A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.

Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.

Although most globins, including the N-terminal domains within chimeric proteins such as flavohemoglobins and globin-coupled sensors, exhibit a 3͞3 helical sandwich structure, many bacterial, plant, and ciliate globins have a 2͞2 helical sandwich structure. We carried out a comprehensive survey of globins in the genomes from the three kingdoms of life. Bayesian phylogenetic trees based on manually aligned sequences indicate the possibility of past horizontal globin gene transfers from bacteria to eukaryotes. BLASTP searches revealed the presence of 3͞3 single-domain globins related to the globin domains of the bacterial and fungal flavohemoglobins in many bacteria, a red alga, and a diatom. Iterated PSI-BLAST searches based on groups of globin sequences found that only the single-domain globins and flavohemoglobins recognize the eukaryote 3͞3 globins, including vertebrate neuroglobins, ␣-and ␤-globins, and cytoglobins. The 2͞2 globins recognize the flavohemoglobins, as do the globin coupled sensors and the closely related single-domain protoglobins. However, the 2͞2 globins and the globin-coupled sensors do not recognize each other. Thus, all globins appear to be distributed among three lineages: (i) the 3͞3 plant and metazoan globins, single-domain globins, and flavohemoglobins; (ii) the bacterial 3͞3 globin-coupled sensors and protoglobins; and (iii) the bacterial, plant, and ciliate 2͞2 globins. The three lineages may have evolved from an ancestral 3͞3 or 2͞2 globin. Furthermore, it appears likely that the predominant functions of globins are enzymatic and that oxygen transport is a specialized development that accompanied the evolution of metazoans.evolution ͉ sequences T hirty years ago, our knowledge of globin sequences was limited to vertebrate ␣-and ␤-globins, myoglobins (Mbs), and the symbiotic Hbs of legume plants. The ensuing years brought the discovery of 3͞3 nonsymbiotic plant Hbs (NsHbs) in plants, symbiotic Hbs in plants other than legumes, and chimeric f lavohemoglobins (FHbs), which are comprised of an Nterminal globin linked to an FAD reductase domain, in bacteria and yeasts (1-8). Concurrently, globins shorter than normal (Ͻ130 aa), the ''truncated'' Hbs, were observed in protozoa and bacteria (9, 10), and globins longer than normal (Ͼ150 aa), which aligned with the truncated Hbs, were found in green alga (11) and plants (12). The crystal structures of these globins (13-15) exhibited a novel globin fold comprised of a 2͞2 helical sandwich secondary structure. The recent rapid accumulation of genomic information has resulted in the discoveries of new types of globins, including the 3͞3 neuroglobins (Ngbs) and 3͞3 cytoglobins (Cygbs) believed to occur in all vertebrates (16), and of globins in organisms in which their presence had not been suspected, such as nematodes (17), an insect (18), and a urochordate (19). Furthermore, genomic data brought to light the existence of 3͞3 single-domain globins (SDgbs), which aligned with the globin domain of the FHbs (20). A class of generegulating, chimeric...

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Background: Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FADbinding domain and the gene-regulating globin coupled sensors, with variable C-terminal domains. The single-domain globins encompass sequences related to chimeric globins and «truncated» hemoglobins with a 2-over-2 instead of the canonical 3-over-3 α-helical fold.

We investigate the genetic structure and molecular selection pattern of a sympatric population of Sinorhizobium meliloti and Sinorhizobium medicae. These bacteria fix nitrogen in association with plants of the genus Medicago. A set of 116 isolates were obtained from a soil sample, from root nodules of three groups of plants representing among-species, within-species and intraline diversity in the Medicago genus. Bacteria were characterized by sequencing at seven loci evenly distributed along the genome of both Sinorhizobium species, covering the chromosome and the two megaplasmids. We first test whether the diversity of host plants influence the bacterial diversity recovered. Using the same data set, we then analyse the selective pattern at each locus. There was no relationship between the diversity of Medicago plants that were used for sampling and the diversity of their symbionts. However, we found evidence of selection within each of the two main symbiotic regions, located on the two different megaplasmids. Purifying selection or a selective sweep was found to occur in the nod genomic region, which includes genes involved in nodulation specificity, whereas balancing selection was detected in the exo region, close to genes involved in exopolysaccharide production. Such pattern likely reflects the interaction between host plants and bacterial symbionts, with a possible conflict of interest between plants and cheater bacterial genotypes. Recombination appears to occur preferentially within and among loci located on megaplasmids, rather than within the chromosome. Thus, recombination may play an important role in resolving this conflict by allowing different selection patterns at different loci.

Due to its proposed basal position in the bilaterian Tree of Life, Acoela may hold the key to our understanding of the evolution of a number of bodyplan features including the central nervous system. In order to contribute novel data to this discussion we investigated the distribution of a-tubulin and the neurotransmitters serotonin and RFamide in juveniles and adults of the sagittiferid Symsagittifera roscoffensis. In addition, we present the expression pattern of the neuropatterning gene SoxB1. Adults and juveniles exhibit six serotonergic longitudinal neurite bundles and an anterior concentration of serotonergic sensory cells. While juveniles show an ''orthogonlike'' arrangement of longitudinal neurite bundles along the anterior-posterior axis, it appears more diffuse in the posterior region of adults. Commissures between the six neurite bundles are present only in the anterior body region of adults, while irregularly distributed individual neurites, often interconnected by serotonergic nerve cells, are found in the posterior region. Anti-RFamide staining shows numerous individual neurites around the statocyst. The orthogon-like nervous system of S. roscoffensis is confirmed by a-tubulin immunoreactivity. In the region of highest neurotransmitter density (i.e., anterior), the HMG-box gene SrSoxB1, a transcription factor known to be involved in neurogenesis in other bilaterians, is expressed in juvenile specimens. Accordingly, SoxB1 expression in S. roscoffensis follows the typical pattern of higher bilaterians that have a brain. Thus, our data support the notion that Urbilateria already had the genetic toolkit required to form brain-like neural structures, but that its morphological degree of neural concentration was still low.

Using nitrogen-fixing Sinorhizobium species that interact with Medicago plants as a model system, we aimed at clarifying how sex has shaped the diversity of bacteria associated with the genus Medicago on the interspecific and intraspecific scales. To gain insights into the diversification of these symbionts, we inferred a topology that includes the different specificity groups which interact with Medicago species, based on sequences of the nodulation gene cluster. Furthermore, 126 bacterial isolates were obtained from two soil samples, using Medicago truncatula and Medicago laciniata as host plants, to study the differentiation between populations of Sinorhizobium medicae, Sinorhizobium meliloti bv. meliloti, and S. meliloti bv. medicaginis. The former two can be associated with M. truncatula (among other species of Medicago), whereas the last organism is the specific symbiont of M. laciniata. These bacteria were characterized using a multilocus sequence analysis of four loci, located on the chromosome and on the two megaplasmids of S. meliloti. The phylogenetic results reveal that several interspecific horizontal gene transfers occurred during the diversification of Medicago symbionts. Within S. meliloti, the analyses show that nod genes specific to different host plants have spread to different genetic backgrounds through homologous recombination, preventing further divergence of the different ecotypes. Thus, specialization to different host plant species does not prevent the occurrence of gene flow among host-specific biovars of S. meliloti, whereas reproductive isolation between S. meliloti bv. meliloti and S. medicae is maintained even though these bacteria can cooccur in sympatry on the same individual host plants.