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<jats:p> This special supplement to <jats:bold>Science</jats:bold> collects together summaries of both current and previous quality research conducted at Tianjin University and supported by the "973" Program, a central government funded initiative initiated by the Chinese Ministry of Science and Technology in June 1997. Its primary goal is to promote the advancement of science and technology in China, emphasizing basic and applied research that is aligned with national interests that will support national economic and social development. The program covers a very diverse range of research areas, from nanotechnology to energy efficiency to agriculture. Although the research covered in this supplement is only a sample of the many projects at Tianjin University, it is intended to provide the reader with a sense of the diversity and depth of work being performed under the "973" Program. As this program grows in the future, further scientific and technological advances will no doubt be forthcoming that benefit not only China and its people, but also researchers and citizens around the world. </jats:p> <jats:p> This booklet brought to you by the <jats:italic>Science</jats:italic> /AAAS Custom Publishing Office. </jats:p>

<jats:p> This special supplement to <jats:bold>Science</jats:bold> collects together summaries of both current and previous quality research conducted at Tianjin University and supported by the "973" Program, a central government funded initiative initiated by the Chinese Ministry of Science and Technology in June 1997. Its primary goal is to promote the advancement of science and technology in China, emphasizing basic and applied research that is aligned with national interests that will support national economic and social development. The program covers a very diverse range of research areas, from nanotechnology to energy efficiency to agriculture. Although the research covered in this supplement is only a sample of the many projects at Tianjin University, it is intended to provide the reader with a sense of the diversity and depth of work being performed under the "973" Program. As this program grows in the future, further scientific and technological advances will no doubt be forthcoming that benefit not only China and its people, but also researchers and citizens around the world. </jats:p> <jats:p> This booklet brought to you by the <jats:italic>Science</jats:italic> /AAAS Custom Publishing Office. </jats:p>

<jats:sec sec-type="intro"> <jats:title>Introduction</jats:title> <jats:p>The notion that species boundaries can be porous to introgression is increasingly accepted. Yet the broader role of introgression in evolution remains contentious and poorly documented, partly because of the challenges involved in accurately identifying introgression in the very groups where it is most likely to occur. Recently diverged species often have incomplete reproductive barriers and may hybridize where they overlap. However, because of retention and stochastic sorting of ancestral polymorphisms, inference of the correct species branching order is notoriously challenging for recent speciation events, especially those closely spaced in time. Without knowledge of species relationships, it is impossible to identify instances of introgression.</jats:p> </jats:sec> <jats:sec sec-type="other1"> <jats:title>Rationale</jats:title> <jats:p> Since the discovery that the single mosquito taxon described in 1902 as <jats:italic>Anopheles gambiae</jats:italic> was actually a complex of several closely related and morphologically indistinguishable sibling species, the correct species branching order has remained controversial and unresolved. This Afrotropical complex contains the world’s most important vectors of human malaria, owing to their close association with humans, as well as minor vectors and species that do not bite humans. On the basis of ecology and behavior, one might predict phylogenetic clustering of the three highly anthropophilic vector species. However, previous phylogenetic analyses of the complex based on a limited number of markers strongly disagree about relationships between the major vectors, potentially because of historical introgression between them. To investigate the history of the species complex, we used whole-genome reference assemblies, as well as dozens of resequenced individuals from the field. </jats:p> </jats:sec> <jats:sec sec-type="results"> <jats:title>Results</jats:title> <jats:p> We observed a large amount of phylogenetic discordance between trees generated from the autosomes and X chromosome. The autosomes, which make up the majority of the genome, overwhelmingly supported the grouping of the three major vectors of malaria, <jats:italic>An. gambiae</jats:italic> , <jats:italic>An. coluzzii</jats:italic> , and <jats:italic>An. arabiensis</jats:italic> . In stark contrast, the X chromosome strongly supported the grouping of <jats:italic>An. arabiensis</jats:italic> with a species that plays no role in malaria transmission, <jats:italic>An. quadriannulatus</jats:italic> . Although the whole-genome consensus phylogeny unequivocally agrees with the autosomal topology, we found that the topology most often located on the X chromosome follows the historical species branching order, with pervasive introgression on the autosomes producing relationships that group the three highly anthropophilic species together. With knowledge of the correct species branching order, we are further able to uncover introgression between another species pair, as well as a complex history of balancing selection, introgression, and local adaptation of a large autosomal inversion that confers aridity tolerance. </jats:p> </jats:sec> <jats:sec sec-type="conclusions"> <jats:title>Conclusion</jats:title> <jats:p> We identify the correct species branching order of the <jats:italic>An. gambiae</jats:italic> species complex, resolving a contentious phylogeny. Notably, lineages leading to the principal vectors of human malaria were among the first in the complex to radiate and are not most closely related to each other. Pervasive autosomal introgression between these human malaria vectors, including nonsister vector species, suggests that traits enhancing vectorial capacity can be acquired not only through de novo mutation but also through a more rapid process of interspecific genetic exchange. <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:p>Time-lapse photographs of an adult anopheline mosquito emerging from its pupal case.</jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="347_1258524_Fa.jpeg" /> </jats:fig> RELATED ITEMS IN <jats:italic>Science</jats:italic> D. E. Neafsey <jats:italic>et al</jats:italic> ., <jats:italic>Science</jats:italic> <jats:bold>347</jats:bold> , 1258522 (2015) </jats:p> </jats:sec>

