the two regions were combined. Four of the five pairs of species not discriminated by sequence data were readily distinguished using a combination of qualitative and quantitative morphological data. The difficulty of barcoding in this group is increased by the presence of intraspecific variation in all three regions studied. In the case of psbA‐trnH, three intraspecific samples had a sequence identical to at least one other species. Overall, psbA‐trnH, currently a candidate for plant barcoding, was the least discriminatory region in our study.

The Evolution of Gene Expression QTL in Saccharomyces cerevisiae

Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.

Genetic variation in the marbled lungfish Protopterus aethiopicus in Lake Victoria and introduction to Lake Baringo, Kenya

Marbled lungfish Protopterus aethiopicus in Lake Victoria and two nearby smaller lakes were found to have high levels of DNA sequence variation in their mitochondrial control regions (35 haplotypes in 61 fish) but no population genetic structure (ΦST= 0·00). In contrast, marbled lungfish in Lake Baringo, Kenya, appeared to be fixed for a single control region haplotype, which occurred at low frequency in the other lakes. Using FLUCTUATE software, the female effective population size in Lake Victoria during the late Pleistocene was estimated to be c. 500 000, similar to the value estimated for the present‐day population. These observations suggest that, during the late Pleistocene dry period, a large marbled lungfish population survived either in wet refugial areas within the lake basin or in surrounding areas. Marbled lungfish were reported to have been introduced into Lake Baringo 30 years ago with a founding population of only three individuals. The lack of control region variation in the Lake Baringo population is consistent with that situation.

Genetic Relationships among species of Populus (Salicaceae) based on nuclear genomic data1

Abstract The genus Populus comprises some of the most commercially exploited, pioneer forest trees distributed throughout the northern-hemisphere. The high level of morphological diversity, extensive inter-species hybridization, and low level of DNA sequence variation among species in this group have impeded the progress of taxonomic and phylogenetic studies. We used nuclear genomic data based upon inter simple sequence repeat (ISSR) variability, a highly variable class of molecular markers to determine the genetic relationships among species of the genus Populus. Species of the section Populus (Leuce) clustered together suggesting monophyly of the section Populus. The Eurasian members of section Populus (P. alba, P. davidiana, and P. tremula) showed closer genetic relationships to each other than to two North American aspens (P. tremuloides and P. grandidentata) of the same section. In contrast to previous phylogenetic studies, P. nigra showed a close genetic relationship to species of the section Tacama...

PHYLOGENETIC AND BIOGEOGRAPHIC RELATIONSHIPS OF MOUSE OPOSSUMS THYLAMYS (DIDELPHIMORPHIA, DIDELPHIDAE) IN SOUTHERN SOUTH AMERICA

Phylogenetic relationships among 51 individuals of South American mouse opossums (Thylamys) were examined by using nucleotide sequence data from the mitochondrial cytochrome-b gene. Parsimony, likelihood, Bayesian, and genetic distance analyses revealed several distinct clades. T. macrurus (subtropical forest of eastern Paraguay) was strongly differentiated from all other species. T. venustus (Yungas forest on eastern slopes of the Andes of Bolivia and Argentina) separated into 2 strongly supported clades, providing support for recognition of 2 species, T. venustus and T. cinderella, but not supporting the distinctness of T. sponsorius. T. tatei (central coast of Peru) was sufficiently different from T. elegans (Matorral of Chile) to support species recognition. The dichotomy between northern (Chile and Bolivia) and southern (Argentina) clades of T. pallidior suggested the presence of 2 subspecies. High levels of DNA sequence variation indicated substantial genetic differentiation among and between clades, and combined with the phylogenetic analyses provide support for the systematic conclusions. Estimates of times since divergence suggest a radiation beginning in the Miocene and continuing through the Pliocene and correspond with changes in climate, vegetation, and geology that occurred during these times.

