1.Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for auditing by neutral parties, which is necessary for dispute resolution. 2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass-PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call 'metabarcoding'. 3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding. 4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.

The sea lamprey (Petromyzon marinus) serves as a comparative model for reconstructing vertebrate evolution. To enable more informed analyses, we developed a new assembly of the lamprey germline genome that integrates several complementary datasets. Analysis of this highly contiguous (chromosome-scale) assembly reveals that both chromosomal and whole-genome duplications have played significant roles in the evolution of ancestral vertebrate and lamprey genomes, including chromosomes that carry the six lamprey HOX clusters. The assembly also contains several hundred genes that are reproducibly eliminated from somatic cells during early development in lamprey. Comparative analyses show that gnathostome (mouse) homologs of these genes are frequently marked by Polycomb Repressive Complexes (PRCs) in embryonic stem cells, suggesting overlaps in the regulatory logic of somatic DNA elimination and repressive/bivalent states that are regulated by early embryonic PRCs. This new assembly will enhance diverse studies that are informed by lampreys’ unique biology and evolutionary/comparative perspective.

The highly anticipated transition from next generation sequencing (NGS) to third generation sequencing (3GS) has been difficult primarily due to high error rates and excessive sequencing cost. The high error rates make the assembly of long erroneous reads of large genomes challenging because existing software solutions are often overwhelmed by error correction tasks. Here we report a hybrid assembly approach that simultaneously utilizes NGS and 3GS data to address both issues. We gain advantages from three general and basic design principles: (i) Compact representation of the long reads leads to efficient alignments. (ii) Base-level errors can be skipped; structural errors need to be detected and corrected. (iii) Structurally correct 3GS reads are assembled and polished. In our implementation, preassembled NGS contigs are used to derive the compact representation of the long reads, motivating an algorithmic conversion from a de Bruijn graph to an overlap graph, the two major assembly paradigms. Moreover, since NGS and 3GS data can compensate for each other, our hybrid assembly approach reduces both of their sequencing requirements. Experiments show that our software is able to assemble mammalian-sized genomes orders of magnitude more quickly than existing methods without consuming a lot of memory, while saving about half of the sequencing cost.