Massive Molecular Parallel Evolution of the HSP90AA1 Gene between High-elevation Anurans

HSP90 AA1 is part of the heat shock protein 90 gene family and has important functions against heat stress. We report a case of molecular level parallel evolution of the HSP90 AA1 gene in high elevation amphibians. HSP90 AA1 gene sequences of four high-elevation anurans, Bufo gargarizans, Nanorana parkeri, Rana kukunoris, and Scutiger boulengeri, were compared along with five of their low-elevation relatives. A total of 16 amino-acid sites were identified as parallel evolution between N. parkeri and R. kukunoris. We generated both model based（Zhang and Kumar＇s test） and empirical data based（parallel/divergence plotting） null distributions for non-parallel evolution, and both methods clearly determined that the observed number of parallel substitutions were significantly more than the null expectation. Furthermore, on the HSP90 AA1 gene tree, N. parkeri and R. kukunoris formed a strongly supported clade that was away from their respective relatives. This study provides a clear case of molecular parallel evolution, which may have significant implications in understanding the genetic mechanisms of high-elevation adaptation.

Strategic flight assignment approach based on multi-objective parallel evolution algorithm with dynamic migration interval

The continuous growth of air traffic has led to acute airspace congestion and severe delays, which threatens operation safety and cause enormous economic loss. Flight assignment is an economical and effective strategic plan to reduce the flight delay and airspace congestion by rea- sonably regulating the air traffic flow of China. However, it is a large-scale combinatorial optimiza- tion problem which is difficult to solve. In order to improve the quality of solutions, an effective multi-objective parallel evolution algorithm （MPEA） framework with dynamic migration interval strategy is presented in this work. Firstly, multiple evolution populations are constructed to solve the problem simultaneously to enhance the optimization capability. Then a new strategy is pro- posed to dynamically change the migration interval among different evolution populations to improve the efficiency of the cooperation of populations. Finally, the cooperative co-evolution （CC） algorithm combined with non-dominated sorting genetic algorithm II （NSGA-II） is intro- duced for each population. Empirical studies using the real air traffic data of the Chinese air route network and daily flight plans show that our method outperforms the existing approaches, multi- objective genetic algorithm （MOGA）, multi-objective evolutionary algorithm based on decom- position （MOEA/D）, CC-based multi-objective algorithm （CCMA） as well as other two MPEAs with different migration interval strategies.

Phylogenomics and integrative taxonomy reveal two new species of Amana(Liliaceae)

Until now the genus Amana(Liliaceae),known as ’East Asian tulips’,has contained just seven species.In this study,a phylogenomic and integrative taxonomic approach was used to reveal two new species,Amana nanyueensis from Central China and A.tianmuensis from East China.A.nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts,but differs in its leaves and anthers.Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers,but differs in aspects of its leaves and bulbs.These four species are clearly separated from each other in principal components analysis based on morphology.Phylogenomic analyses based on plastid CDS further support the species delimitation of A.nanyueensis and A.tianmuensis and suggests they are closely related to A.edulis.Cytological analysis shows that A.nanyueensis and A tianmuensis are both diploid(2n=2x=24),different from A edulis,which is either diploid(northern populations) or tetraploid(southern populations,2n=4x=48).The pollen morphology of A.nanyueensis is similar to other Amana species(single-groove germination aperture),but A.tianmuensis is quite different because of the presence of a sulcus membrane,which creates the illusion of double grooves.Ecological niche modelling also revealed a niche differentiation between A.edulis,A.nanyueensis and A.tianmuensis.

一种基于并行搜索策略的苍狼算法

作为一种新型群体智能方法,苍狼算法模拟了苍狼在群体捕食过程中的搜索跟踪、包围、攻击等行为,具有结构简单、寻优能力强的特点。分析了该算法的优化机理,并对算法优化过程进行了数学定义及描述;提出了一种基于并行搜索策略的改进型苍狼算法,将狼群分组,在整个搜索过程中同时进行局部开发和全局探索活动,以更好地满足目标搜寻的要求。通过典型的基准测试函数对算法进行了性能仿真测试,实验结果表明,与其他群体智能优化方法相比,改进型苍狼算法在收敛速度、收敛精度及鲁棒性等方面均具有一定优势。

AERODYNAMIC OPTIMIZATION DESIGN OF LOW ASPECT RATIO TRANSONIC TURBINE STAGE

The advanced optimization method named as adaptive range differential evolution （ARDE） is developed. The optimization performance of ARDE is demonstrated using a typical mathematical test and compared with the standard genetic algorithm and differential evolution. Combined with parallel ARDE, surface modeling method and Navier-Stokes solution, a new automatic aerodynamic optimization method is presented. A low aspect ratio transonic turbine stage is optimized for the maximization of the isentropic efficiency with forty-one design variables in total. The coarse-grained parallel strategy is applied to accelerate the design process using 15 CPUs. The isentropic efficiency of the optimum design is 1.6% higher than that of the reference design. The aerodynamic performance of the optimal design is much better than that of the reference design.

