1,721,130 research outputs found
Evolutionary genomics of the crustacean Triops cancriformis (Branchiopoda, Notostraca)
No full textWHO? Triops cancriformis is a crustacean of the class Branchiopoda, order Notostraca. The order comprises only two genera (Triops and Lepidurus) world-wide distributed owing to their ancient origin. T. cancriformis lives in freshwater ponds that may be subjected to dry period during which the tadpole shrimps survive as encysted egg resistant stages. It is also well known for
its high morphological stasis, compared with fossil forms; hence
the debated status of "living fossil". WHY? Aside from the peculiar morphological stasis, T. cancriformis represents an interesting framework to address evolutionary studies: i) across its European range it is present with bisexual, parthenogenetic, hermaphroditic and androdioecious populations: it would be, thus, interesting to check whether di erent reproductive strategies leave genomic signatures such as di erential evolutionary rates and/or trans- posable element accumulation; ii) Branchiopod crustaceans are phylogenetically close to Hexapoda, in most analyses resulting
their sister clade. The study of T. cancriformis genomic features
in comparison with those of early-branching Hexapoda could tell about the origin of hexapods and their most represented taxon, Insecta. HOW? Genomic resources on T. cancriformis and related species are slowly accumulating (transcriptomes, RAD-sequencing and one genome draft), although a comprehensive and co-or- dinated project of a genomic evolutionary study is still lacking.
We therefore, undertaken Illumina sequencing of T. cancriformis genomes, starting from Italian parthenogenetic samples and Spanish bisexual ones. Moreover, we included two species from the related genus Lepidurus (L. apus lubbocki and L. arcticus) in order to have a clearer picture of Notostraca genomes. Further sequencing will be performed on transcriptome and already published data will be also included in the analyses. TO GET WHAT? A total evidence picture on the hardwares (genomes) and softwares (transcriptomes) evolution, with a special focus on repetitive DNA (transposable elements and satellite DNA), in the same species presenting genomes subject to di erent reproductive milieau. We have already some results indicating that transposable elements (R2 lineages) are di erently evolving in di erent T. cancriformis genomes. The full genome sequencing of further population/ species will help drawing a more complete picture, including the possibility to study all transposable element lineages as well as satellite DNAs. Moreover, the strengthening of the genomic dataset with new branchiopod species will likely result in a more stable phylogenetic relationship of Branchiopoda with closer taxa. Finally, we will get knowledge on the genome structure and composition that will be compared with the close relatives, the Hexapoda
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Phylogeography and colony structure of dry-wood dwelling termites of the genus Kalotermes (Isoptera, Kalotermitidae) in Southern Europe
No full textAccording to the most recent phylogenetic and phylogeographic investigations, the Kalotermes genus (Kalotermitidae) includes three different mitochondrial lineages of K. flavicollis and the new K. italicus species. In some Italian populations extreme colony fusion events were observed, with mixed families composed by up to nine maternal lines belonging to different genetic lineages or even to different species. In termites with the same nesting type, colony fusions lead to the death of queens and kings allowing false workers (pseudoergates) to evolve into reproducers and to inherit the colony (Accelerated Nest Inheritance). To widen the analyses on Kalotermes phylogeography and colony structure, we sequenced 912 bp of the mitochondrial genome, corresponding to COI/tRNA-Leu/COII, in two individuals from each of the 21 colonies collected in 11 European localities. In four colonies showing haplotypes of different genetic lineages/species, five-eight individuals per colony were further analyzed. A more detailed biogeographic scenario is obtained, with overlapping distribution areas of the considered lineages/species. Moreover, data confirm that mixed colonies with haplotypes of different genetic lineages/species may show more than two maternal lines. On the whole, colony fusions appear to occur more frequently than expected on the basis of eusociality models. Moreover, the possibility of hybridization between different genetic lineages or species could facilitate the fusion of more than two colonies wiping out mechanisms of nest-mate recognition. This analysis, therefore, demonstrates that dry-wood dwelling termites might be an interesting framework to study the evolution and maintenance of eusociality
Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera
Full text linkThe class Branchiopoda, whose origin dates back to Cambrian, includes ~ 1200 species which mainly occupy freshwater habitats. The phylogeny and systematics of the class have been debated for long time, until recent phylogenomic analyses allowed to better clarify the relationships among major clades. Based on these data, the clade Anostraca (fairy and brine shrimps) is sister to all other branchiopods, and the Notostraca (tadpole shrimps) results as sister group to Diplostraca, which includes Laevicaudata + Spinicaudata (clam shrimps) and Cladoceromorpha (water fleas + Cyclestherida). In the present analysis, thanks to an increased taxon sampling, a complex picture emerges. Most of the analyzed mitogenomes show the Pancrustacea gene order while in several other taxa they are found rearranged. These rearrangements, though, occur unevenly among taxa, most of them being found in Cladocera, and their taxonomic distribution does not agree with the phylogeny. Our data also seems to suggest the possibility of potentially homoplastic, alternative gene order within Daphniidae
Molecular taxonomy and phylogeny of the 'living fossil' lineages Triops and Lepidurus (Branchiopoda: Notostraca)
