Dental Eruption Sequences in Fossil Colobines and the Evolution of Primate Life Histories

Unlike other catarrhines, colobines show early molar eruption relative to that of the anterior dentition. The pattern is variable, with Asian genera (Presbytina) showing a greater variability than the African genera (Colobina). The polarity of early relative molar eruption, as well as the degree to which it is related to phylogeny, are unclear. Schultz (1935) suggested that the trend reflects phylogeny and is primitive for catarrhines. More recently, however, researchers have proposed that life history and dietary hypotheses account for early relative molar eruption. If the colobine eruption pattern is primitive for catarrhines, it implies that cercopithecines and hominoids converged on delayed relative molar eruption. Alternatively, if the colobine condition is derived, factors such as diet and mortality patterns probably shaped colobine eruption patterns. Here we update our knowledge on eruption sequences of living colobines, and explore the evolutionary history of the colobine dental eruption pattern by examining fossil colobine taxa from Eurasia (Mesopithecus) and Africa (Kuseracolobus aramisi and Colobus sp.) and the basal cercopithecoid Victoriapithecus macinnesi. We scored specimens per Harvati (2000). The Late Miocene-Early Pliocene Mesopithecus erupts the second molar early relative to the incisors, while the Early Pliocene Kuseracolobus aramisi does not. These results demonstrate that the common colobine tendency for early molar eruption relative to the anterior dentition had appeared by the Late Miocene, and that some of the diversity observed among living colobines was already established in the Late Miocene/Early Pliocene. We discuss the implications of these results for phylogenetic, life history, and dietary hypotheses of dental development.     

Evolutionary Implications of Dental Eruption in Dasypus (Xenarthra)

Late eruption of the permanent dentition was recently proposed as a shared anatomical feature of endemic African mammals (Afrotheria), with anecdotal reports indicating that it is also present in dasypodids (armadillos). In order to clarify this question, and address the possiblity that late eruption is shared by afrotherians and dasypodids, we quantified the eruption of permanent teeth in Dasypus, focusing on growth series of D. hybridus and D. novemcinctus. This genus is the only known xenarthran that retains two functional generations of teeth. Its adult dentition typically consists of eight upper and eight lower ever-growing (or euhypsodont) molariforms, with no premaxillary teeth. All but the posterior-most tooth are replaced, consistent with the identification of a single molar locus in each series. Comparison of dental replacement and skull metrics reveals that most specimens reach adult size with none or few erupted permanent teeth. This pattern of growth occurring prior to the full eruption of the dentition is similar to that observed in most afrotherians. The condition observed in Dasypus and many afrotherians differs from that of most other mammals, in which the permanent dentition erupts during (not after) growth, and is complete at or near the attainment of sexual maturity and adult body size. The suture closure sequence of basicranial and postcranial epiphyses does not correlate well with dental eruption. The basal phylogenetic position of the taxon within dasypodids suggests that diphyodonty and late dental replacement represent the condition of early xenarthrans. Additionally, the inferred reduction in the number of molars to a single locus and the multiplication of premolars represent rare features for any living mammal, but may represent apomorphic characters for Dasypus.     

Eruption Sequence of the Lower Permanent Dentition of Lufengpithecus lufengensis

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Sequence Dependent Hole Evolution in DNA

The paper examines thedynamical behavior of a radical cation(G ^+*) generated in adouble stranded DNA for differentoligonucleotide sequences. The resonancehole tunneling through an oligonucleotidesequence is studied by the method ofnumerical integration of self-consistentquantum-mechanical equations. The holemotion is considered quantum mechanicallyand nucleotide base oscillations aretreated classically. The results obtaineddemonstrate a strong dependence of chargetransfer on the type of nucleotidesequence. The rates of the hole transferare calculated for different nucleotidesequences and compared with experimentaldata on the transfer from (G ^+*)to a GGG unit.     

Evolution of an Arbitrary Sequence in Solubility

We have investigated the evolvability of an insoluble random polypeptide, RP3-34, to a soluble form through iterative mutation and selection with the aid of the green fluorescent protein (GFP) folding reporter. To assess the solubility of the polypeptides in the selected clones of each generation, the polypeptide genes were detached from the GFP fusions and expressed with a His₆ tag. The solubility of the variant random polypeptides increased in each generation within the scope of the evolutionary process, and the polypeptides assumed a soluble form from the fourth generation. Analysis of the synonymous and nonsynonymous mutations found in the deduced amino acid sequence of the selected polypeptides revealed that selection had accelerated the evolutionary rate. The solubility and hydrophobicity of the polypeptides and the 25 arbitrarily chosen random polypeptides found in a previously prepared library were determined, analyzed, and interpreted from the landscape on the protein sequence space. This study showed the evolvability of an insoluble arbitrary sequence toward a soluble one, hence, it provides a new perspective on the field of artificial evolution.     

