Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis

Microsatellite sequences were cloned and sequenced from Cicer reticulatum, the wild annual progenitor of chickpea (C. arietinum L.). Based on the flanking sequences of the microsatellite motifs, 11 sequence-tagged microsatellite site (STMS) markers were developed. These markers were used for phylogenetic analysis of 29 accessions representing all the nine annual Cicer species. The 11 primer pairs amplified distinct fragments in all the annual species demonstrating high levels of sequence conservation at these loci. Efficient marker transferability (97%) of the C. reticulatum STMS markers across other species of the genus was observed as compared to microsatellite markers from the cultivated species. Variability in the size and number of alleles was obtained with an average of 5.8 alleles per locus. Sequence analysis at three homologous microsatellite loci revealed that the microsatellite allele variation was mainly due to differences in the copy number of the tandem repeats. However, other factors such as (1) point mutations, (2) insertion/deletion events in the flanking region, (3) expansion of closely spaced microsatellites and (4) repeat conversion in the amplified microsatellite loci were also responsible for allelic variation. An unweighted pairgroup method with arithmetic averages (UPGMA)-based dendrogram was obtained, which clearly distinguished all the accessions (except two C. judaicum accessions) from one another and revealed intra- as well as inter-species variability in the genus. An annual Cicer phylogeny was depicted which established the higher similarity between C. arietinum and C. reticulatum. The placement of C. pinnatifidum in the second crossability group and its closeness to C. bijugum was supported. Two species, C. yamashitae and C. chorassanicum, were grouped distinctly and seemed to be genetically diverse from members of the first crossability group. Our data support the distinct placement of C. cuneatum as well as a revised classification regarding its placement.     

Among-site rate variation and its impact on phylogenetic analyses

Although several decades of study have revealed the ubiquity of variation of evolutionary rates among sites, reliable methods for studying rate variation were not developed until very recently. Early methods fit theoretical distributions to the numbers of changes at sites inferred by parsimony and substantially underestimate the rate variation. Recent analyses show that failure to account for rate variation can have drastic effects, leading to biased dating of speciation events, biased estimation of the transition:transversion rate ratio, and incorrect reconstruction of phylogenies.     

Studying plant genome variation using molecular markers

The authors' studies on the organization and variation of plant genome with the use of molecular markers are briefly reviewed with special emphasis on random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), sequence characterized amplified region (SCAR), and cleaved amplified polymorphic sequence (CAPS) markers detected with the use of polymerase chain reaction (PCR). These markers have been demonstrated to be promising for identifying cultivars and determining the purity of genetic strains of pea. Genetic relationships between strains, cultivars, and mutants of pea have been studied. The role of molecular markers in molecular genetic mapping and localizing the genes of commercially important characters of pea has been shown. The possibility of the use of molecular markers for studying somaclonal variation and detecting mutagenic factors in plants during long-term spaceflights is considered. The prospects of using DNA markers for understanding the organization and variability of higher plant genomes are discussed.     

Studying plant genome variation using molecular markers

The authors studies on the organization and variation of plant genome with the use of molecular markers are briefly reviewed with special emphasis on random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR), sequence characterized amplified region (SCAR), and cleaved amplified polymorphic sequence (CAPS) markers detected with the use of polymerase chain reaction (PCR). These markers have been demonstrated to be promising for identifying cultivars and determining the purity of genetic strains of pea. Genetic relationships between strains, cultivars, and mutants of pea have been studied. The role of molecular markers in molecular genetic mapping and localizing the genes of commercially important characters of pea has been shown. The possibility of the use of molecular markers for studying somaclonal variation and detecting mutagenic factors in plants during long-term spaceflights is considered. The prospects of using DNA markers for understanding the organization and variability of higher plant genomes are discussed.__________Translated from Genetika, Vol. 41, No. 4, 2005, pp. 480–492.Original Russian Text Copyright © 2005 by Gostimsky, Kokaeva, Konovalov.     

New partial sequences of phosphoenolpyruvate carboxylase as molecular phylogenetic markers

To better understand the evolution of the enzyme phosphoenolpyruvate carboxylase (PEPC) and to test its versatility as a molecular character in phylogenetic and taxonomic studies, we have characterized and compared 70 new partial PEPC nucleotide and amino acid sequences (about 1100 bp of the 3' side of the gene) from 50 plant species (24 species of Bryophyta, 1 of Pteridophyta, and 25 of Spermatophyta). Together with previously published data, the new set of sequences allowed us to construct the up to now most complete phylogenetic tree of PEPC, where the PEPC sequences cluster according to both the taxonomic positions of the donor plants and the assumed specific function of the PEPC isoforms. Altogether, the study further strengthens the view that PEPC sequences can provide interesting information for the reconstruction of phylogenetic relations between organisms and metabolic pathways. To avoid confusion in future discussion, we propose a new nomenclature for the denotation of PEPC isoforms.     