<jats:sec sec-type="intro"> <jats:title>INTRODUCTION</jats:title> <jats:p> Control of mosquito vectors has historically proven to be an effective means of eliminating malaria. Human malaria is transmitted only by mosquitoes in the genus <jats:italic>Anopheles</jats:italic> , but not all species within the genus, or even all members of each vector species, are efficient malaria vectors. Variation in vectorial capacity for human malaria among <jats:italic>Anopheles</jats:italic> mosquito species is determined by many factors, including behavior, immunity, and life history. </jats:p> </jats:sec> <jats:sec sec-type="other1"> <jats:title>RATIONALE</jats:title> <jats:p> This variation in vectorial capacity suggests an underlying genetic/genomic plasticity that results in variation of key traits determining vectorial capacity within the genus. Sequencing the genome of <jats:italic>Anopheles gambiae</jats:italic> , the most important malaria vector in sub-Saharan Africa, has offered numerous insights into how that species became highly specialized to live among and feed upon humans and how susceptibility to mosquito control strategies is determined. Until very recently, similar genomic resources have not existed for other anophelines, limiting comparisons to individual genes or sets of genomic markers with no genome-wide data to investigate attributes associated with vectorial capacity across the genus. </jats:p> </jats:sec> <jats:sec sec-type="results"> <jats:title>RESULTS</jats:title> <jats:p> We sequenced and assembled the genomes and transcriptomes of 16 anophelines from Africa, Asia, Europe, and Latin America, spanning ~100 million years of evolution and chosen to represent a range of evolutionary distances from <jats:italic>An. gambiae</jats:italic> , a variety of geographic locations and ecological conditions, and varying degrees of vectorial capacity. Genome assembly quality reflected DNA template quality and homozygosity. Despite variation in contiguity, the assemblies were remarkably complete and searches for arthropod-wide single-copy orthologs generally revealed few missing genes. Genome annotation supported with RNA sequencing transcriptomes yielded between 10,738 and 16,149 protein-coding genes for each species. Relative to <jats:italic>Drosophila,</jats:italic> the closest dipteran genus for which equivalent genomic resources exist, <jats:italic>Anopheles</jats:italic> exhibits a dynamic genomic evolutionary profile. Comparative analyses show a fivefold faster rate of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses in <jats:italic>Anopheles</jats:italic> . Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. We also document evidence of variation in important reproductive phenotypes, genes controlling immunity to <jats:italic>Plasmodium</jats:italic> malaria parasites and other microbes, genes encoding cuticular and salivary proteins, and genes conferring metabolic insecticide resistance. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. </jats:p> </jats:sec> <jats:sec sec-type="conclusions"> <jats:title>CONCLUSIONS</jats:title> <jats:p> Anopheline mosquitoes exhibit a molecular evolutionary profile very distinct from <jats:italic>Drosophila</jats:italic> , and their genomes harbor strong evidence of functional variation in traits that determine vectorial capacity. These 16 new reference genome assemblies provide a foundation for hypothesis generation and testing to further our understanding of the diverse biological traits that determine vectorial capacity. </jats:p> <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:title>Geography, vector status, and molecular phylogeny of the 16 newly sequenced anopheline mosquitoes and selected other dipterans.</jats:title> <jats:p>The maximum likelihood molecular phylogeny of all sequenced anophelines and two mosquito outgroups was constructed from the aligned protein sequences of 1085 single-copy orthologs. Shapes between branch termini and species names indicate vector status and are colored according to geographic ranges depicted on the map.</jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="347_1258522_Fa.jpeg" /> </jats:fig> </jats:sec>

