The Hardwood Genomics Database (HGD, www.hardwoodgenomics.org) serves forest tree scientists by providing online access to hardwood tree genomic and genetic data. HGD currently houses data for economically and phylogenetically important hardwood species including assembled reference genomes, transcriptomes, and genetic mapping information. The results of bioinformatic analysis including functional annotation of genes, ontology assignment, analysis of gene expression patterns across RNASeq libraries and simple sequence repeat (SSR) identification are available to enhance the utility of the information. The web site provides access to online tools for mining and visualization of these data sets, including BLAST for comparing sequences, Jbrowse1 for browsing genomes, Apollo2 for community annotation and SyMAP3 for comparative genomics. However, these tools are limited in scope. To maximize the ability for users of community databases to harness this information and perform their own custom analysis, we are collaborating with other genome databases to build an interface to the Galaxy data analysis platform4. Users will be able to select and transfer data from the HGD to a Galaxy instance or run a pre-designed Galaxy workflow on selected datasets.

Online community genome databases offer curated and mission-specific data and information to scientists with shared basic and applied research goals. In an effort to share a common code base, standardize storage formats, and simplify site construction, a coalition of genome databases have developed the software Tripal . Tripal is an open-source platform that bridges Drupal , a popular content management system (CMS), and Chado , a standardized relational database for storage of biological data. There is a need for users of community databases to not only discover, visualize and download genomic information but to directly port it to analysis workflow software such as the Galaxy platform. Through development of the new Tripal Galaxy module, site visitors will be able to select custom datasets from within and across Tripal databases and import those directly to a Galaxy instance from within a Tripal-based site. Additionally, a set of pre-designed workflows for common analyses needed by users of community databases will be made publicly available, including functional annotation of gene sequences, genomic variant discovery and genotype/phenotype association. Current efforts are focused on enabling authenticated users to move data from within a Tripal community database to the Tripal community Galaxy instance or a public Galaxy instance, creation of PHP bindings for the Galaxy API, and establishment of the most commonly needed analysis workflows for database users.

BACKGROUND:Rhynchocypris oxycephalus is a cold water fish with a wide geographic distribution including the relatively warm temperate regions of southern China. It also occurs in second- and third-step geomorphic areas in China. Previous studies have postulated that high-altitude populations of R. oxycephalus in southern China are Quaternary glacial relics. In this study, we used the mitochondrial gene Cytb and the nuclear gene RAG2 to investigate the species phylogeographical patterns and to test two biogeographic hypotheses: (1) that divergence between lineages supports the three-step model and (2) climatic fluctuations during the Quaternary resulted in the present distribution in southern China.RESULTS:Phylogenetic analysis detected three major matrilines (A, B, and C); with matrilines B and C being further subdivided into two submatrilines. Based on genetic distances and morphological differences, matriline A potentially represents a cryptic subspecies. The geographic division between matrilines B and C coincided with the division of the second and third geomorphic steps in China, suggesting a historical vicariance event. Pliocene climatic fluctuations might have facilitated the southwards dispersal of R. oxycephalus in matriline C, with the subsequent warming resulting in its split into submatrilines C1 and C2, leaving submatriline C2 as a relic in southern China.CONCLUSIONS:Our study demonstrates that geological events (three steps orogenesis) and climate fluctuations during the Pliocene were important factors in shaping phylogeographical patterns in R. oxycephalus. Notably, no genetic diversity was detected in several populations, all of which possessed unique genotypes. This indicates the uniqueness of local populations and calls for a special conservation plan for the whole species at the population level.

The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1-2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish.

Global climate change has been suggested to cause decrease of distribution area of many species. However, this has not been tested for East Asian inland coldwater fish. Chinese minnow (Rhynchocypris oxycephalus) is a small typical coldwater fish, which is endemic to East Asia and generally inhabits stream headwaters. Due to its occurrence in temperate south China, there is growing concern about its future fate in the face of global warming. In this study, we employed maximum entropy approach to analyze how distribution of this species would be impacted by future climate change. We collected data of 310 independent distribution points and 20 environmental variables, and conducted modeling under three general circulation models assuming two gas emission scenarios for 2020s, 2050s, and 2080s. The results showed that the Min temperature of coldest month was the most important climatic variable for potential distribution of the Chinese minnow. Modeling predicted geographical distribution of the Chinese minnow would shrink over time and become much more limited in all the situations especially in South-eastern China, and there would be little suitable habitat left in this region by 2080s. Our results confirm that climate change clearly poses a severe threat to the Chinese minnow, and we suggest that conservation efforts should focus on lower temperature areas within the current range, because these areas will remain relatively cool and may be still suitable for the Chinese minnow even under the most drastic climate change scenarios.