PCR derived molecular markers and phylogenetic relationships in theSecale genus

DNA from 22 different species, accessions, cultivars and lines included in theSecale genus were analyzed by the polymerase chain reaction (PCR), using as primers five pairs of oligonucleotides derived from specific sequences. A total of 42 amplified bands were considered, and some of them appeared to be potentially useful as molecular markers for some of the analyzed groups. These amplified bands were used to generate molecular phenograms inside theSecale genus.     

An examination of phylogenetic models of substitution rate variation among lineages

Molecular evolutionary rates can show significant variation among lineages, complicating the task of estimating substitution rates and divergence times using phylogenetic methods. Accordingly, relaxed molecular clock models have been developed to accommodate such rate heterogeneity, but these often make the assumption of rate autocorrelation among lineages. In this paper, I examine the validity of this assumption.     

The effect of dilution rate variation on the performance of continuous fermentation

The effect of dilution rate variation on the performance of bioreactors used for continuous biomass producton is discussed. Calculations based on Powell's model of microbial dynamics show that such a mode of operation does not improve the performance of the process. Remarkable improvement of the process performance reported in literature is caused by incorrectness of the dynamic model of microbial growth which has been used in the calculations.     

The effects of rate variation on ancestral inference in the coalescent

We describe a Markov chain Monte Carlo approach for assessing the role of site-to-site rate variation in the analysis of within-population samples of DNA sequences using the coalescent. Our framework is a Bayesian one. We discuss methods for assessing the goodness-of-fit of these models, as well as problems concerning the separate estimation of effective population size and mutation rate. Using a mitochondrial data set for illustration, we show that ancestral inference concerning coalescence times can be dramatically affected if rate variation is ignored.     

Codon and rate variation models in molecular phylogeny

This article generalizes previous models for codon substitution and rate variation in molecular phylogeny. Particular attention is paid to (1) reversibility, (2) acceptance and rejection of proposed codon changes, (3) varying rates of evolution among codon sites, and (4) the interaction of these sites in determining evolutionary rates. To accommodate spatial variation in rates, Markov random fields rather than Markov chains are introduced. Because these innovations complicate maximum likelihood estimation in phylogeny reconstruction, it is necessary to formulate new algorithms for the evaluation of the likelihood and its derivatives with respect to the underlying kinetic, acceptance, and spatial parameters. To derive the most from maximum likelihood analysis of sequence data, it is useful to compute posterior probabilities assigning residues to internal nodes and evolutionary rate classes to codon sites. It is also helpful to search through tree space in a way that respects accepted phylogenetic relationships. Our phylogeny program LINNAEUS implements algorithms realizing these goals. Readers may consult our companion article in this issue for several examples.     

Exceptional among-lineage variation in diversification rates during the radiation of Australia's most diverse vertebrate clade

The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. 'beetles'), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.     

Genetic variation among pumpkin landraces based on seed qualities and molecular markers

Molecular Biology Reports - Germplasm identification is an essential connection linking the conservation and exploitation of crop genetic resources in several plant breeding programs. This study...     

Among-site rate variation and phylogenetic analysis of 12S rRNA in sigmodontine rodents

We analyze sequences from two mitochondrial genes, cytochrome b (cyt b) and 12S rRNA (12S), for a group of sigmodontine rodents among which phylogenetic relationships are well understood based on concordance of morphological, chromosomal, allozyme, and other DNA data sets. Because these two genes are physically linked on the nonrecombining mitochondrial genome, they necessarily share the same history. Phylogenetic analysis of the cyt b gene recovers the well-corroborated relationships, generally with strong support. None of the methods that we employed, including variously weighted parsimony, neighbor joining on both single-rate and gamma-corrected distances, and maximum likelihood, were able to recover these relationships for the 12S gene. Parsimony analyses of the 12S data resulted in a relatively strongly supported placement of Peromyscus eremicus that conflicts with that suggested by cyt b and all other data. There is extreme among-site rate variation in the 12S sequences and moderate levels in the cyt b sequences. This highly skewed distribution of rates in the 12S gene makes phylogenetic analyses of these sequences particularly susceptible to the misleading effects of nonindependence and other nonrandom noise, suggesting that phylogenetic analyses of data sets that contain a great deal of among-site rate variation be interpreted with caution.      

Genetic analysis of morphological variation in Brassica oleracea using molecular markers

A cross between the open-pollinated Brassica oleracea cabbage cultivar Wisconsin Golden Acre and the hybrid broccoli cultivar Packman was used with molecular markers to investigate the genetic control of morphological variation. Twenty-two traits derived from leaf, stem, and flowering measurements were analyzed in 90 F₂ individuals that were also classified for genotype by restriction fragment length polymorphism (RFLP) markers. Seventy-two RFLP loci, which covered the mapped genome at an average of 10 map-unit intervals on all nine linkage groups, were tested individually for associations to phenotypic measurements by single factor ANOVA, and markers with significant associations (P<0.05) were used to develop multilocus models. These data were utilized to describe the location, parental contribution of alleles, magnitude of effect, and the gene action of trait loci. Single marker loci that were significantly associated (P<0.05) with trait measurements accounted for 6.7–42.7% of the phenotypic variation. Multilocus models described as much as 60.1% of the phenotypic variation for a given trait. In some cases, different related traits had common marker-locus associations with similar gene action and genotypic class ranking. The numbers, action, and linkages, of genes controlling traits estimated with marker loci in this population corresponded to estimates based on classical genetic methods from other studies using similar, or similarly-wide, crosses. There was no evidence that genome duplication accounted for a significant portion of multiple genes controlling trait loci over the entire genome, but possible duplications of trait loci were identified for two regions with linked, duplicated marker loci.     

