No description available.

Complete DNA sequences were determined for the mitochondrial (mt) genomes of the sea anemones, Mesactinia genesis ¡]20,544 bp¡^, Heteractis aurora (19,800 bp) and partial mtDNA between cox2 and nad4 of the Calliactis sp. (3,713 bp). In addition, complete mtDNA sequences were determined for the sea squirt, Eudistoma gilboviride (14,203 bp). The circular, sea anemones genomes contain the genes for 13 energy pathway proteins and two ribosomal RNAs and two transfer RNAs. H. aurora contains a previously undescribed ORF between the cox2 and nad4 genes encoding a putative protein of 646 amino acids. In M. geneisis and Calliactis sp. encodes two separate smaller ORFs of 259 and 243 as well as 269 and 345 in the corresponding regions, respectively. Possible control region of the mitochondrial genomes of M. geneisis and H. aurora were identified in the intergenic region 13. The sea squirt genomes contain the genes for 11 energy pathway proteins and two rRNAs and 22 tRNAs. All genes are encoded by the heavy strand, except for trnM, trnK, and trnV, which are encoded by the light strand. The ascidians showed frequent and extensive gene rearrangement. The gene order in E. gilboviride are very much different from the other ascidians mt-genome. The E. gilboviride mtDNA does not encode the nad6 and a tpyical atp8. Molecular phylogenetic analyses based on nucleic acid and amino acid sequences of the deuterostome (echinoderms, chordate and Xenoturbella), and cnidaria coincide with the morphological characters.

Abstract Analyses of mitochondrial control region sequences were used to infer phylogeny of Anser species, phylogeography of the lesser white-fronted goose, and genetic background of a captive stock. The genetic distances among the Anser species ranged from 0.9 to 5.5% in the complete control region sequences and supported the view of close relatedness of these species. Among the four most closely related species, the bean, pink-footed, white-fronted and lesser white-fronted goose, the branching order is uncertain. The short internal branches and low support for the branching order suggest that the species have diverged recently within short time-intervals. The mtDNA tree obtained is incongruent with the traditional view of the species relationships, but the reasons for this remain to be clarified. Two diverged mitochondrial lineages were found in the lesser white-fronted goose and a refugial origin was proposed. Basal haplotypes are geographically widespread and indicate a recent common ancestry for populations. The derived haplotypes are confined to singular breeding populations and suggest restrictions to the present female gene flow. A shift in the frequency of the mtDNA lineages approximately coincides with a migratory divide in the Taimyr Peninsula. Low mtDNA diversity and significant difference in the haplotype frequencies observed in Fennoscandian subpopulation suggested that it should be considered as a management unit. The fossil record was examined to gain additional information about the colonisation history of the species, but was found to be of limited use. The captive lesser white-fronted goose stock used for reintroduction/restocking was shown to be incompatible with the Fennoscandian wild population. Some captive individuals carried the mtDNA of the white-fronted goose suggesting a hybrid origin. Hybridisation has probably occurred during captive propagation, but to clarify further the extent of introgression, nuclear markers should be applied. The structure and evolution of the control region were studied by comparing complete avian sequences. Saturation was found to occur at pairwise divergences of 10% as shown for third codon positions of the mitochondrial genes previously. In pairwise comparisons of the control region and cytochrome b sequences, the rate of divergence varied among the lineages. Two conserved sequence blocks showed considerable sequence conservation when compared to mammalian sequences.

