Abstract: Nucleotide sequences of the nuclear-encoded small subunit (18S rDNA) and partial large subunit (28S rDNA) ribosomal
DNA were determined in 30 different species of the haptophyte genera Prymnesium, Chrysocampanula, Chrysochromulina,
Imantonia and Platychrysis, all belonging to the order Prymnesiales. Phylogenies based on these and other available haptophyte
18S, 28S and plastid 16S rDNA sequences were reconstructed, and compared with available morphological and ultrastructural data. The rDNA phylogenies indicate that the genus Chrysochromulina is paraphyletic and is divided into two major clades. This is supported by ultrastructural and morphological data. There is a major split between Chrysochromulina species with a saddle-shaped cell form (clade B2) and the remaining species in the genus (clade B1). Clade B2 includes the type species C. parva and taxa belonging to this clade thus retain the name Chrysochromulina. The non-saddle-shaped Chrysochromulina species analysed are closely related to Hyalolithus, Prymnesium and Platychrysis species. Imantonia species are sister taxa to these species within clade B1. An amendment to the classification of the order Prymnesiales and the genera Prymnesium, Platychrysis and Chrysochromulina is proposed with one new and one emended family (Chrysochromulinaceae and Prymnesiaceae, respectively), two new genera (Haptolina and Pseudohaptolina), and one new species (Pseudohaptolina arctica). We suggest a revision of the taxonomy of the Prymnesiales that is in accordance with available molecular evidence and supported by morphological data.
Abstract: The Na/K pump, or Na,K-ATPase, is a key enzyme to the homeostasis of osmotic pressure, cell volume, and the maintenance of electrochemical gradients. Its α subunit, which holds most of its functions, belongs to a large family of ATPases known as P-type, and to the subfamily IIC, which also includes H,K-ATPases. In this study, we attempt to describe the evolutionary history of IIC ATPases by doing phylogenetic analysis with most of the currently available protein sequences (over 200), and pay special attention to the relationship between their diversity and their osmoregulatory role. We include proteins derived from many completed or ongoing genome projects, many of whose IIC ATPases have not been phylogenetically analyzed previously. We show that the most likely origin of IIC proteins is prokaryotic, and that many of them are present in non-metazoans, such as algae, protozoans or fungi. We also suggest that the pre-metazoan ancestor, represented by the choanoflagellate Monosiga brevicollis, whose genome has been sequenced, presented at least two IIC-type proteins. One of these proteins would have given rise to most current animal IIC ATPases, whereas the other apparently evolved into a lineage that, so far, has only been found in nematodes. We also propose that early deuterostomes presented a single IIC gene, from which all the extant diversity of vertebrate IIC proteins originated by gene and genome duplications.
Abstract: Our increasing access to the identification and manipulation of genes keeps paving the way to our understanding of species and speciation. In my view, following two different threads in recent times: On the one hand, DNA barcoding - a systematic, molecular and complementary approach to species identification - is revealing a great deal of biodiversity, much of it previously unsuspected and morphologically cryptic. Secondly, a functional view of how genes shape microevolutionary changes is emphasizing the role of natural selection in the formation and evolution of species, even in the face of abundant gene flow.
Abstract: Background: Dietary restriction (DR) results in increased longevity, reduced fecundity and reduced growth in many organisms. Though many studies have examined the effects of DR on longevity and fecundity, few have investigated the effects on growth. Results: Here we use Caenorhabditis elegans to determine the mechanisms that regulate growth under DR. We show that rather than a reduction in cell number, decreased growth in wild type C. elegans under DR is correlated with lower levels of hypodermal polyploidization. We also show that mutants lacking wild type sensory ciliated neurons are small, exhibit hypo-polyploidization and more importantly, when grown under DR, reduce their levels of endoreduplication to a lesser extent than wild type, suggesting that these neurons are required for the regulation of hypodermal polyploidization in response to DR. Similarly, we also show that the cGMP-dependent protein kinase EGL-4 and the SMA/MAB signalling pathway regulate polyploidization under DR. Conclusions: We show C. elegans is capable of actively responding to food levels to regulate adult ploidy. We suggest this response is dependent on the SMA/MAB signalling pathway.
