BackgroundThe process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly.ResultsIn Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies.ConclusionsMany current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

a b s t r a c t Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032 bp (COI + 28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.

Ancient climatic £uctuations have caused changes in the demography and distribution of many species. The genetic di¡erentiation between populations of the same species and of sister species is often attributed largely to the more recent Pleistocene £uctuations. Recent interpretations, which implicate earlier episodes, have proved controversial. We address the timing of genetic divergence in the Iberian lizard Lacerta schreiberi by studying the phylogeography of the cytochrome b sequence. The species has a remarkable morphological uniformity, yet our evidence suggests that earlier events in the Pliocene initiated the main divergence between populations. This interpretation implies that the di¡erent populations survived through the Pleistocene in separate localities. This conclusion is robust to di¡erent molecular clock calibrations. The persistence of earlier di¡erentiation through the Pleistocene has wide implications for our understanding of Pleistocene refugia in this species and, by extension, to the biogeography of the whole region.

The schism between North Africa and Southern Europe caused by the opening of the Strait of Gibraltar and the consequent refilling of the Mediterranean basin at the end of Messinian salinity crisis (MSC), 5.33 million years ago, has been advocated as the main event shaping biogeographical patterns in the western Mediterranean as exemplified by the distribution of species and subspecies and genetic variation within the ocellated lizard group. To reassess the role of the MSC, partial sequences of three mitochondrial DNA genes (cytochrome b, 12S and 16S ribosomal RNA) and two nuclear genes (b-fibrinogen and C-mos) from species of the ocellated lizard group were analysed. Three alternative hypotheses were tested: that divergence was initiated (i) by post-MSC vicariance as the basin filled, (ii) when separate populations established either side of the strait by pre-MSC overseas dispersal, and (iii) by post-MSC overseas dispersal. The pattern and level of divergence detected clearly refute the post-MSC vicariance hypothesis, and support a model of divergence initiated by earlier overseas dispersal. Indeed, our best estimate is that the basal Euro-African divergence predates the MSC event by several million years. The estimated divergence times among the populations in former Miocene Mediterranean islands, the current Betic and Rifian mountains, from adjacent mainland populations suggest overseas dispersal for the former and overland dispersal, or perhaps vicariance, for the latter. These results suggest that the MSC may have played a much less important role in shaping the current western Mediterranean biogeographical patterns than might have been anticipated from the dramatic nature of the episode.