Sequence variation of a 238 bp segment of the mitochondrial control region was analyzed for 1,568 Steller sea lions (2.8% of the estimated species population) sampled from 50 rookeries representing nearly every locality at which Steller sea lions are known to breed in significant numbers. Haplotype diversity (H = 0.9164 ± 0.0035) was high and nucleotide diversity (π = 0.00967 ± 0.00586) was moderate. No evidence was observed for significant genetic bottleneck effects. Rookeries were grouped into regions and stocks to examine structure at different spatial scales. F- and Φ-statistics were computed for all pairwise comparisons of rookeries, regions and stocks. Significant (P<0.05) divergence of eastern stock (southeastern Alaska to California) animals from western stock animals was supported in analyses at all spatial scales. Likewise, rookeries and regions from Asia were found to be significantly different from all other western stock rookeries. This was most clearly demonstrated using Φ-statistics at the regional level. The Commander Islands clearly associate with Alaskan western stock rookeries, not with the Asian rookeries. Within each of the three stocks there is significant isolation by distance among rookeries. This relationship does not hold for inter-stock comparisons indicating that there are important barriers to gene flow among stocks. Mitochondrial DNA analysis supports the recognition of three stocks for appropriate conservation of the species. The currently recognized eastern stock is unaffected, but the western stock is now partitioned west of the Commander Islands yielding a western stock which ranges from Prince William Sound west to the Commander Islands, and an Asian stock including rookeries from the Kamchatka Peninsula, Kuril Islands, and Sea of Okhtosk.

Genetic analyses of two endangered species of mammals in the Lower Keys of Florida (Lower Keys marsh rabbit, LKMR, Sylvilagus palustris hefneri; silver rice rat, SRR, Oryzomys palustris natator) were performed to evaluate the genetic structure of their populations. Mitochondrial sequence data (control region; 763 base pairs (bp), LKMR; 788 bp, SRR) were used to explore patterns of genetic variation within and among island populations in both species. Analysis of the SRR also included 8 polymorphic nuclear microsatellite loci (9 to 16 alleles). Phylogenetic analyses of mitochondrial sequence data for both species revealed two main lineages corresponding to eastern and western localities, with high levels of genetic structuring (LKMR FST = 0.982, SRR ΦST = 0.916). The two species differed in the level of sequence divergence between eastern and western populations (LKMR, 19 bp; SRR 4 bp). In addition to an overall similar pattern of genetic subdivision, populations of both species possessed low levels of mtDNA variation (haplotypic diversity in the LKMR = 66.1%, SRR = 58.6%). Microsatellite analyses of the SRR revealed subdivision between eastern and western regions. Although less pronounced than the structure observed in mtDNA, the overall pattern was still apparent. Additional examination of divergence between mainland and Lower Keys rice rats revealed a genetic division that indicated a lack of recent gene exchange between the regions (i.e. no shared haplotypes, the presence of private alleles, and distinctive separation in numerous analyses). Although this degree of division does not warrant species designation, the levels and patterns of divergence, both morphological and genetic, do suggest genetic isolation of mainland and island forms. This fact, along with restricted gene flow between the Lower Keys and the Everglades, suggests that the SRR is on an evolutionary trajectory separate from its mainland counterparts and validates its identification as a separate subspecies, Oryzomys palustris natator. Finally, the genetic division between eastern and western populations of the SRR and LKMR suggests that populations of both species in these two regions of the Lower Keys should be treated as separate management units, especially when considering the enhancement of populations via translocations.

Sequence variation of a 238 bp segment of the mitochondrial control region was analyzed for 1,568 Steller sea lions (2.8% of the estimated species population) sampled from 50 rookeries representing nearly every locality at which Steller sea lions are known to breed in significant numbers. Haplotype diversity (H = 0.9164 ± 0.0035) was high and nucleotide diversity (π = 0.00967 ± 0.00586) was moderate. No evidence was observed for significant genetic bottleneck effects. Rookeries were grouped into regions and stocks to examine structure at different spatial scales. F- and Φ-statistics were computed for all pairwise comparisons of rookeries, regions and stocks. Significant (P<0.05) divergence of eastern stock (southeastern Alaska to California) animals from western stock animals was supported in analyses at all spatial scales. Likewise, rookeries and regions from Asia were found to be significantly different from all other western stock rookeries. This was most clearly demonstrated using Φ-statistics at the regional level. The Commander Islands clearly associate with Alaskan western stock rookeries, not with the Asian rookeries. Within each of the three stocks there is significant isolation by distance among rookeries. This relationship does not hold for inter-stock comparisons indicating that there are important barriers to gene flow among stocks. Mitochondrial DNA analysis supports the recognition of three stocks for appropriate conservation of the species. The currently recognized eastern stock is unaffected, but the western stock is now partitioned west of the Commander Islands yielding a western stock which ranges from Prince William Sound west to the Commander Islands, and an Asian stock including rookeries from the Kamchatka Peninsula, Kuril Islands, and Sea of Okhtosk.

