Preliminary analysis of the mitochondrial genome evolutionary pattern in primates

Since the birth of molecular evolutionary analysis,primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features.Surprisingly,to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates.Here,we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank.The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons.Likewise,an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes.Within 13 protein-coding genes,the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence,while synonymous changes differed only for individual genes,indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites.Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes,and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias.Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene,consistent with near neutrality.Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species.Thus,with the exception of rate heterogeneity among mitochondrial genes,evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

Whole genome re-sequencing reveals evolutionary patterns of sacred lotus (Nelumbo nucifera)

Sacred lotus(Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystems. As a foundation for exploring genomic variation and evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups(rhizome,seed and flower lotus), one wild temperate lotus subgroup(wild lotus), one tropical lotus group(Thai lotus) and an outgroup(Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, we confirmed that wild and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus. Rhizome lotus had the lowest genomic diversity and a closer relationship to wild lotus, whereas the genomes of seed and flower lotus were admixed. Genes in energy metabolism process and plant immunity evolved rapidly in lotus, reflecting local adaptation.We established that candidate genes in genomic regions with significant differentiation associated with temperate and tropical lotus divergence always exhibited highly divergent expression pattern. Together, this study comprehensive and credible interpretates important patterns of genetic diversity and relationships, gene evolution, and genomic signature from ecotypic differentiation of sacred lotus.

New insights into the evolutionary history of Megacodon:Evidence from a newly discovered species

Megacodon is an ideal genus to study speciation and ecological adaptation in the Sino-Himalayan region.The genus contains two species distributed at different elevations and in two separate areas.However,studies of this genus have long been impeded by a lack of fieldwork on one of its species,Megacodon venosus.In this study,we collected specimens of two Megacodon species and found an extraordinary new species of Megacodon in Lushui county of north-west Yunnan province,which we have since named Megacodon lushuiensis.We propose new species based on both morphological and molecular evidence.The finding of this new species emphasized the importance of ecological divergence in the divergence of Megacodon stylophorus and its parapatric low-elevation Megacodon species.To identify genetic determinants that underlie adaptations to different elevations,we characterized transcriptomes of the new species M.lushuiensis,which is distributed at low elevations,and M.stylophorus,which is distributed at high elevations.Comparative transcriptome analysis identified 8926 orthogroups containing single-copy genes,and 370 orthogroups containing significantly positively selected genes.The set of positively selected genes was enriched into 25 Gene Ontology terms,including "response to water deprivation","response to osmotic stress",and "cellular response to external stimulus".Our results provide new insights into how ecological adaptation and speciation occurred in Megacodon and highlight the role of heterogeneous habitats in the speciation of plants in the Sino-Himalayan region.

Adaptive backtracking search optimization algorithm with pattern search for numerical optimization

The backtracking search optimization algorithm（BSA） is one of the most recently proposed population-based evolutionary algorithms for global optimization. Due to its memory ability and simple structure, BSA has powerful capability to find global optimal solutions. However, the algorithm is still insufficient in balancing the exploration and the exploitation. Therefore, an improved adaptive backtracking search optimization algorithm combined with modified Hooke-Jeeves pattern search is proposed for numerical global optimization. It has two main parts： the BSA is used for the exploration phase and the modified pattern search method completes the exploitation phase. In particular, a simple but effective strategy of adapting one of BSA＇s important control parameters is introduced. The proposed algorithm is compared with standard BSA, three state-of-the-art evolutionary algorithms and three superior algorithms in IEEE Congress on Evolutionary Computation 2014（IEEE CEC2014） over six widely-used benchmarks and 22 real-parameter single objective numerical optimization benchmarks in IEEE CEC2014. The results of experiment and statistical analysis demonstrate the effectiveness and efficiency of the proposed algorithm.

Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple

Sucrose phosphate synthase(SPS)is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase(SPP)for sucrose synthesis,and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality.However,studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking.In the present study,a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1.The gene structures and their promoter cis-elements,protein conserved motifs,subcellular localizations,physiological functions and biochemical properties were analyzed.A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication(WGD)and segmental duplication played vital roles in MdSPS gene family expansion.The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication.Furthermore,three SPS gene subfamilies were classified based on phylogenetic relationships,and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies.In addition,a major gene related to sucrose accumulation(MdSPSA2.3)was identified according to the highly consistent trends in the changes of its expression in four apple varieties(‘Golden Delicious’,‘Fuji’,‘Qinguan’and‘Honeycrisp’)and the correlation between gene expression and soluble sugar content during fruit development.Furthermore,the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit.The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.

