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The evolution of the placenta is an excellent model to examine the evolutionary processes underlying adaptive complexity due to the recent, independent derivation of placentation in divergent animal lineages. In fishes, the family Poeciliidae offers the opportunity to study placental evolution with respect to variation in degree of post-fertilization maternal provisioning among closely related sister species. In this study, we present a detailed examination of a new reference transcriptome sequence for the live-bearing, matrotrophic fish, Poeciliopsis prolifica, from multiple-tissue RNA-seq data. We describe the genetic components active in liver, brain, late-stage embryo, and the maternal placental/ovarian complex, as well as associated patterns of positive selection in a suite of orthologous genes found in fishes. Results indicate the expression of many signaling transcripts, "non-coding" sequences and repetitive elements in the maternal placental/ovarian complex. Moreover, patterns of positive selection in protein sequence evolution were found associated with live-bearing fishes, generally, and the placental P. prolifica, specifically, that appear independent of the general live-bearer lifestyle. Much of the observed patterns of gene expression and positive selection are congruent with the evolution of placentation in fish functionally converging with mammalian placental evolution and with the patterns of rapid evolution facilitated by the teleost-specific whole genome duplication event.

Wide-ranging marine species are often described as having a low effective population size ([N.sub.e]) to census size (N) ratio. This genetic phenomenon is typically attributed to large variation among individuals in reproductive success because of the high mortality rates and unpredictable environments associated with larval dispersal. In this study, we examined patterns of genetic variation in gag (Mycteroperca microlepis) on the West Florida Shelf across year classes of post-settlement juveniles and spawning adults. With no significant genetic differentiation among year classes despite varying recruitment dynamics, little evidence for chaotic genetic patchiness, and no truncation of adult genetic diversity in subsequent juvenile cohorts, there was little support for large variation among individual in reproductive success contributing to a low [N.sub.e]/N ratio. In fact, the consistent lack of significant differences in annual recruitment classes indicated that reproductive success among individuals was resistant to skewing. among the various evolutionary forces that may be affecting Ne, changes to demography due to fishing pressure are posited as a likely mechanism affecting current levels of genetic variation., Introduction Understanding the population genetics of widespread marine species is essential for describing species cohesion and the regulation of genetic diversity. However, the spatial ecology and genetics of many marine [...]

Gag (Mycteroperca microlepis) from the eastern Gulf of Mexico and northwestern Atlantic are managed as separate stocks, although evidence for their demographic isolation remains equivocal. Several hundred individuals were genotyped at 11 microsatellite loci and it was found that gag across these regions were genetically indistinguishable (FST < 0.001). A coalescent-based computer simulation was employed to quantitatively assess the relative importance of dispersal rate, population size, and time since divergence on gag genetic homogeneity. Using empirical estimates of long-term effective population size (16 500), a range of dispersal rates and divergence times (500 to 500 000 generations) was modeled, and it was concluded that present-day genetic homogeneity must be maintained by dispersal rates of at least 20-30 migrants per generation and up to hundreds or thousands per generation. This study also documents the absence of significant temporal genetic structure and inbreeding in the Atlantic when comparing cohorts separated in time from weeks to 20 years. This suggests that the long-standing practice of overfishing gag has yet to manifest as an inbreeding effect. Overall, gag dispersal rates remain uncertain, and consequently, this study can neither support nor refute management schemes that independently regulate gag in the eastern Gulf of Mexico and northwestern Atlantic. Les badeches baillou (Mycteroperca microlepis) de l'est du golfe du Mexique et du nord-ouest de l'Atlantique sont gerees comme des stocks distincts, bien que les donnees sur leur isolement demographique restent equivoques. Nous avons determine le genotype a 11 locus microsatellites de plusieurs centaines d'individus et nous n'arrivons pas a distinguer genetiquement les badeches baillou dans l'ensemble de ces regions (FST < 0,001). Une simulation sur ordinateur basee sur la coalescence nous a servi a evaluer quantitativement l'importance relative du taux de dispersion, de la taille de la population et du temps depuis la divergence pour l'homogeneite genetique de la badeche. En utilisant des estimations empiriques de la taille effective de la population a long terme (16 500), nous avons modelise une gamme de taux de dispersion et de temps depuis la divergence (500 a 500 000 generations); il en ressort que l'homogeneite genetique actuelle doit etre maintenue par des taux de dispersion d'au moins 20-30 migrants par generation jusqu'a des centaines ou des milliers de migrants par generation. Notre etude note aussi l'absence de structure genetique temporelle significative et de consanguinite dans l'Atlantique dans des comparaisons de cohortes separees dans le temps par des periodes allant de semaines a 20 annees. Cela indique que la pratique de longue date de surpeche de la badeche baillou ne s'est pas encore manifeste e comme un effet de consanguinite. Globalement, les taux de dispersion de la badeche demeurent incertains et, en consequence, notre etude ne peut ni appuyer, ni rejeter les propositions de gestion qui controlent de facon independante les badeches baillou de l'est du golfe du Mexique et du nord-ouest de l'Atlantique. [Traduit par la Redaction], Introduction Fisheries managers use several criteria to determine whether species should be managed as a single stock or as multiple units (Begg and Waldman 1999; Fraser and Bernatchez 2001). From [...]

Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression ratio of X- and A-linked genes has been relatively well studied in humans and mice, despite controversial results over the existence of upregulation of X-linked genes. Here we report the first comprehensive test of Ohno's hypothesis in bovine preattachment embryos, germline, and somatic tissues. Overall an incomplete dosage compensation (0.5 < X:A < 1) of expressed genes and an excess X dosage compensation (X:A > 1) of ubiquitously expressed "dosage-sensitive" genes were seen. No significant differences in X:A ratios were observed between bovine female and male somatic tissues, further supporting Ohno's hypothesis. Interestingly, preimplantation embryos manifested a unique pattern of X dosage compensation dynamics. Specifically, X dosage decreased after fertilization, indicating that the sperm brings in an inactive X to the matured oocyte. Subsequently, the activation of the bovine embryonic genome enhanced expression of X-linked genes and increased the X dosage. As a result, an excess compensation was exhibited from the 8-cell stage to the compact morula stage. The X dosage peaked at the 16-cell stage and stabilized after the blastocyst stage. Together, our findings confirm Ohno's hypothesis of X dosage compensation in the bovine and extend it by showing incomplete and over-compensation for expressed and "dosage-sensitive" genes, respectively. [ABSTRACT FROM AUTHOR]

A preliminary genome sequence has been assembled for the Southern Ocean salp, Salpa thompsoni (Urochordata, Thaliacea). Despite the ecological importance of this species in Antarctic pelagic food webs and its potential role as an indicator of changing Southern Ocean ecosystems in response to climate change, no genomic resources are available for S. thompsoni or any closely related urochordate species. Using a multiple-platform, multiple-individual approach, we have produced a 318,767,936-bp genome sequence, covering >50% of the estimated 602 Mb (±173 Mb) genome size for S. thompsoni. Using a nonredundant set of predicted proteins, >50% (16,823) of sequences showed significant homology to known proteins and ~38% (12,151) of the total protein predictions were associated with Gene Ontology functional information. We have generated 109,958 SNP variant and 9,782 indel predictions for this species, serving as a resource for future phylogenomic and population genetic studies. Comparing the salp genome to available assemblies for four other urochordates, Botryllus schlosseri, Ciona intestinalis, Ciona savignyi and Oikopleura dioica, we found that S. thompsoni shares the previously estimated rapid rates of evolution for these species. High mutation rates are thus independent of genome size, suggesting that rates of evolution >1.5 times that observed for vertebrates are a broad taxonomic characteristic of urochordates. Tests for positive selection implemented in PAML revealed a small number of genes with sites undergoing rapid evolution, including genes involved in ribosome biogenesis and metabolic and immune process that may be reflective of both adaptation to polar, planktonic environments as well as the complex life history of the salps. Finally, we performed an initial survey of small RNAs, revealing the presence of known, conserved miRNAs, as well as novel miRNA genes; unique piRNAs; and mature miRNA signatures for varying developmental stages. Collectively, these resources provide a genomic foundation supporting S. thompsoni as a model species for further examination of the exceptional rates and patterns of genomic evolution shown by urochordates. Additionally, genomic data will allow for the development of molecular indicators of key life history events and processes and afford new understandings and predictions of impacts of climate change on this key species of Antarctic pelagic ecosystems. [ABSTRACT FROM AUTHOR]

We present a full genome sequence for the thermophilic denitrifier Geobacillus thermodenitrificans subsp. calidus DSM 22629 T (3,408,575 bp, 48.94% GC). This genome includes 3,615 predicted genes, including those needed to reduce nitrate to nitrogen gas. This organism and genome sequence provide valuable resources for future phylogenetic, genomic, and biotechnological research., Competing Interests: The authors declare no conflict of interest.