Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.

Whole-genome shotgun assembly has been a long-standing issue for highly polymorphic genomes, and the advent of nextgeneration sequencing technologies has made the issue more challenging than ever. Here we present an automated pipeline, HaploMerger, for reconstructing allelic relationships in a diploid assembly. HaploMerger combines a LASTZChainNet alignment approach with a novel graph-based structure, which helps to untangle allelic relationships between two haplotypes and guides the subsequent creation of reference haploid assemblies. The pipeline provides flexible parameters and schemes to improve the contiguity, continuity, and completeness of the reference assemblies. We show that HaploMerger produces efficient and accurate results in simulations and has advantages over manual curation when applied to real polymorphic assemblies (e.g., 4%-5% heterozygosity). We also used HaploMerger to analyze the diploid assembly of a single Chinese amphioxus (Branchiostoma belcheri ) and compared the resulting haploid assemblies with EST sequences, which revealed that the two haplotypes are not only divergent but also highly complementary to each other. Taken together, we have demonstrated that HaploMerger is an effective tool for analyzing and exploiting polymorphic genome assemblies.

N-α-acetyltransferase 10 protein, Naa10p, is an N-acetyltransferase known to be involved in cell cycle control. We found that Naa10p was expressed lower in varieties of malignancies with lymph node metastasis compared with non-lymph node metastasis. Higher Naa10p expression correlates the survival of lung cancer patients. Naa10p significantly suppressed migration, tumor growth, and metastasis independent of its enzymatic activity. Instead, Naa10p binds to the GIT-binding domain of PIX, thereby preventing the formation of the GIT-PIX-Paxillin complex, resulting in reduced intrinsic Cdc42/Rac1 activity and decreased cell migration. Forced expression of PIX in Naa10-transfected tumor cells restored the migration and metastasis ability. We suggest that Naa10p functions as a tumor metastasis suppressor by disrupting the migratory complex, PIX-GIT- Paxillin, in cancer cells.

The ability to form cooperative societies may explain why humans and social insects have come to dominate the earth. Here we examine the ecological consequences of cooperation by quantifying the fitness of cooperative (large groups) and non-cooperative (small groups) phenotypes in burying beetles (Nicrophorus nepalensis) along an elevational and temperature gradient. We experimentally created large and small groups along the gradient and manipulated interspecific competition with flies by heating carcasses. We show that cooperative groups performed as thermal generalists with similarly high breeding success at all temperatures and elevations, whereas non-cooperative groups performed as thermal specialists with higher breeding success only at intermediate temperatures and elevations. Studying the ecological consequences of cooperation may not only help us to understand why so many species of social insects have conquered the earth, but also to determine how climate change will affect the success of these and other social species, including our own.DOI: http://dx.doi.org/10.7554/eLife.02440.001

Studies on the evolution of tropical taxa emphasize the role of vicariance and the break‐up of Gondwana in explaining modern distributions. Earlier studies on figs (Ficus spp.) support this view. In the current study, we used an expanded sample (208 spp.) and improved molecular dating techniques to reconstruct the phylogenetic and biogeographic history of Ficus. Consistent with previous studies, our biogeographic analysis indicated that the ancestor of Ficus was present in Gondwana. However, a relaxed clock analysis relying on uncorrelated rates in BEAST suggested that the Neotropical section Pharmacosycea split‐off in South America 86.67 Mya, and that other Ficus lineage ancestors originated in India. Most of the basal lineages appeared to have diverged following KT extinction, then rapidly diversified after India collided with continental Asia. The Afrotropical species most likely evolved initially in the Indian subcontinent then dispersed to Africa, either in the late Cretaceous of Madagascar or even later, following the Eocene collision of India with Asia. The Neotropical section Americana, either island‐hopped to South America or took a northern route to the Americas through Europe prior to the terminal Eocene global cooling event. Ficus may have arrived in eastern Malesia following the collision of India with Asia, then widely dispersed thereafter. Given the wide ranges in our date estimates, several other scenarios are possible. However, contrary to earlier reports, our analyses suggest that vicariance played a relatively minor role compared with ecological opportunity and dispersal in the diversification of genus Ficus.

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The species of the firefly genus Vesta occurring in Taiwan are revised. Three species are recognized: Vesta scutellonigra Olivier (nomen emendatum), V. impressicollis Fairmaire, and V. rufiventris (Motschulsky). Vesta chevrolatii var. scutello nigro Olivier is automatically emended to scutellonigra under ICZN rules. Okada described as a distinct species V. scutellonigra, employing the same name and material as Olivier, thereby automatically rendering his taxon a junior synonym (n. syn.). The name V. scutellonigro, simultaneously employed by Okada, is considered an incorrect subsequent spelling and therefore unavailable. Vesta formosana Pic (n. syn.) is a new junior synonym of V. scutellonigra. The spelling chevrolati, employed by Gemminger and Harold, is determined to be an incorrect subsequent spelling of chevrolatii and thus unavailable. Lectotypes are newly designated for V. scutellonigra Olivier, V. impressicollis Fairmaire, and V. formosana Pic. A key to the species of Taiwan is provided. Vesta flaviventris (Fairmaire) (n. comb.) from China is transferred from Lucernuta.

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