No full textEuropean Triops cancriformis and Lepidurus apus were analysed for 12S and 16S mitochondrial genes and compared to North American and Japanese taxa. There are no cryptic species among European T. cancriformis populations, which are highly homogeneous in comparison to conspecific Japanese samples. T. cancriformis differs from congeneric taxa all over its range, which can be explained by its antiquity. In contrast, the parapatric subspecies L. apus apus and L. apus lubbocki are morphologically conserved and differ substantially at the mtDNA level. The genetic distance values between them are of the same order of magnitude as those observed between American Lepidurus species. Their subspecific status therefore requires further analysis. L. apus apus is more closely related to a L. arcticus sample from Iceland than to L. apus lubbocki. It is also related to a Canadian L. couesii population. Further analyses of populations from the whole range of L. arcticus and the European range of L. couesii are needed to understand the relationships among these notostracan taxa. When considering the two genera, it is clear that Lepidurus is a well supported monophyletic unit, while Triops is polyphyletic, embodying very divergent taxa
Reproductive biology versus transposable elements load: the role of host reproductive strategy in the study of R2 dynamics in Bacillus stick insects (Phasmida, Bacillidae)
No full textTransposable elements (TEs) are known to promote genome evolution, even if they are often defined as “genomic parasites”. According to the Red Queen hypothesis, conflicts between parasite TEs and the host genome are at equilibrium through strict competitive efforts. Host reproductive strategy is significantly involved in this dynamics. The R2 non-LTR retrotransposon activity was estimated, through insertions display analyses, in populations of the strictly gonochoric Bacillus grandii maretimi, the facultative parthenogenetic B. rossius and the obligatory parthenogenetic B. atticus. R2 activity was also evaluated in the progeny of parthenogenetic isolates of B. rossius and B. atticus, and in the male progeny of crosses between gonochoric individuals of B. rossius. Gonochoric populations showed higher R2 loads than the parthenogenetic ones, the lowest value being scored in B. atticus. In all samples low frequency insertions are the majority, with the only exception of a bisexual B. rossius population. R2 load was similar in unisexual and bisexual B. rossius offspring but lower in B. atticus progeny. Moreover, in B. rossius unisexual offspring high-frequency insertions were the most represented. Data on facultative unisexuals evidenced a low R2 elimination rate, with recombination having a major role, although a bisexual-like insertion profile emerge at the population level. In this regard, natural selection seems to predominate in bisexuals. Stick-insects obligatory parthenogenesis seems to allow only a very low R2 load, with possible burst of retrotransposition buffered at the population level. Our data agree in indicating TE dynamics deeply linked with host reproductive strategies
SDS-PAGE identification of raw and cooked clams of the Veneridae family
No full textClam species belonging to the family Veneridae (Mollusca: Bivalvia) represent very important marine products, especially in the European countries. The increasing economic interest in marine edible molluscs has strongly enhanced the need for a routine method of unambiguous recognition of species in Fresh and preserved material, mainly intended to prevent mislabelling and commercial frauds. Here a procedure for identification of soft parts is proposed, by means of SDS-PAGE total protein patterning. In fresh material, this technique allowed recognition of four main regions of diagnostic bands, which have been named V1 (111-99 kDa), V2 (44 kDa), V3 (33-30 kDa) and V4 (19-13 kDa). The main diagnostic region appears to be the V3 band series. SDS-PAGE analysis allows the same technique to be used with denatured samples, such as cooked and preserved soft parts, giving reproducible results, very similar to those of fresh material
Molecular taxonomy and phylogeny of Italian Lepidurus taxa (Branchiopoda: Notostraca)
No full textNotostraca taxonomy is controversial, mainly owing to the high intraspecific variability of morphological characters; other complexity factors are represented by the consistent rate of reproductive variation. We undertook the molecular analyses of Italian Lepidurus taxa through the characterization of 12S, 16S and COI mitochondrial genes in new L. apus demes and in the L. couesii populations recently discovered in Southern Italy. For L. apus, the analysis of a wider data set (both in terms of molecular markers and of analysed populations) confirms the previously suggested specific rank of differentiation between its so far recognized subspecies, the Italian L. apus lubbocki and the European L. apus apus. The Italian L. couesii samples pertain to a well-defined taxonomic entity, strictly related to Canadian L. couesii. In 12S dendrograms, this taxon strongly diverges from the other North American Lepidurus species, but the relationships among nearctic taxa are unresolved. On the other hand, a high affinity between Italian/Canadian L. couesii and the circumpolar species L. arcticus is scored and a possible descent from a common ancestor is hypothesized. © 2009 Unione Zoologica Italiana
Recombine and survive: evolutionary history of the V highly conserved domain in the mammalian genome after the V-SINE superfamily extinction
No full textShort interspersed elements (SINEs) are non-autonomous retrotransposons. Because of high turnover rate, they exhibit widely divergent nucleotide sequences but highly conserved domains (HCDs) may occur. Three different HCDs originated before the Radiata-Bilateria split and two underwent repeatedly to exaptation. The "V" HCD has been retrieved in 16 nonamniotes'SINE families and within a miniature inverted-repeat transposon, MER6, in the human genome. Through in silico searches in sequenced genomes and transcriptomes, we found MER6 in all primates and its variant, MER6A, in bats and in the star-nosed mole. Moreover, we found evidence of MER6 in a salamander and retrieved its parental Tc1/ mariner element in the painted turtle. Data indicate that MER6 originated by recombination between a V- SINE and the parental Tc1/mariner element. Nucleotide substitution rate, computed on 10 primates orthologous insertions, places MER6 main activity burst as contemporary to Placentalia diversification. Moreover, age analyses suggest that MER6 was no longer active in mammals, except in the tarsier where a recent replication burst originated a new MER6A subfamily. Finally, unlike frog and fishes V-SINEs, genomic distribution of MER6 does not appear biased toward genic regions in human, chimp and mole genomes. Present data show how the V domain managed to survive and replicate after V-SINEs extinction. Although the impact of HCDs is still unclear, their wide conservation suggests some role; the study of V- elements with different replicative biology may help to disentangle transposon- related aspects from putative HCD function
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