340 research outputs found
Evolution of the dystrophin muscular promoter and 5 ' flanking region in primates
No full textAbout 1.6 kb of the noncoding region upstream of the muscular dystrophin gene was sequenced in human and other primates. The alignment showed the existence of many stretches of conserved sequences among the compared species distributed all along the investigated fragment, including the 5' end. In correspondence to these conserved boxes, we identified several new putative cis-acting elements that have similarity to known control regions of other muscle-specific genes. In some cases, however, the conserved sequences did not correspond to any known transcription factor binding sites. The rate of evolution estimated site by site all along the investigated region revealed a nonhomogeneous distribution of the substitution rate, several sequences exhibited a very slow rate of evolution suggesting that evolutionary forces of different nature may be at work. On the basis of the sequence alignment, we reconstructed the phylogenetic relationships within the hominoid lineage. In addition, we estimated the relative rate of evolution between hominoid and Old World monkeys, confirming the existence of an evolutionary slowdown in the hominoid lineage
Krill: a possible model for investigating the effects of ocean currents on the genetic structure of a pelagic invertebrate
No full textThis paper reviews the information available on the population genetics and systematics of krill (Euphausiidae, Crustacea), integrating the published data with new data collected in our laboratory. Phylogenetic analysis of several Antarctic and sub-Antarctic Euphausia species indicates the importance of dispersal in determining the present-day geographic distribution. Dating speciation events suggest that the formation of the Antarctic Convergence, the oceanographic barrier isolating the Southern Ocean, may have played a role in separating the ancestral Antarctic and sub-Antarctic lineages. Intraspecific data show that the Antarctic krill (Euphausia superba) is characterized by weak genetic differentiation, whereas the northern krill (Meganyctiphanes norvegica) is more structured showing discrete genetic pools. This difference can be explained, at least partly, by the oceanographic conditions in the areas inhabited by the two species
Optimization of single-strand conformation polymorphism and sequence analysis of the mitochondrial control region in Pagellus bogaraveo (Sparidae, Teleostei): Rationalized tools in fish population biology
No full textWe report the isolation and sequencing of 400-550 base pairs (bp) of the mitochondrial DNA (mtDNA) control region of eight species of Sparidae (Perciformes, Teleostei). This sequence information allowed us to design specific primers to one of these species (Pagellus bogaraveo). The new set of primers was used to test a rationalized approach to study the mtDNA nucleotide variability at the intraspecific level. The single-strand conformation polymorphism (SSCP) technique was applied to detect sequence variation in two non-overlapping fragments of the control region of 32 individuals of P. bogaraveo. To assess the sensitivity of the method, the nucleotide sequence of the analysed region was determined for all the specimens. The results showed that, for one of the two fragments, SSCP analysis was able to detect 100% of the underlying genetic variability. In sharp contrast, nucleotide variation of the second DNA fragment was completely unresolved by SSCP under different experimental conditions. This suggests that the resolution power of SSCP is crucially dependent on the nature of the fragment subjected to the analysis; therefore, a preliminary test of the sensitivity of the method should be performed on each specific DNA fragment before starting a large-scale survey. A rationalized approach, combining the SSCP technique and a simplified sequencing procedure, is proposed for studying intraspecific polymorphism at the mtDNA control region in fish
The mitochondrial genome of the ascalaphid owlfly <it>Libelloides macaronius </it>and comparative evolutionary mitochondriomics of neuropterid insects
No full textAbstract Background The insect order Neuroptera encompasses more than 5,700 described species. To date, only three neuropteran mitochondrial genomes have been fully and one partly sequenced. Current knowledge on neuropteran mitochondrial genomes is limited, and new data are strongly required. In the present work, the mitochondrial genome of the ascalaphid owlfly Libelloides macaronius is described and compared with the known neuropterid mitochondrial genomes: Megaloptera, Neuroptera and Raphidioptera. These analyses are further extended to other endopterygotan orders. Results The mitochondrial genome of L. macaronius is a circular molecule 15,890 bp long. It includes the entire set of 37 genes usually present in animal mitochondrial genomes. The gene order of this newly sequenced genome is unique among Neuroptera and differs from the ancestral type of insects in the translocation of trnC. The L. macaronius genome shows the lowest A+T content (74.50%) among known neuropterid genomes. Protein-coding genes possess the typical mitochondrial start codons, except for cox1, which has an unusual ACG. Comparisons among endopterygotan mitochondrial genomes showed that A+T content and AT/GC-skews exhibit a broad range of variation among 84 analyzed taxa. Comparative analyses showed that neuropterid mitochondrial protein-coding genes experienced complex evolutionary histories, involving features ranging from codon usage to rate of substitution, that make them potential markers for population genetics/phylogenetics studies at different taxonomic ranks. The 22 tRNAs show variable substitution patterns in Neuropterida, with higher sequence conservation in genes located on the α strand. Inferred secondary structures for neuropterid rrnS and rrnL genes largely agree with those known for other insects. For the first time, a model is provided for domain I of an insect rrnL. The control region in Neuropterida, as in other insects, is fast-evolving genomic region, characterized by AT-rich motifs. Conclusions The new genome shares many features with known neuropteran genomes but differs in its low A+T content. Comparative analysis of neuropterid mitochondrial genes showed that they experienced distinct evolutionary patterns. Both tRNA families and ribosomal RNAs show composite substitution pathways. The neuropterid mitochondrial genome is characterized by a complex evolutionary history.</p
Isolation and characterization of microsatellite loci in the icefish Chionodraco rastrospinosus (Perciformes, Notothenioidea, Channichthyidae)