Abstract:
The braconid subfamily Rogadinae is a large, cosmopolitan group of endoparasitoid wasps characterised by 'mummifying' their lepidopteran host larvae, from which the adult subsequently emerges. Rogadines attack a variety of both macro- and microlepidopteran taxa, although the speciose genus Aleiodes almost exclusively attacks macrolepidopterans. Here, we investigate the phylogenetic history of the Rogadinae, revise their higher-level classification and assess the evolution of their host ranges and mummy types. We also assess the divergence times within the subfamily and discuss the reasons for the extraordinary evolutionary diversification of Aleiodes.
Results
Our Bayesian analyses weakly support the monophyly of the subfamily. A clade comprising all Aleiodes species and some other taxa is not nested within the tribe Rogadini as previously supposed, but instead is recovered as sister to the Yeliconini, with the remaining Rogadini genera being recovered as sister to the Stiropiini. The Rogadinae is estimated to have originated during the mid to late Eocene, 36.1â51.62 MYA. Molecular dating gives a more recent origin for the Aleiodes clade (17.98â41.76 MYA) compared to the origins proposed for two of its principal lepidopteran host groups (Noctuidae: 60.7â113.4 MYA; Geometridae 48â62 MYA). The Bayesian ancestral reconstruction of the emergence habits from the mummified hosts weakly recovered an anterior emergence as the ancestral condition for the subfamily. Producing a hard mummy has evolved at various times independently, though most of the species with this biology belong to the Aleiodes clade.
Conclusion
Based on our results, we erect the tribe Aleiodini nov. to include Aleiodes and Heterogamus stat. rev. Cordylorhogas, Pholichora and Hemigyroneuron are synonymised with Aleiodes. The molecular dating of clades and the ancestral reconstruction of host ranges support the hypothesis that radiation within Aleiodes s. s. was due to host recruitment leading to host range expansion followed by speciation, and not to parasitoid-host coevolution. Within the Rogadinae, variation in the site of emergence from the mummified host probably evolved as a consequence of the mummy's site and mode of formation, and the extent of mummy tanning/hardness to the degree of protection needed in relation to the cost of providing it.
Abstract: The taxonomy of the Asian genera of the subfamily Betylobraconinae, a small and understudied group within the hymenopteran family Braconidae, is revised. A new genus exclusive from the Asian region, Asiabregma gen. nov., containing three species (A. makiharai sp. nov., A. ryukyuensis sp. nov., and A. sulaensis (van Achterberg), comb. nov.) is described. One new species of Aulosaphobracon, A. striatus sp. nov. from Vietnam, and one of Facitorus, F. amamioshimus sp. nov. from Japan, are also described. Based on molecular phylogenetic analyses using COI mtDNA and 28S rRNA sequences, the three genera previously placed in the tribe Facitorini, Facitorus, Conobregma and Jannya, together with Asiabregma gen. nov., are transferred to the rogadine tribe Yeliconini.
Abstract: Within the marine phytoplankton community, coccolithophores are important players in the carbon cycle, because of their great abundance and unusual ability to form an external cover of calcium carbonate. Most described species are oceanic, and so little attention has been devoted to coastal species, the majority of which belong to two families: Pleurochrysidaceae and Hymenomonadaceae. Here, we study the biodiversity and evolutionary relationships within the Pleurochrysidaceae, for which we have compiled DNA sequences from a total of 18 strains plus three members of the Hymenomonadaceae. Most of the analysed sequences have been obtained for this study and belong to three genetic fragments: 18S rDNA, elongation factor Tu (tufA), and internal transcribed spacers 1 and 2, which include the 5.8S rDNA. We find some discordance between the current taxonomy of the group and our molecular analyses. First, we observe that several different recognised species are in fact highly similar taxa, probably belonging to the same evolutionary lineages. Secondly, we show some unexpected phylogenetic relationships. In the light of these results, we suggest that, when possible, DNA sequences be considered in future taxonomic classifications of the Pleurochrysidaceae and other planktonic organisms.