No description available.

ABSTRACT Spiny softshell turtles (Apalone spinifera) occur at the northwest limit of their range in Lake Champlain. This species, although widespread across North America, is listed as threatened in Vermont due to habitat destruction and disturbances of anthropogenic origin. The population of spiny softshell turtles in Lake Champlain is isolated from other North American populations and is considered as an independent management unit. Efforts to obtain information on the biology of spiny softshell turtles in Lake Champlain precede 1936 with conservation measures being initiated in 1987. Methods of studying spiny softshell turtles in Lake Champlain have included direct observation, mark-recapture, nest beach monitoring, winter diving, and radio telemetry. Each of these approaches has provided some information to the sum of what is known about A. spinifera in Lake Champlain. For example major nesting beaches, hibernacula, and home range size have been determined. Currently spiny softshell turtles primarily inhabit two areas within Lake Champlain, Missisquoi Bay and the mouth of the Lamoille River. However, the population structure and gene flow between spiny softshell turtles inhabiting the Lamoille and Missisquoi regions remained unknown. A GIS model was created and tested in order to identify additional nesting beaches used by spiny softshell turtles along the Vermont shores of Lake Champlain. Although some additional small potential nesting beaches were found, no additional major nesting sites were found. The GIS model identified the mouth of the Winooski River (the site of a historical population) as potentially suitable nesting habitat; however, no evidence of spiny softshell turtle nesting was found at this site. A series of methods developed for collecting molecular and population genetic data about spiny softshell turtles in Lake Champlain are described, including techniques for DNA extraction of various tissue types and the design of new primers for PCR amplification and sequencing of the mitochondrial control region (mtD-loop). Techniques for circumventing problems associated with DNA sequence alignment in regions of a variable numbers of tandem repeats (VNTRs) and the presence of heteroplasmy within some individuals are also described. The mtD-loop was found to be a suitable marker to assess the genetic structure of the Lake Champlain population of spiny softshell turtles. No significant genetic sub-structuring was found (FST=0.082, p=0.223) and an indirect estimate of the migration rate between Lamoille and Missisquoi regions of Lake Champlain was high (Nm>5.576). In addition to consideration of A. spinifera in Lake Champlain, the mtD-loop was modeled across 46 species in 14 families of extant turtles. The primary structure was obtained from DNA sequences accessed from GenBank and secondary structures of the mtD-loop were inferred, (from thermal stabilities) using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order of turtles; however, the inclusion of an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop was common across all turtle families considered. The Cryptodira showed conservation in the primary structure at regular conserved sequence blocks (CSBs), but the Pluerodira displayed little conservation in the primary structure of the mtD-loop. Overall, greater conservation in secondary structure than primary structure was observed in turtle mtD-loop. The AT-rich secondary structural element near the 3' terminus of the mtD-loop may be conserved across turtles due to it serving a functional role during mtDNA transcription.