Sequence Evolution of Drosophila Mitochondrial DNA

We have compared nucleotide sequences of corresponding segments of the mitochondrial DNA (mtDNA) molecules of Drosophila yakuba and Drosophila melanogaster, which contain the genes for six proteins and seven tRNAs. The overall frequency of substitution between the nucleotide sequences of these protein genes is 7.2%. As was found for mtDNAs from closely related mammals, most substitutions (86%) in Drosophila mitochondrial protein genes do not result in an amino acid replacement. However, the frequencies of transitions and transversions are approximately equal in Drosophila mtDNAs, which is in contrast to the vast excess of transitions over transversions in mammalian mtDNAs. In Drosophila mtDNAs the frequency of C----T substitutions per codon in the third position is 2.5 times greater among codons of two-codon families than among codons of four-codon families; this is contrary to the hypothesis that third position silent substitutions are neutral in regard to selection. In the third position of codons of four-codon families transversions are 4.6 times more frequent than transitions and A----T substitutions account for 86% of all transversions. Ninety-four percent of all codons in the Drosophila mtDNA segments analyzed end in A or T. However, as this alone cannot account for the observed high frequency of A----T substitutions there must be either a disproportionately high rate of A----T mutation in Drosophila mtDNA or selection bias for the products of A----T mutation. --Consideration of the frequencies of interchange of AGA and AGT codons in the corresponding D. yakuba and D. melanogaster mitochondrial protein genes provides strong support for the view that AGA specifies serine in the Drosophila mitochondrial genetic code.     

Deciduous Dentitions of Eocene Cebochoerid Artiodactyls and Cetartiodactyl Relationships

Deciduous lower premolars (milk teeth) of the Eocene artiodactyl family Cebochoeridae possess accessory denticles and are remarkably similar to both deciduous and adult teeth of the cetacean family Basilosauridae, suggesting that morphological characters of juvenile dentitions are important to understanding the phylogenetic origin of whales and morphological transitions in the cetartiodactyl lineage. Incorporation of these new characters into a larger phylogenetic analysis of morphological characters of artiodactyls, mesonychids, and basal and recent whales supports a monophyletic Cetartiodactyla, but does not directly support a whale–hippo relationship. However, the presence of accessory denticles on some artiodactyl dentitions weakens the morphological support for a monophyletic Artiodactyla, suggesting either that whales and cebochoerids may be more closely related than had been thought, or that cebochoerids share a developmental pathway with cetaceans.     

Evolution Analysis of Simple Sequence Repeats in Plant Genome

Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.     

The Evolution of Dental Journals from 2003 to 2012: A Bibliometric Analysis

Bibliometrics are a set of methods, which can be used to analyze academic literature quantitatively and its changes over time. The objectives of this study were 1) to evaluate trends related to academic performance of dental journals from 2003 to 2012 using bibliometric indices, and 2) monitor the changes of the five dental journals with the highest and lowest impact factor (IF) published in 2003. Data for the subject category "Dentistry, Oral Surgery & Medicine" was retrieved from the Journal Citation Reports (JCR) published from 2003 to 2012. Linear regressions analysis was used to determine statistical trends over the years with each bibliometric indicator as the dependent variable and the JCR year as the predictor variable. Statistically significant rise in the total number of dental journals, the number of all articles with the steepest rise observed for research articles, the number of citations and the aggregate IF was observed from 2003 to 2012. The analysis of the five top and five bottom-tire dental journals revealed a rise in IF however, with a wide variation in relation to the magnitude of this rise. Although the IF of the top five journals remained relatively constant, the percentile ranks of the four lowest ranking journals in 2003 increased significantly with the sharpest rise being noted for the British Journal of Oral & Maxillofacial Surgery. This study revealed significant growth of dental literature in absolute terms, as well as upward trends for most of the citation-based bibliometric indices from 2003 to 2012.     

融合位置特征与序列进化信息的磷酸化位点预测

磷酸化是蛋白质翻译后的主要修饰,可分为激酶特异性和非激酶特异性两种类型．以非激酶特异性磷酸化位点Dou数据集为基础,本文发展了一种基于位置的卡方差表特征χ²-pos,融合伪氨基酸序列进化信息PsePSSM表征序列,构建正负样本均衡的支持向量机分类器,S, T, Y独立测试Matthew相关系数、ROC曲线下面积分及准确率分别达到了(0.59、0.87、79.74%),(0.55、0.85、77.68%)和(0.50、0.81、75.22%),明显优于文献报道结果． χ²-pos、PsePSSM两种特征的融合在蛋白质磷酸化位点预测中有广泛应用前景．     

The Campanian Ignimbrite Eruption: New Data on Volcanic Ash Dispersal and Its Potential Impact on Human Evolution