Genome-wide identification,molecular evolution, and expression divergence of the hexokinase gene family in apple

Hexokinase(HXK)is the first irreversible catalytic enzyme in the glycolytic pathway,which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes.However,the evolutionary pattern of the HXK gene family in apple remains unknown.In this study,a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1.The physiological and biochemical properties,exonintron structures,conserved motifs,and cis-elements of the MdHXK genes were determined.Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria,cytoplasm,and nucleus.Gene duplication revealed that whole-genome duplication(WGD)and segmental duplication played vital roles in MdHXK gene family expansion.Theωvalues of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication.Additionally,five subfamilies were classified,and recent/old duplication events were identified based on phylogenetic tree analysis.Different evolutionary rates were estimated among the various HXK subfamilies.Moreover,divergent expression patterns of the MdHXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation.Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.

Strata Architectural Variability and Facies Distribution in a Structural Transfer Zone: A Case Study of Fushan Sag, Northern South China Sea

Structural transfer zones in a half-graben rift basin play a significant role in controlling sandy sediments and providing a target for hydrocarbon exploration. Previous studies have classified the transfer zone in lacustrine environments into two different patterns: synthetic approaching transfer zones and synthetic overlapping transfer zones. However, the evolution of the depositional pattern and the controlling factors of the above transfer zones are still unclear. In the Fushan Sag, the northern South China Sea, an overlapping transfer zone developed in the early Eocene Epoch, while a synthetic approaching transfer zone developed in the late Eocene, due to tectonic uplift. This evolutionary process provided an opportunity to study the stacking pattern of strata architectural variability and facies distribution in the structural transfer zone of the Eocene lacustrine basin. In this study, following the indications of the oriented sedimentary structures in core samples and heavy mineral assemblages of 18 wells, the evolution of the paleo-hydrodynamic distribution during the early and late Eocene has been reconstructed. The sequence-stratigraphy was then divided and the sand body parameters calculated, according to the seismic data and well log interpretations. During the early Eocene, the lake level was at a low stand, the faults broken displacement in the East block being over 50 m. The prograding delta and turbidites are oriented perpendicular to the structural transfer zone. According to the quantitative analysis of the flow rate and the depositional parameters, we speculate that gravity transportation of the sediment and the sediment-supply are the dominating factors during this period. Up to the late Eocene, the rising lake level and the decreased fault displacement leads the flow to divert to a NE-direction, resulting in it being parallel to the axis of the transfer zone. Thus, we speculate that the accommodation space is predominant in this period. In comparison with the above two periods, a braided river delta with an isolated sand body and turbidites developing in the deep area is prominent in the overlapping transfer zone, while a meandering river delta is characteristic of the synthetic approaching transfer zone.

Callovian-Oxfordian sedimentary microfacies in the middle of Block B on the right bank of the Amu Darya Basin,Turkmenistan

The right bank of the Amu Darya Basin enjoys abundant natural gas resources,on which the Callovian-Oxfordian strata in the middle of Block B serve as the major horizons for natural gas production.However,the characteristics and distribution patterns of the sedimentary microfacies in these strata are yet to be further explored.Based on the analysis of data on drilling,logging,cores,and thin sections from 29 typical wells,as well as the regional sedimentary background,this study inferred that the middle of Block B evolved from the Callovian ramp platform into the Oxfordian rimmed platform.Moreover,this study determined that the inner-ramp intertidal-subtidal shallow-water subfacies mainly developed during the Callovian and transitioned into the shallow shelf subfacies during the Oxfordian.This study identified eight sedimentary microfacies,namely reef knoll,reef-shoal complex,bioclastic shoal,psammitic shoal,bioherm,lime mud mound,intershoal(intermound),and static-water mud.Based on research into the high-precision sequence-sedimentary microfacies framework,this study built a geological model for the development of sedimentary microfacies in the study area.According to this geological model,the sedimentary microfacies in the study area are characterized by vertical alternation of reef-shoal complex,bioclastic(psammitic)shoal,bioherm,and intershoal microfacies.Moreover,they show the development of reef knoll,reef-shoal complex,bioclastic(psammitic)shoal,and bioherm(or lime mud mound)laterally from west to east,with the physical properties of the reservoirs deteriorating from west to east accordingly.The microfacies of reef-shoal complex and the bioclastic(psammitic)shoal predominate in the study area,and their deposition and development are controlled by sequence boundaries and are also affected by paleo-landforms.The Oxfordian reef-shoal complexes were largely inherited from the Callovian uplifts and show lateral seaward progradation.