ABSTRACT Ethanol is a classic teratogen capable of inducing a wide range of developmental abnormalities that vary in severity, from the barely perceptible to spontaneous abortion. These defects are collectively referred to as foetal alcohol spectrum disorders (FASD). Foetal alcohol syndrome (FAS) lies at the extreme end of this spectrum and is associated with three broad domains: prenatal and/or postnatal growth retardation, distinctive facial features and brain damage. Epidemiological and animal studies clearly indicate that the clinical variability of FASD is related to four distinct window periods: preconception, preimplantation, gastrulation and postorganogenesis. These developmental windows are correlated with peak periods of epigenetic reprogramming, suggesting a common mechanism of ethanol teratogenesis. Together with experimental evidence that ethanol inhibits DNA-methyltransferase, as well as folate metabolism, this suggests an ‘epigenetic model of FASD’. The aim of the present study was to explore the validity of this model by investigating the relationship between ethanol-induced growth retardation and imprinting, following ethanol exposure during the preimplantation period. Employing an experimental study design, together with a hybrid mouse model, embryos and placentae were harvested at 10.5 days post coitus (dpc). The weights of embryos and placentae, as well as methylation profiles at the H19 imprinting control region (ICR) – an important regulator of growth - were measured. It was found that ethanol-treated embryos and placentae were severely growth retarded in comparison to controls: r=-0.760 (p<0.01, one-tailed) and r=-0.816 (p<0.05, two-tailed), respectively. Bisulphite genomic sequencing revealed that the methylation profile at the H19 ICR was unaffected in ethanol-treated embryos, in comparison to saline-treated controls. Conversely, methylation at the paternal and maternal alleles in placentae was found to be reduced and increased, respectively, in comparison to embryos. These results imply that mechanisms for the maintenance of imprinting in the embryo are more robust than in the placenta. This is consistent with the relatively longlived nature of the embryo, which must maintain imprinting for a considerably longer period of time than the placenta. Bisulphite sequencing also revealed that the paternal allele of the H19 ICR had significantly decreased levels of methylation, while the maternal allele had increased levels of methylation, in ethanol treated-placentae, in comparison to saline controls. The changes observed at the paternal allele were localized to the CTCF1 DNA-binding site, while a trend for increased methylation at the maternal allele was observed at the CTCF2 site. A partial correlation further revealed that demethylation at the paternal allele in placentae partly mediated the effect of ethanol on placental weight. An ‘epigenetic switch model’, whereby paternal Igf2 is downregulated by the epigenetic switching of the paternal allele to the maternal epigenotype, is proposed to explain this relationship. However, partial correlations also indicated that demethylation at the paternal allele of the H19 ICR, as well as placental growth retardation, did not mediate the effect of ethanol on embryo growth. Collectively, these data suggest that imprinting at the H19 ICR is not a mechanism of embryo growth retardation prior to 10.5 dpc. In explaining these results, it is proposed that the growth retarded placenta was able to meet the nutritional demands of the similarly growth retarded embryo up until 10.5 dpc. However, an important question for future research would be to examine the relationship between ethanol-induced growth retardation and imprinting during late gestation. During the final growth spurt (>14.5 dpc) the growth retarded placenta may become unable to meet the increased demands for nutrition, which would exacerbate foetal growth restriction. In sum, the present study revealed a novel mechanism of ethanol-induced growth retardation in the placenta but indicated that imprinting at the H19 ICR does not mediate the effect of ethanol on the early embryo. Further research is required to resolve the relationship between imprinting and ethanol-induced growth retardation.