<jats:sec sec-type="other1"> <jats:title>Background</jats:title> <jats:p> The integration of graphene in photovoltaic modules, fuel cells, batteries, supercapacitors, and devices for hydrogen generation offers opportunities to tackle challenges driven by the increasing global energy demand. Graphene’s two-dimensional (2D) nature leads to a theoretical surface-to-mass ratio of ~2600 m <jats:sup>2</jats:sup> /g, which combined with its high electrical conductivity and flexibility, gives it the potential to store electric charge, ions, or hydrogen. Other 2D crystals, such as transition metal chalcogenides (TMDs) and transition metal oxides, are also promising and are now gaining increasing attention for energy applications. The advantage of using such 2D crystals is linked to the possibility of creating and designing layered artificial structures with “on-demand” properties by means of spin-on processes, or layer-by-layer assembly. This approach exploits the availability of materials with metallic, semiconducting, and insulating properties. </jats:p> </jats:sec> <jats:sec sec-type="other2"> <jats:title>Advances</jats:title> <jats:p>The success of graphene and related materials (GRMs) for energy applications crucially depends on the development and optimization of production methods. High-volume liquid-phase exfoliation is being developed for a wide variety of layered materials. This technique is being optimized to control the flake size and to increase the edge-to-surface ratio, which is crucial for optimizing electrode performance in fuel cells and batteries. Micro- or nanocrystal or flake edge control can also be achieved through chemical synthesis. This is an ideal route for functionalization, in order to improve storage capacity. Large-area growth via chemical vapor deposition (CVD) has been demonstrated, producing material with high structural and electronic quality for the preparation of transparent conducting electrodes for displays and touch-screens, and is being evaluated for photovoltaic applications. CVD growth of other multicomponent layered materials is less mature and needs further development. Although many transfer techniques have been developed successfully, further improvement of high-volume manufacturing and transfer processes for multilayered heterostructures is needed. In this context, layer-by-layer assembly may enable the realization of devices with on-demand properties for targeted applications, such as photovoltaic devices in which photon absorption in TMDs is combined with charge transport in graphene.</jats:p> </jats:sec> <jats:sec sec-type="other3"> <jats:title>Outlook</jats:title> <jats:p> Substantial progress has been made on the preparation of GRMs at the laboratory level. However, cost-effective production of GRMs on an industrial scale is needed to create the future energy value chain. Applications that could benefit the most from GRMs include flexible electronics, batteries with efficient anodes and cathodes, supercapacitors with high energy density, and solar cells. The realization of GRMs with specific transport and insulating properties on demand is an important goal. Additional energy applications of GRMs comprise water splitting and hydrogen production. As an example, the edges of MoS <jats:sub>2</jats:sub> single layers can oxidize fuels—such as hydrogen, methanol, and ethanol—in fuel cells, and GRM membranes can be used in fuel cells to improve proton exchange. Functionalized graphene can be exploited for water splitting and hydrogen production. Flexible and wearable devices and membranes incorporating GRMs can also generate electricity from motion, as well as from water and gas flows. </jats:p> <jats:fig fig-type="figure" orientation="portrait" position="float"> <jats:caption> <jats:title>Tailored GRMs for energy applications.</jats:title> <jats:p> The ability to produce GRMs with desired specific properties paves the way to their integration in a variety of energy devices. Solution processing and chemical vapor deposition are the ideal means to produce thin films that can be used as electrodes in energy devices (such as <jats:italic /> solar panels, batteries, fuel cells, or in hydrogen storage). Chemical synthesis is an attractive route to produce “active” elements in solar cell or thermoelectric devices. </jats:p> </jats:caption> <jats:graphic xmlns:xlink="http://www.w3.org/1999/xlink" orientation="portrait" position="float" xlink:href="347_1246501_Fa.jpeg" /> </jats:fig> </jats:sec>

<jats:p> During 2014, <jats:italic>Science</jats:italic> worked with members of the research community, other publishers, and representatives of funding agencies on many initiatives to increase transparency and promote reproducibility in the published research literature. Those efforts will continue in 2015. Connected to that progress, and an essential element to its success, an additional focus will be on making data more open, easier to access, more discoverable, and more thoroughly documented. My own commitment to these goals is deeply held, for I learned early in my career that interpretations come and go, but data are forever. </jats:p>

<jats:p>A roundup of weekly science policy and related news.</jats:p>

<jats:p>Maps of DNA's loops and folds advance—but may disagree.</jats:p>