The Campanian Ignimbrite (CI) volcanic eruption was the most explosive in Europe in the last 200,000 years. The event coincided with the onset of an extremely cold climatic phase known as Heinrich Event 4 (HE4) approximately 40,000 years ago. Their combined effect may have exacerbated the severity of the climate through positive feedbacks across Europe and possibly globally. The CI event is of particular interest not only to investigate the role of volcanism on climate forcing and palaeoenvironments, but also because its timing coincides with the arrival into Europe of anatomically modern humans, the demise of Neanderthals, and an associated major shift in lithic technology. At this stage, however, the degree of interaction between these factors is poorly known, based on fragmentary and widely dispersed data points. In this study we provide important new data from Eastern Europe which indicate that the magnitude of the CI eruption and impact of associated distal ash (tephra) deposits may have been substantially greater than existing models suggest. The scale of the eruption is modelled by tephra distribution and thickness, supported by local data points. CI ashfall extends as far as the Russian Plain, Eastern Mediterranean and northern Africa. However, modelling input is limited by very few data points in Eastern Europe. Here we investigate an unexpectedly thick CI tephra deposit in the southeast Romanian loess steppe, positively identified using geochemical and geochronological analyses. We establish the tephra as a widespread primary deposit, which blanketed the topography both thickly and rapidly, with potentially catastrophic impacts on local ecosystems. Our discovery not only highlights the need to reassess models for the magnitude of the eruption and its role in climatic transition, but also suggests that it may have substantially influenced hominin population and subsistence dynamics in a region strategic for human migration into Europe.     

A Phylogenetic Perspective on Sequence Evolution in Microsatellite Loci

We examined the evolution of the repeat regions of three noncoding microsatellite loci in 58 species of the Polistinae, a subfamily of wasps that diverged over 140 million years ago. A phylogenetic approach allows two new kinds of approaches to studying microsatellite evolution: character mapping and comparative analysis. The basic repeat structure of the loci was highly conserved, but was often punctuated with imperfections that appear to be phylogenetically informative. Repeat numbers evolved more rapidly than other changes in the repeat region. Changes in number of repeats among species seem consistent with the stepwise mutation model, which is based on slippage during replication as the main source of mutations. Changes in repeat numbers can occur even when there are very few tandem repeats but longer repeats, especially perfect repeats led to greater rates of evolutionary change. Species phylogenetically closer to the one from which we identified the loci had longer stretches of uninterrupted repeats and more different motifs, but not longer total repeat regions. The number of perfect repeats increased more often than it decreased. However, there was no evidence that some species have consistently greater numbers of repeats across loci than other species have, once ascertainment bias is eliminated. We also found no evidence for a population size effect posited by one form of the directionality hypothesis. Overall, phylogenetic variation in repeat regions can be explained by adding neutral evolution to what is already known about the mutation process. The life cycle of microsatellites appears to reflect a balance between growth by slippage and degradation by an essentially irreversible accumulation of imperfections. Received: 13 April 1999 / Accepted: 8 September 1999     

Statistical Alignment with a Sequence Evolution Model Allowing Rate Heterogeneity along the Sequence

We present a stochastic sequence evolution model to obtain alignments and estimate mutation rates between two homologous sequences. The model allows two possible evolutionary behaviors along a DNA sequence in order to determine conserved regions and take its heterogeneity into account. In our model, the sequence is divided into slow and fast evolution regions. The boundaries between these sections are not known. It is our aim to detect them. The evolution model is based on a fragment insertion and deletion process working on fast regions only and on a substitution process working on fast and slow regions with different rates. This model induces a pair hidden Markov structure at the level of alignments, thus making efficient statistical alignment algorithms possible. We propose two complementary estimation methods, namely, a Gibbs sampler for Bayesian estimation and a stochastic version of the EM algorithm for maximum likelihood estimation. Both algorithms involve the sampling of alignments. We propose a partial alignment sampler, which is computationally less expensive than the typical whole alignment sampler. We show the convergence of the two estimation algorithms when used with this partial sampler. Our algorithms provide consistent estimates for the mutation rates and plausible alignments and sequence segmentations on both simulated and real data.     

DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton

Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved resolution of 34 deeply re-sequenced genomes. We also explore the evolution of homoeologous regions in the A_T- and D_T-genomes and especially the phenomenon of conversion between genomes. We did not find any compelling evidence for homoeologous conversion between genomes. These findings are very different from other recent reports of frequent conversion events between genomes. We also identified several distinct regions of the genome that have been introgressed between G. hirsutum and G. barbadense, which presumably resulted from breeding efforts targeting associated beneficial alleles. Finally, the genotypic data resulting from this study provides access to a wealth of diversity sorely needed in the narrow germplasm of cotton cultivars.     

An Empirical Codon Model for Protein Sequence Evolution

Mol. Biol. Evol. 2007 24:1464-1479 The first affiliation should have appeared as EMBL-EuropeanBioinformatics Institute, Hinxton, United Kingdom. On page     

序列消除与异源多倍体植物基因组的进化

经杂交后多倍化形成的异源多倍体植物,被认为在其形成的早期阶段经历了DNA序列消除过程。发生消除的序列既涉及到高拷贝的序列也有低拷贝的序列,而且大多数情况下倾向于消除来自其中一个亲本的序列。序列消除的模式因基因组组成和物种的不同而有差异,并且可能受到细胞质的影响。尽管序列消除的分子机制还不是很清楚,但很多证据已表明非同源染色体之间的互作不是主要的原因。目前认为,序列消除增加了非同源染色体之间的差异,为多倍化后在减数分裂过程中快速恢复二倍化的染色体配对模式提供了物质基础,这样更有利于多倍体在自然界快速稳定。