Abstract: A molecular clock has been constructed for the haptophyte algae using the 18S rDNA gene and calibrated using the fossil record of the coccolithophorid algae, which have the best fossil record of any microalgal group. There is high consistency between the molecular genetic estimates of relative timing of divergence and palaeontological estimates of divergence times, so ages can be inferred for undated nodes in the tree with a reasonable degree of confidence. The placement of the K/T boundary across the tree strongly supports the palaeontological model that extant coccolithophorid algae diversified after this event and are the survivors of a few lineages that survived this major extinction. In contrast, the non-calcifying haptophytes are diverse before and after the extinction, with no evidence of bottlenecking associated with the event. This result is surprising, because it has been assumed that ability to produce resting stages was a key determinant of phytoplankton survival across the K/T boundary, but in this regard the coccolithophores and non-calcifying haptophytes are similar. The adaptation of non-calcifying haptophytes to eutrophic coastal environments and their ability to switch modes of nutrition from autotrophy to mixotrophy are discussed as possible explanations for their survival during this abrupt global change event.
Abstract: One of the first reported gall-associated braconids, from 1910, Bracon mendocinus Kieffer and Jorgensen, is removed from the subfamily Braconinae and transferred to the doryctine genus Allorhogas, A. mendocinus (Kieffer and Jorgensen) comb. nov. A new species morphologically similar to A. mendocinus, A. joergenseni Martinez and Zaldivar-Riveron sp. nov., is also described. Additionally a neotype is designated for B. mendocinus Kieffer and Jorgensen. We base our conclusions on the morphological examination of recently collected specimens from central Argentina associated with galls on Lycium chilense (Solanaceae), as well as on the DNA variation at 28S ribosomal RNA and cytochrome oxidase subunit I (COI) mitochondrial DNA genes.
Abstract: Some animals, such as the larvae of Drosophila melanogaster, the larvae of the Appendicularian chordate Oikopleura, and the adults of the nematode Caenorhabditis elegans, are unusual in that they grow largely by increases in cell size. The giant cells of such species are highly polyploid, having undergone repeated rounds of endoreduplication. Since germline polyploid strains tend to have large cells, it is often assumed that endoreduplication drives cell growth, but this remains controversial. We have previously shown that adult growth in C. elegans is associated with the endoreduplication of nuclei in the epidermal syncitium, hyp 7. We show here that this relationship is causal. Manipulation of somatic ploidy both upwards and downwards increases and decreases, respectively, adult body size. We also establish a quantitative relationship between ploidy and body size. Finally, we find that TGF-beta (DBL-1) and cyclin E (CYE-1) regulate body size via endoreduplication. To our knowledge, this is the first experimental evidence establishing a cause-and-effect relationship between somatic polyploidization and body size in a metazoan.
Abstract: Several coccolithophore species are known to exhibit heteromorphic life cycles. In certain species, notably Emiliania huxleyi, the heterococcolith-bearing phase alternates with a non-calcifying stage, whereas in others the heterococcolith-bearing phase alternates with a holococcolith-bearing phase. Heterococcolithophore-holococcolithophore life cycles have previously been observed for only one species in culture, but have also been inferred from an increasing number of observations of combination coccospheres. 18S rDNA sequences from pure cultures of both the heterococcolith-bearing and holococcolith-bearing phases of Coccolithus pelagicus were identical, providing an additional indication of their identity as different life cycle stages of the same species. Flow cytometric analyses have been undertaken on SybrGreen-stained nuclei isolated from pure cultures of the two phases of four coccolithophore species (Coccolithus pelagicus, Calcidiscus leptoporus, Coronosphaera mediterranea and Emiliania huxleyi) in order to determine relative DNA content. Results confirm the hypothesis that holococcolithophore-heterococcolithophore life cycles are haplo-diploid in nature. Light microscope observations of the processes of sexual fusion and meiosis are reported for two of the experimental species. The results are discussed in the context of the evolution of biomineralization in the coccolithophores and the possible ubiquity of haplo-diploidy in the haptophytes.
Abstract: Coccolithophores are a group of calcifying unicellular algae that constitute a major fraction of oceanic primary productivity, play an important role in the global carbon cycle, and are key biostratigraphic marker fossils. Their taxonomy is primarily based on the morphology of the minute calcite plates, or coccoliths, covering the cell. These are diverse and include widespread fine scale variation, of which the biological/taxonomic significance is unknown. Do they represent phenotypic plasticity, genetic polymorphisms, or species-specific characters? Our research on five commonly occurring coccolithophores supports the hypothesis that such variation represents pseudocryptic speciation events, occurring between 0.3 and 12.9 million years ago from a molecular clock estimation. This finding suggests strong stabilizing selection acting on coccolithophorid phenotypes. Our results also provide strong support for the use of fine scale morphological characters of coccoliths in the fossil record to improve biostratigraphic resolution and paleoceanographic data retrieval.