Multiple Genetically Distinct Groups Revealed among Clinical Isolates Identified as Atypical Aspergillus fumigatus

To investigate whether genetic variants of A. fumigatus are found among clinical isolates, four isolates that were originally identified as poorly sporulating strains of Aspergillus fumigatus were subjected to molecular analysis. DNA sequence analysis of the alkaline protease genes of these isolates showed that each is genetically distinct and each shows substantial variation (7 to 11%) from the A. fumigatus nucleotide sequence. Subsequent morphological examination suggested that all of the isolates could be classified as Aspergillus viridinutans. To clarify the taxonomic status of these four clinical isolates and of two previously identified as atypical A. fumigatus isolates, partial beta-tubulin and 18S rRNA gene sequences were determined. Each of the six atypical strains had a unique beta-tubulin sequence, whereas the sequences of three standard isolates of A. fumigatus, which were included as controls, were identical to the published A. fumigatus beta-tubulin sequence. The very low level of DNA sequence variation detected in standard isolates of A. fumigatus compared with other isolates from members of Aspergillus section Fumigati suggests that it may be a relatively recently evolved species. The 18S rRNA gene of two of the atypical isolates differed from that of A. fumigatus at a single nucleotide position. Phylogenetic analyses do not support the classification of all of these isolates as A. viridinutans. Thus, some of these isolates represent new species which are potential opportunistic pathogens.

Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara

Species in the genus Tangara are distributed throughout the New World tropics and vary in their morphology, behavior, and ecology. We used data from the cytochrome b and ND 2 genes to provide the first phylogenetic perspective on the evolution of this diversity. Reconstructions based on parsimony, maximum likelihood, and Bayesian approaches were largely congruent. The genus is monophyletic and consists of two main clades. Within these clades, DNA sequence data confirm the monophyly of most previously recognized species groups within Tangara, indicating general concordance between molecular data and impressions based on geographic distribution, morphology, and behavior. Within some currently recognized species, levels of DNA sequence variation are larger than expected, suggesting multiple taxa may be involved. In contrast, some currently recognized species are only weakly differentiated from their sister species. Biogeographic analyses indicate that many early speciation events occurred in the Andes. More recently, dispersal events followed by subsequent speciation have occurred in other geographic areas of the Neotropics. Assuming a molecular clock, most speciation events occurred well before Pleistocene climatic cycles. The time frame of Tangara speciation corresponds more closely to a period of continued uplift in the Andes during the late Miocene and Pliocene.

Patterns of DNA sequence variation suggest the recent action of positive selection in the janus-ocnus region of Drosophila simulans.

Levels of nucleotide polymorphism in three paralogous Drosophila simulans genes, janusA (janA), janusB (janB), and ocnus (ocn), were surveyed by DNA sequencing. The three genes lie in tandem within a 2.5-kb region of chromosome arm 3R. In a sample of eight alleles from a worldwide distribution we found a significant departure from neutrality by several statistical tests. The most striking feature of this sample was that in a 1.7-kb region containing the janA and janB genes, 30 out of 31 segregating sites contained variants present only once in the sample, and 29 of these unique variants were found in the same allele. A restriction survey of an additional 28 lines of D. simulans revealed strong linkage disequilibrium over the janA-janB region and identified six more alleles matching the rare haplotype. Among the rare alleles, the level of DNA sequence variation was typical for D. simulans autosomal genes and showed no departure from neutrality. In addition, the rare haplotype was more similar to the D. melanogaster sequence, indicating that it was the ancestral form. These results suggest that the derived haplotype has risen to high worldwide frequency relatively recently, most likely as a result of natural selection.