Applications of codon and rate variation models in molecular phylogeny

The current article illustrates the practical advantages of some new models and statistical algorithms for codon substitution and spatial rate variation in molecular phylogeny. Our companion paper in this issue discusses at length the mathematical properties of these models for nucleotide and codon substitution, for site-to-site and branch-to-branch heterogeneity in rates of evolution, and for spatial correlation in the assignment of rates. In this study we summarize the theoretical background and apply the models and algorithms to data on beta-globin, the complete HIV genome, and the mitochondrial genome. Our complex but realistic models enhance biological interpretation of sequence data and show substantial improvements in model fit over existing models. All the new statistical algorithms applied are incorporated in our phylogeny software LINNAEUS, which is tuned for performance and modeling flexibility.     

Molecular phylogenetic study of the Iranians based on polymorphic markers

The application of polymorphic markers in construction of phylogenetic trees has been documented. Five polymorphic markers located in the PAH gene region including PAH-BglII, PAH-PvuII(A), PAH-EcoRI, PAH-MspI and PAH-STR were selected for analysis of phylogenetic relationships of the Iranians with 15 other populations of the world. The lowest genetic distance was observed between the Iranians and populations residing in Adygei (an ethnic group of the Russian Caucasus), Russia and Druze (a Middle Eastern group). However, East Asian populations including Han, Japanese and Cambodians, Khmer or the Oceanians (Melanesian, Nasioi) showed high genetic distance with the Iranians. The data suggested that the Iranians might have relatively close evolutionary history with the populations residing in Russia rather than East Asian populations. This study provided the first new molecular insight into the evolutionary history of the Iranian population.     

Time of night effects on heart rate variation in normal neonates

Circadian patterns have been observed in infants as early as the first few postnatal days. We hypothesized that, in each sleep-waking state, heart rate variation in several distinct frequency bands would show consistent variations across a night in newborn infants. Twelve-hour night-time recordings of EEG, ECG, EOG, digastric EMG, respiratory movements, and CO2 were obtained from 25 normal full-term infants at 2-7 days postnatal age. The extents of three types of heart rate variation were determined for all epochs identified as quiet sleep, rapid eye movement (REM) sleep, and waking during each 4-hr period of the night. In particular states, the extent of all three types of heart rate variation decreased from the evening (7-11pm) to the late night (11pm-3am). Heart rate variation at the respiratory frequency showed such a time-of-night effect in quiet sleep only, resulting in a significant sleep state effect on respiratory sinus arrhythmia during the evening that disappeared later in the night. Previous studies have indicated that respiratory sinus arrhythmia is enhanced during quiet sleep, relative to other states, after 3 mo of age; the present findings suggest that the tendency for enhancement during quiet sleep is present even in the neonate, although this tendency is only expressed during the evening. Results indicate that time-of-night effects on heart rate variation are not constant across physiological states in neonates, and heart rate variation during the waking state is particularly unresponsive to these time-of-night influences.     

Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities

The detection and analysis of nucleic acids extracted from microbial communities are the ultimate ways to determine the diversity and functional capability of microbial communities in the environments. However, it remains a challenge to use molecular techniques for unequivocal determination and quantification of microbial species composition and functional activities. Considerable efforts have been made to enhance the capability of molecular techniques. Here an update of the recent developments in molecular techniques for environmental microbiology is provided.     

Analysis of phylogenetic relationship among five mulberry (Morus) species using molecular markers.

Species identification in mulberry (Morus) continues to be a point of great debate among scientists despite the number of criteria such as floral characters, wood, and leaf anatomical and biochemical characters used to identify the species within this genus. However, no consensus system of classification has emerged. Hence, an investigation was undertaken with inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers to find out the possibility of using these DNA markers to confirm the identity of genotypes in a particular species. Fifteen ISSR and 15 RAPD primers generated 86% and 78% polymorphism, respectively, among 19 mulberry genotypes. The polymorphism among the species varied from 50% to 57% in ISSR markers and 31% to 53% in RAPD markers. Similarity coefficients were higher among the genotypes of M. latifolia, M. bombycis and M. alba. Cluster analyses separated genotypes of M. laevigata and M. indica from those of the other species. Population structure analysis of these species further showed high genetic differentiation coefficients (GST), high heterozygosity between two species (DST), and total heterozygosity among populations (Ht) coupled with considerably low gene flow (Nm) when M. laevigata was paired with other species. Based on these parameters and the result of cluster analysis it is concluded that M. laevigata can be considered as a separate species of mulberry, whereas the other four species may be grouped together and treated as subspecies.