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Crassostrea (Sacco, 1897) é o gênero mais importante do mundo de ostras de cultivo e consiste de 34 espécies distribuídas pelas regiões tropicais e temperadas do globo. C. gasar e C. rhizophorae são as duas espécies nativas que estão distribuídas ao longo de toda a costa do Brasil até o Caribe. C. gasar também ocorre na costa da Africa. Ainda que sua distribuição seja extensa e com disponibilidade abundante, o cultivo de ostras nativas no Brasil ainda é incipiente e a delimitação correta dos estoques mantém-se incerta. O sucesso do desenvolvimento da malacocultura, que é recomendada internacionalmente como forma sustentável de aquicultura, depende da resolução desses problemas. Assim, com o objetivo de determinar geneticamente seus estoques no Atlântico como também estimar sua história demográfica, dois diferentes marcadores moleculares foram empregados: sequências de DNA da região controle mitocondrial e loci de microssatélites espécie-especifícos, desenvolvidos no presente estudo. Foram sequenciados fragmentos da região controle de um total de 930 indivíduos de C. gasar e C. rhizophorae coletados em 32 localidades que incluíram o Caribe, a Guiana Francesa, a costa brasileira e a África. Também foram realizadas genotipagens de 1178 indivíduos, e ambas as espécies, com 9 e 11 loci de microssatélites para C. gasar e C. rhizophorae, respectivamente. Os dados genéticos foram analisados através de diferentes abordagens (índices de estruturação (FST) e de (Jost D), análise molecular de variância (AMOVA), análise espacial molecular de variância (SAMOVA), Bayesian Skyline Plots (BSP), análise fatorial de correspondência (AFC) e análise de atribuição Bayesiana (STRUCTURE)). Os resultados indicaram um padrão geral de estruturação, onde dois diferentes estoques foram detectados para ambas as espécies: grupos do norte e do sul, onde o Rio de Janeiro seria a região limitante entre os dois estoques. Os maiores valores dos índices de estruturação foram encontrados para C. gasar, indicando que esta espécie estaria mais estruturada do que C. rhizophorae. As análises demográficas indicaram uma provável expansão das populações durante o ultimo período glacial e uma possível origem americana das populações africanas. Todos os resultados sugeriram a existência de uma barreira geográfica próxima ao Rio de Janeiro, que poderia ser a cadeia de Vitória-Trindade e o fenômeno de ressurgência que ocorre em Cabo Frio (RJ). Esses resultados serão de grande utilidade para estabelecer critérios para seleção de sementes para cultivo ao longo da costa do Brasil que permitirá o manejo adequado dos estoques ostreícolas, prevenindo seu desaparecimento como já ocorrido em outros recifes no mundo. / Crassostrea (Sacco, 1897) is the most important genus of cultivated oysters in the world and consisting of 34 species distributed by tropical and temperate regions of the globe. C. gasar and C. rhizophorae are the two native species which have wide distribution along the entire Brazilian coast up to the Caribbean. C. gasar also occurs on coast of Africa. Despite its extensive distribution and abundant availability, cultivation of those oysters in Brazil is incipient, and the correct delimitation of the existing stocks is still uncertain. The successful development of malacoculture which is recommended internationally as an environmentally sustainable form of aquaculture depends on the resolution of these issues. Thus, in order to genetically determinate their stocks in the Atlantic and to estimate their demographic history, two different molecular markers were employed: sequences of the mitochondrial DNA control region and species-specific microsatellite loci, developed in the present study. We have sequenced a fragment of the mitochondrial control region from a total of 930 individuals of C. gasar and C. rhizophorae collected in 32 localities including the Caribbean, French Guyana, Brazilian coast and Africa. We have also genotyped 1178 individuals of both species with 9 and 11 loci of microsatellites for C. gasar and C. rhizophorae, respectively. Genetic data were analyzed with different approaches (fixation (FST) and differentiation (Jost D) indices, analysis of molecular variance (AMOVA), spatial analysis of molecular variance (SAMOVA), Bayesian Skyline Plots (BSP), factorial correspondence analysis (AFC) and Bayesian attribution analysis (STRUCTURE)). The results indicated a general structure pattern, where two different stocks were detected for both species: north and south groups, where Rio de Janeiro would be the limited region between them. Higher values of fixation indices were found for C. gasar, indicating that this species would be more structured than C. rhizophorae. Demographic analyses showed a probable expansion of populations during the last glacial period and a probable American origin of African populations. All results suggested the existence of a barrier next to Rio de Janeiro, which could be Vitoria-Trindade chain and the upwelling in the region of Cabo Frio (RJ). These results will be useful to establish criteria for the selection of seeds for cultivation along the Brazilian coast which will allow proper management of stocks of oysters preventing its disappearance as in other reefs around the world.