Abstract: Variations in the HPLC-derived pigment composition of cultured Pavlovophyceae (Cavalier-Smith) Green et Medlin were compared with phylogenetic relationships inferred from 18S rDNA sequencing, morphological characteristics, and current taxonomy. The four genera described for this haptophyte class (Diacronema Prauser emend. Green et Hibberd, Exanthemachrysis Lepailleur, Pavlova Butcher, and Rebecca Green) were represented by nine different species (one of which with data from GeneBank only). Chlorophylls a, c1, c2 and MgDVP (Mg-[3,8-divinyl]-phytoporphyrin-132-methylcarboxylate) and the carotenoids fucoxanthin, diadinoxanthin, diatoxanthin, and β,β-carotene were detected in all cultures. Species only differed in the content of an unknown (diadinoxanthin-like) xanthophyll and two polar chl c forms, identified as a monovinyl (chl c1-like) and a divinyl (chl c2-like) compound. This is the first observation of the monovinyl form in haptophytes. Based on distribution of these two chl c forms, species were separated into Pavlovophyceae pigment types A, B, and C. These pigment types crossed taxonomic boundaries at the generic level but were in complete accordance with species groupings based on molecular phylogenetic relationships and certain ultrastructural characteristics (position and nature of pyrenoid, stigma, and flagella). These results suggest that characterization of the pigment signature of unidentified culture strains of Pavlovophyceae can be used to predict their phylogenetic affinities and vice versa. Additional studies have been initiated to evaluate this possibility for the haptophyte class Prymnesiophyceae.
Abstract: We survey DNA sequence polymorphisms at the Sod locus and four neighboring regions of Drosophila melanogaster, spanning 55,513 base pairs (bp), in 15 strains from a natural population, plus one reference laboratory strain and one strain of Drosophila simulans. Our objective is to characterize a proposed selective sweep that occurred at a locus close to Sod in D. melanogaster and to characterize the strength of the selection event, its time, and the size of the hitchhiked region. Two regions, 1819 and 6kbr3r, show a pattern of polymorphism very similar to the one of Sod, implying that they have been affected by the same evolutionary process that impacted Sod. A third fragment, 2021 seems unaffected by the event. A fourth one, 4039, on the opposite flank of Sod in relation to 2021, is only partially affected. We estimate that the length of the chromosomal segment impacted by the selective sweep is 41-54 kb, the age of the selective sweep is 2,600-22,000 years, and the selective advantage is 0.020 < s < 0.103.
Abstract: We have examined the patterns of polymorphism at two linked loci, Sod and Est-6, separated by nearly 1000 kb on the left arm of chromosome 3 of Drosophila melanogaster. The evidence suggests that natural selection has been involved in shaping the polymorphisms. At the Sod locus, a fairly strong (s>0.01) selective sweep, started >or=2600 years ago, increased the frequency of a rare haplotype, F(A), to about 50% frequency in populations of Europe, Asia, and the Americas. More recently, an F(A) allele mutated to an S allele, which has increased to frequencies 5-15% in populations of Europe, Asia and North America. All S alleles are identical (or very nearly) in sequence and differ by one nucleotide substitution (which accounts for the F-->S electrophoretic difference) from F(A) alleles. At the Est-6 locus, the evidence indicates both directional and balancing selection impacting separately the promoter and the coding regions of the gene, with linkage disequilibrium occurring within each region. Some linkage disequilibrium also exists between the two genes.
Abstract: The marine coccolithophorid Emiliania huxleyi is an important component of the marine carbon cycle because bloom development results in the export of calcium carbonate from the ocean surface to the abyss. Laboratory and field studies demonstrate significant biogeographical, ecological, physiological and morphological plasticity in E. huxleyi and suggest high underlying genetic variability. Here we describe seven polymorphic microsatellite loci from the E. huxleyi genome and their degree of polymorphism in clonal isolates of different geographical origin. Our results indicate a high degree of genetic diversity within E. huxleyi.