Habitat-dependent diversification and parallel molecular evolution： Water scavenger beetles as a case study

Habitat shift is a key innovation that has contributed to the extreme diversification of insects. Most groups are well-adapted to more or less specific environments and shifts usually only happen between similar habitats. To colonize a pro- foundly different habitat type does not only present ecological opportunities but also great challenges. We used Hydrophiloidea （water scavenger beetles） as a system to study transitions between terrestrial and aquatic environments. We estimated the diversi- fication rate of different clades using phylogenetic trees based on a representative taxon sampling and six genes. We also investi- gated possible evolutionary changes in candidate genes following habitat shifts. Our results suggest that the diversification rate is relatively slow （0.039-0.050 sp/My） in the aquatic lineage, whereas it is distinctly increased in the secondarily terrestrial clade （0.055-0.075 sp/My）. Our results also show that aquatic species have a G （Glycine） or S （Serine） amino acid at a given site of COI, while terrestrial species share an A （Alanine） amino acid with terrestrial outgroups. This indicates that habitat factors may create selection pressure on the evolution of functional genes and cause homoplasy in molecular evolution [Current Zoology 60 （5）： 561-570, 2014 ]

The chromosome-scale assembly of the Notopterygium incisum genome provides insight into the structural diversity of coumarins

Coumarins,derived from the phenylpropanoid pathway,represent one of the primary metabolites found in angiosperms.The alignment of the tetrahydropyran(THP)and tetrahydrofuran(THF)rings with the lactone structure results in the formation of at least four types of complex coumarins.However,the mechanisms underlying the structural diversity of coumarin remain poorly understood.Here,we report the chromosome-level genome assembly of Notopterygium incisum,spanning 1.64 Gb,with a contig N50 value of 22.7 Mb and 60,021 annotated protein-coding genes.Additionally,we identified the key enzymes responsible for shaping the structural diversity of coumarins,including two p-coumaroyl CoA 2′-hydroxylases crucial for simple coumarins basic skeleton architecture,two UbiA prenyltransferases responsible for angular or linear coumarins biosynthesis,and five CYP736 cyclases involved in THP and THF ring formation.Notably,two bifunctional enzymes capable of catalyzing both demethylsuberosin and osthenol were identified for the first time.Evolutionary analysis implies that tandem and ectopic duplications of the CYP736 subfamily,specifically arising in the Apiaceae,contributed to the structural diversity of coumarins in N.incisum.Conclusively,this study proposes a parallel evolution scenario for the complex coumarin biosynthetic pathway among different angiosperms and provides essential synthetic biology elements for the heterologous industrial production of coumarins.

Evolutionary relationships of Pemphigus and allied genera （Hemiptera： Aphididae： Eriosomatinae） and their primary endosymbiont, Buchnera aphidicola

Aphids harbor primary endosymbionts, Buchnera aphidicola, in specialized cells within their body cavities. Aphids and Buchnera have strict mutualistic relationships in nutrition exchange. This ancient association has received much attention from researchers who are interested in endosymbiotic evolution. Previous studies have foundparallel phylogenetic relationships between non-galling aphids and Buchnera at lower taxonomic levels （genus, species）. To understand whether relatively isolated habitats such as galls have effect on the parallel relationships between aphids and Buchnera, the present paper investigated the phylogenetic relationships of gall aphids from Pemphigus and allied genera, which induce pseudo-galls or galls on Populus spp. （poplar） and Buchnera. The molecular phylogenies inferred from three aphid genes （COI, COII and EF-la） andtwo Buchnera genes （gnd, 16S rRNA gene） indicated significant congruence between aphids and Buchnera at generic as well as interspecific levels. Interestingly, both aphid andBuchnera phylogenies supported three main clades corresponding to the galling locations of aphids, namely leaf, the joint of leaf blade and petiole, and branch of the host plant.The results suggest phylogenetic conservatism of gall characters, which indicates gall characters are more strongly affected by aphid phylogeny, rather than host plants.

Molecular phylogeny of the genus Sticta (lichenized Ascomycota: Lobariaceae) in Colombia

We present a molecular phylogenetic study of the lichen genus Sticta focusing on Colombia,using the ITS fungal barcoding gene for a total of 370 ingroup OTUs,with 322 newly generated sequences.The topology resulting from a maximum likelihood approach does not support current species concepts in Sticta,which use a morphological concept,but in contrast shows that similar morphodemes evolved multiple times independently within the genus.As a consequence,currently applied names such as S.fuliginosa and S.weigelii comprise numerous(up to more than 20)unrelated species-level lineages,which can be distinguished also phenotypically using previously unrecognized characters such as lobe configuration,lobe surface structure,tomentum type,and anatomy of the basal membrane of the cyphellae.We conclude that the genus Sticta contains about four to five times the number of species currently recognized.In Colombia alone,approximately 150 species of Sticta are present.