Genetic linkage and molecular evolution

The different models make similar predictions which makes it difficult to ascribe an observation to just one process. Are there any observations that allow one to identify which process is operating? It turns out that the distribution of frequencies of neu-tral variants in a sample of sequences (the frequency spectrum) is model-dependent. A large distortion of the frequency spectrum towards rare variants is more likely with selective sweeps (Fig. 1Fig. 1). And when there is some recombination, so that initially rare variants are not necessarily swept to complete fixation, a transient sig-nature of a sweep is provided by the occurrence of an excess of ‘derived’ variants at a high frequency within a sample. (One can infer if a variant is derived or ancestral from the sequence of a closely related species.) Other features of genetic variation, such as patterns of linkage disequilibrium, may also be useful in testing alternative models. Perhaps the best way to quantify the relative importance of these processes is to get solid estimates of the rate at which deleterious mutations occur, and of the distribution of their effects on fitness. Although this is a simple question to ask, it is hard to answer. But given such information, and using the increasing amount of information on DNA sequence variation and evolution, one can perhaps try to answer an even harder question: what is the rate at which advantageous mutations occur, and what are their effects on fitness?Key references

Low levels of DNA sequence variation among adapted genotypes of hexaploid wheat

PCR products from regions corresponding to sequences hybridising to wheat RFLP probes were sequenced in order to establish the level of DNA sequence variation among adapted wheat genotypes. Hexaploid bread wheat shows a very low rate of nucleotide polymorphism, approximately 1 polymorphic nucleotide per 1000 basepairs. Differences in PCR product length can be exploited to design genome-specific amplicons, which may have use in gene tagging or in diagnostic applications. Interpretation of results may be complicated by the simultaneous amplification of orthologous and paralogous sequences. These findings have significant implications for the use of STS markers in wheat and other polyploid species.

Distribution and relative abundance of Pseudocalanus moultoni and P. newmani (Copepoda: Calanoida) on Georges Bank using molecular identification of sibling species

The sibling species, Pseudocalanus moultoni (Frost, 1989) and P. newmani (Frost, 1989), occur sympatrically on Georges Bank. Taxonomic discrimination of the species relies on subtle morphological characteristics, making routine identification of the species very difficult. DNA sequence variation of two mitochondrial genes, 16S rRNA and cytochrome oxidase I (COI), reliably discriminated P. moultoni and P.␣newmani. Levels of DNA sequence variation for both genes were consistent with those between species of calanoid copepods. A molecular systematic protocol (based on allele-specific PCR amplification) was designed from the COI sequences and used to discriminate females of the two species. The distributions and relative abundances of the two species were mapped for April 1996 based on samples of 15 to 30 females from 12 collections across Georges Bank. The results of this study indicated that P. moultoni females predominated along the northern flank of Georges Bank, while P. newmani females were common on the southern flank, deeper than the 60-m isobath.

The hitchhiking effect on the site frequency spectrum of DNA polymorphisms.

The level of DNA sequence variation is reduced in regions of the Drosophila melanogaster genome where the rate of crossing over per physical distance is also reduced. This observation has been interpreted as support for the simple model of genetic hitchhiking, in which directional selection on rare variants, e.g., newly arising advantageous mutants, sweeps linked neutral alleles to fixation, thus eliminating polymorphisms near the selected site. However, the frequency spectra of segregating sites of several loci from some populations exhibiting reduced levels of nucleotide diversity and reduced numbers of segregating sites did not appear different from what would be expected under a neutral equilibrium model. Specifically, a skew toward an excess of rare sites was not observed in these samples, as measured by Tajima's D. Because this skew was predicted by a simple hitchhiking model, yet it had never been expressed quantitatively and compared directly to DNA polymorphism data, this paper investigates the hitchhiking effect on the site frequency spectrum, as measured by Tajima's D and several other statistics, using a computer simulation model based on the coalescent process and recurrent hitchhiking events. The results presented here demonstrate that under the simple hitchhiking model (1) the expected value of Tajima's D is large and negative (indicating a skew toward rare variants), (2) that Tajima's test has reasonable power to detect a skew in the frequency spectrum for parameters comparable to those from actual data sets, and (3) that the Tajima's Ds observed in several data sets are very unlikely to have been the result of simple hitchhiking. Consequently, the simple hitchhiking model is not a sufficient explanation for the DNA polymorphism at those loci exhibiting a decreased number of segregating sites yet not exhibiting a skew in the frequency spectrum.