Abstract:
We have studied the plastid genome of Ochrosphaera neapolitana (Hymenomonadaceae, Prymnesiophyta), a member of the chlorophyll a+c-containing algae. Total DNA from O. neapolitana was fractionated in a CsCl density gradient and the âlighterâ upper band (which is typically of plastid origin) was unusually abundant relative to the âheavierâ nuclear one. Denaturation and renaturation experiments done with DNA isolated from the upper band showed that it had a base composition of 43.6 mol% G + C (molar fraction of guanosine plus cytosine), compared to 60.5 mol% G + C in the lower band, and that it lacked a substantial fraction of repetitive sequences; this DNA had a size of c. 10 Mb, which is more than an order of magnitude larger than has been reported for any plastid genome. Using Pulse Field Gel Electrophoresis (PFGE) of total DNA, we resolved a plastid genome size of approximately 165 kb for O. neapolitana. Although this is within the range reported for other plastid genomes, there is an increase of about 40 kb compared to related algae. Using the upper band from the CsCl gradient as a probe for the PFGE blots, we showed that this upper band is apparently a mixture of nuclear DNA with a small fraction of plastid DNA. The nuclear genome of Ochrosphaera neapolitana thus appears to have a distinctive heterogeneity in G+C content, with two DNA types differing by c. 17 mol%
Abstract: We previously reported that the Na/K-ATPase alpha 1 subunit coding gene showed signs of being a very polymorphic locus in Artemia franciscana. This species is adapted to highly saline waters, and the Na/K-ATPase alpha 1 isoform presumably plays a key role in this adaptation. Therefore, we were interested in further study of the alpha 1 Na/K-ATPase polymorphisms to examine whether they might be due to an adaptation to salt resistance driven by natural selection. Using coding sequences from 10 genomic clones and 3 cDNAs, we observed that most substitutions are in synonymous positions (88.8%). The 12 nonsynonymous substitutions code for conservative amino acid replacements with an apparent scattered distribution across functional domains of the protein. Interspecific comparison between these sequences and two genomic clones from Artemia parthenogenetica containing 1,122 bp of the alpha 1 Na/K-ATPase locus coding sequence showed independence of the synonymous/nonsynonymous ratio in the comparison within A. franciscana and between A. franciscana and A. parthenogenetica, which fits the neutral model of evolution. Since there were no previous studies on DNA polymorphism for other A. franciscana genes, we also studied variability at the Actin 302 locus for comparison. Both loci were amplified by reverse transcription-polymerase chain reaction, and 20 sequences were obtained for each. This study shows that the amplified region of the alpha 1 Na/K-ATPase gene is 3.5 times as polymorphic as the Actin 302 gene and 2.9 times as heterozygotic. Interestingly, under a model of neutral evolution, the data observed would be expected with a probability of approximately 0.05, suggesting an excess of intraspecific variation of alpha 1 Na/K-ATPase with respect to Actin 302. Restriction fragment length polymorphism studies show similar patterns of polymorphism along the approximately 41-kb span of the alpha 1 Na/K-ATPase locus. Most of the nucleotide differences are linked in a few haplotypes, although recombination events are also inferred from the data. We propose a possible explanation for the high polymorphic levels at the alpha 1 Na/K-ATPase locus which invokes positive selection acting tightly to the locus in transiently isolated or semi-isolated subpopulations.
Abstract: Cs, a gene with unknown function, and amd and Ddc, which encode decarboxylases, are among the most closely spaced genes in D. melanogaster. Untranslated 3' ends of the convergently transcribed genes Cs and Ddc are known to overlap by 88bp. A number of questions arise about the organization of this tightly-packed gene region and about the evolution and function of the Cs gene. We have now investigated this three-gene cluster in Scaptodrosophila lebanonensis (which diverged from D. melanogaster 60-65 MYA), as well as in D. melanogaster and D. simulans. Gene order and direction of transcription is the same in all three species. The Cs gene codes, in Scaptodrosophila, for a polypeptide of 544 amino acids; in D. melanogaster, it consists of 504 amino acids, which is twice as long as previously suggested, which makes the gene density even more spectacular. The Cs sequences exhibit higher number of non-synonymous substitutions between species, higher ratios of non-synonymous to synonymous substitutions, and lower codon usage bias than other genes, suggesting that Cs is less functionally constrained than the other genes. This is consistent with the failure of inducing phenotypic mutations in D. melanogaster. The function of Cs remains to be identified, but a high degree of similarity indicates that it is homologous to genes coding for a corticosteroid-binding protein in yeast and a polyamine oxidase in maize.