No full textWe characterized eight polymorphic microsatellites in the icefish Chionodraco rastrospinosus (Perciformes, Notothenioidea, Channichthyidae). Microsatellites were isolated from a partial genomic library enriched for an AC motif. Chionodraco rastrospinosus is an endemic species inhabiting southern ocean waters surrounding the Antarctic Peninsula, the South Shetland Islands, and the South Orkney Islands. An excess of homozygotes was observed in seven out of the eight investigated loci; however, presence of null alleles was detected only for three of them suggesting that other factors may act in reducing heterozygosity. These molecular markers will be useful to investigate icefish genetic structure, possibly providing insights on its effective population size and demographic history
GENETICS OF NORTHERN KRILL (MEGANYCTIPHANES NORVEGICA SARS)
No full textUnderstanding the origin and maintenance of genetic diversity in the oceanic realm is difficult because barriers to gene flow are far less obvious in marine compared to terrestrial species This is particularly so for planktonic species such as euphausiids with no fossil record and high rates of dispersal and in which paleobiology and evolutionary history remains largely obscure Population genetics may play an important role in this respect elucidating population connectivity and shedding light on the historical demography of the investigated species In turn the relevant factors that can promote speciation over both at short and long evolutionary timescales can be identified In this chapter we outline the available approaches for gathering population genetics information on marine organisms with a particular focus on the recent achievements in the study of Meganyctiphanes norvegica For population structure we review the data available for mitochondrial DNA (mtDNA) markers that show the presence of four temporally stable and genetically distinct gene pools one in the Mediterranean samples and three others in the North Atlantic Ocean potentially associated with the basin scale pattern of circulation Unpublished data on some nuclear microsatellite markers adds support to this conclusion In addition we apply a newly introduced Bayesian coalescent approach and demonstrate that previously reported mitochondrial sequence diversity is indicative of a recent expansion at the Northern edge of the species distribution This does not hold for the Southern and Mediterranean populations that appear to be stable over time We also review the literature reporting new advances on the analysis of M norvegica genes and genes products involved in metabolic pathways that may underline differences at the population level possibly linked to environmental variation and local adaptation
Effects of pollution on heterozygosity in the barnacle Balanus amphitrite Darwin (Cirripedia: Thoracica)
No full textThe effects of thermal and chemical pollution on gene and genotype frequencies and on multilocus structure were studied in 3 populations of the barnacle Balanus amphitrite Darwin from the lagoon of Venice, Italy. One of these populations (A) was subjected to high chemical pollution; the second (B) was constantly exposed to temperatures about 10-degrees-C higher than the rest of the lagoon since it was settled in front of an electric power plant outflow; and the third (C) was sampled in an unpolluted area of the lagoon as a control. Juvenile and adult age classes of each of the 3 samples were studied by electrophoretic analysis of the polymorphic loci Mpi, Pgi and Pgm. Significant differences were found between Population A adults and both B and C adults for the majority of the genetic comparisons. B and C adult populations did not differ significantly. Statistical comparisons among the 3 juvenile populations showed a high genetic homogeneity. Comparisons between the 2 age classes within each of the 3 populations exhibited significant differences only between adults and juveniles of Population A at the level of gene and genotype frequencies. Moreover, in Population A a significantly higher survival of the multi-homozygote class was observed. No differences were detected between adults and juveniles of B and C samples. These results suggest the action, in Population A, of some selective factor during the post-settlement period. Thermal pollution does not seem to play any important selective role. The hypothesis is advanced that selection is operated by heavy metals
Antarctic fish hemoglobins: evidence of adaptive evolution at subzero temperature
No full textNotothenioids represent a large group of marine teleosts that are mostly endemic to the Antarctic Ocean. In this environment, the low metabolic demand and the high oxygen concentration reduce the need for hemoglobin(s) [Hb(s)]. The extreme condition is represented by the icefish (Channichthyidae, Notothenioidei), the only vertebrates that lack Hb. We obtained the nucleotide sequence coding for the beta-globin chain of the single major Hb form in six red-blooded notothenioids. These included Gymnodraco acuticeps, one of the closest species to the Hb-less icefish, which is also the only known fish having a single Hb without Bohr effect. This species shows a higher rate of nonsynonymous substitutions (K-A), in contrast with the homogeneity of synonymous substitution (K-S) rates, and K-A/K-S ratios significantly greater than one in the majority of comparisons. These results are suggestive of positive selection, diversifying the single major Hb toward specialized functions. A single Hb that is free to diversify means that its role in routine oxygen transport can be reduced in the presence of a combination of physiological, ecological, and environmental factors. Although a reduced "routine" function for Hb, as is apparent in G. acuticeps, might, indeed, evoke the lack of Hb in icefish, evidence of diversifying selection reported here is at variance with the hypothesis of a simple trend from a single Hb toward the Hb-less condition
Inherited disease in dogs: molecular genetics applied to diagnosis
No full textThe recent progresses of molecular genetics and biotechnology allowed to significantly advance in the field of biomedical sciences. These extraordinary progresses also regarded species of veterinary interest such as dog, the genome of which was completely sequenced. More than 350 dog-breed gene pools combined to new powerful technologies represent a unique opportunity to investigate the molecular basis of inherited canine disorders as well as to develop appropriate test for quick and accurate molecular diagnosis
Strategies for microsatellite isolation: a review
No full textIn the last few years microsatellites have become one of the most popular molecular markers used with applications in many different fields. High polymorphism and the relative ease of scoring represent the two major features that make microsatellites of large interest for many genetic studies. The major drawback of microsatellites is that they need to be isolated de novo from species that are being examined for the first time. The aim of the present paper is to review the various methods of microsatellite isolation described in the literature with the purpose of providing useful guidelines in making appropriate choices among the large number of currently available options. In addition, we propose a fast and easy protocol which is a combination of different published methods
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