How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained?

Different regions of the Drosophila genome have very different rates of recombination. For example, near centromeres and near the tips of chromosomes, the rates of recombination are much lower than in other regions. Several surveys of polymorphisms in Drosophila have now documented that levels of DNA polymorphism are positively correlated with rates of recombination; i.e., regions with low rates of recombination tend to have low levels of DNA polymorphism within populations of Drosophila. Three hypotheses are reviewed that might account for these observations. The first hypothesis is that regions of low recombination have low neutral mutation rates. Under this hypothesis between-species divergences should also be low in regions of low recombination. In fact, regions of low recombination have diverged at the same rate as other regions of the genome. On this basis, this strictly neutral hypothesis is rejected. The second hypothesis is that the process of fixation of favorable mutations leads to the observed correlation between polymorphism and recombination. This occurs via genetic hitchhiking, in which linked regions of the genome are swept along with the selectively favored mutant as it increases in frequency and eventually fixes in the population. This hitchhiking model with fixation of favorable mutations is compatible with major features of the data. By assuming this model is correct, one can estimate the rate of fixation of favorable mutations. The third hypothesis is that selection against continually arising deleterious mutations results in reduced levels of polymorphism at linked loci. Analysis of this background selection model shows that it can produce some reduction in levels of polymorphism but cannot explain some extreme cases that have been observed. Thus, it appears that hitchhiking of favorable mutations and background selection against deleterious mutations must be considered together to correctly account for the patterns of polymorphism that are observed in Drosophila.

Reduced natural selection associated with low recombination in Drosophila melanogaster.

Synonymous codons are not used equally in many organisms, and the extent of codon bias varies among loci. Earlier studies have suggested that more highly expressed loci in Drosophila melanogaster are more biased, consistent with findings from several prokaryotes and unicellular eukaryotes that codon bias is partly due to natural selection for translational efficiency. We link this model of varying selection intensity to the population-genetics prediction that the effectiveness of natural selection is decreased under reduced recombination. In analyses of 385 D. melanogaster loci, we find that codon bias is reduced in regions of low recombination (i.e., near centromeres and telomeres and on the fourth chromosome). The effect does not appear to be a linear function of recombination rate; rather, it seems limited to regions with the very lowest levels of recombination. The large majority of the genome apparently experiences recombination at a sufficiently high rate for effective natural selection against suboptimal codons. These findings support models of the Hill-Robertson effect and genetic hitchhiking and are largely consistent with multiple reports of low levels of DNA sequence variation in regions of low recombination.

Structure and expression of the maize gene encoding the phosphoenolpyruvate carboxylase isozyme involved in C4 photosynthesis

We have determined the structure of the maize (Zea mays L. subsp.mays line B73) nuclear gene encoding the phosphoenolpyruvate (PEP) carboxylase isozyme involved in C4 photosynthesis. The gene is 5.3 kb long and has ten exons that range in size from 85 to 999 bp. The nine introns vary from 97 to 872 bp. The sequence of 663 bp of 5'-flanking and 205 bp of 3'-flanking DNA is reported along with the entire gene sequence. Several short repetitive sequences were found in the 5'-flanking DNA that have characteristics similar to elements important in the light regulation of pea genes encoding the small subunit of ribulose 1,5-bisphosphate carboxylase. In addition, some 5'-flanking sequence similarities were found in a comparison with other light-regulated genes from maize and wheat.The level of DNA sequence variation among different PEP carboxylase alleles is similar to the allelic variation observed for several other maize nuclear genes. The data suggest modern maize variaties have retained much of the genetic variation present in their ancestral forms.Finally, accumulation of transcripts encoding the PEP carboxylase isozyme involved in C4 photosynthesis is quite high in several structures besides leaves, including inner leaf sheaths, tassels and husks. This indicates that expression of this gene is not leaf-specific and may not necessarily be coupled to the development of Kranz anatomy.