Abstract: Patterns of variation at the Sod locus of Drosophila melanogaster suggest that the protein polymorphism at this locus has very recently arisen. In addition, it appears that a previously rare DNA variant has been recently and rapidly driven to intermediate frequency. From the size of the region (>20 kb) that has been swept along with this rare variant, and patterns of linkage disequilibrium in the region, it is inferred that strength of selection was large (s > 0.01) and that the sweep occurred more than 25,000 generations ago. In addition, there are striking similarities to patterns of variation observed at the Est6 and Est-P loci, which are located approximately 1,000 kb from Sod.
Abstract: Genomic clones coding for one of the two identified Artemia franciscana Na/K-ATPase alpha subunits, the alpha 1 subunit, have been isolated. Several overlapping clones were obtained, although their restriction maps showed a large heterogeneity. Sequencing of their exons showed that they differ in up to 3.46% of their nucleotides in translated regions and 8.18% in untranslated regions. Southern blot analysis of DNA purified from different lots of A. franciscana cysts and from isolated individuals suggests that the variation is due to the existence of multiple Na/K-ATPase alpha 1 subunit alleles in A. franciscana. The Na/K-ATPase alpha 1 subunit gene is divided into 15 exons. Ten of the 14 introns are located in identical positions in this gene as in the human Na/K-ATPase alpha 3 subunit gene. Analysis of the 5' flanking region of the gene has allowed identification of the transcription-initiation sites. The adjacent upstream region has been shown to have functional promoter activity in cultured mammalian cells, suggesting the evolutionary conservation of some of the promoter regulatory sequences.
Abstract: The spatial pattern of expression of the mRNA encoded by the Na,K-ATPase alpha-subunit cDNA clone pArATNa136 was determined by in situ hybridization of first, second, and third instar Artemia franciscana larvae. This mRNA was expressed at high levels in the salt gland, the antennal gland, and the end of the midgut, which are the three main osmoregulatory organs in Artemia at these stages of development. The pattern of expression was similar at the three stages of development analyzed, although the level of expression increased during development, especially in the salt and antennal glands. The expression of the mRNA coding for another Na, K-ATPase alpha-subunit isoform, the proposed alpha 2-isoform, was also determined and was shown to be limited to the salt gland. These results suggest that the clone pArATNa136 codes for the biochemically defined alpha 1-isoform of the Na,K-ATPase alpha-subunit and reinforce the importance of this isoform in osmoregulation at the three larval stages studied. The alpha 2-isoform may also be involved in osmoregulation during the first stages of larval development.
Abstract: The steady-state levels of six different mRNAs have been studied during Artemia franciscana development. Some of these mRNAs are present in the cryptobiotic cyst, like those coding for cytoplasmic actins, sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPase, and the Na+, K(+)-ATPase alpha-subunit isoform coded by the clone pArATNa136. The expression of these mRNAs is markedly induced during cyst development. A small increase in mRNA levels can be observed for some genes at very early stages of development (2 h). The main increase is observed between 4 and 16 h of development for all these genes, although the time course of mRNA accumulation is different for each one of the genes studied. Some other genes, like those coding for muscle actin (actin 3) or the Na+, K(+)-ATPase alpha-subunit isoform coded by the cDNA clone alpha 2850, are not expressed in the cyst before resumption of development and their expression is induced after 10 or 6 h of development, respectively. These data on the kinetic of mRNA accumulation provide the information required to determine transcriptionally active developmental stages, necessary to study in more detail the mechanisms of transcriptional regulation during activation of cryptobiotic cysts and resumption of embryonic development.
Abstract: It is common to find articles in which phylogenetic studies based on DNA sequences use particular evolutionary models of nucleotide substitution without any rationale for choosing among these models. However, there are phylogenetic techniques that allow us to test the suitability of different models of nucleotide substitution for particular data sets. Importantly these techniques have recently been proved effective through simulation analyses. We summarize these developments and provide ârules of thumbâ for their predictive ability.
