Claudia A. M. Russo

DOES COSMOPOLITANISM RESULT FROM OVERCONSERVATIVE SYSTEMATICS? A CASE STUDY USING THE MARINE SPONGE CHONDRILLA NUCULA

The sponge species Chondrilla nucula has a simple morphology and a very wide geographical distribution. To verify whether the latter might be an artifact of the former, samples of this species were collected across 10,000 km of its range, in the Mediterranean, the Caribbean, and the southwestern atlantic. The classical (spicule morphology) and molecular (allozymes) systematic approaches were compared, to try to define the geographic limits between populations and detect possible cryptic species. We found five distinct genetic forms within C. nucula that sometimes showed morphological homogeneity and other times plasticity. The difference in size of spicules could not be related to the clear‐cut genetic differences, suggesting that the use of spicule sizes for sponge systematics should be reappraised. The population of one of the genetic forms along 3000 km of the Brazilian coast was highly structured (FST = 0.21; Nem = 0.96). Our results reject the null hypothesis of cosmopolitanism of C. nucula and indicate that the putative worldwide distribution of some marine sponges, and possibly many other benthic invertebrates, may be the result of overly conservative systematics. Cryptic species appear to be particularly prevalent when genera are well defined but species are characterized by only a few morphological characters.

Evolution of the B3 DNA Binding Superfamily: New Insights into REM Family Gene Diversification

Background The B3 DNA binding domain includes five families: auxin response factor (ARF), abscisic acid-insensitive3 (ABI3), high level expression of sugar inducible (HSI), related to ABI3/VP1 (RAV) and reproductive meristem (REM). The release of the complete genomes of the angiosperm eudicots Arabidopsis thaliana and Populus trichocarpa, the monocot Orysa sativa, the bryophyte Physcomitrella patens,the green algae Chlamydomonas reinhardtii and Volvox carteri and the red algae Cyanidioschyzon melorae provided an exceptional opportunity to study the evolution of this superfamily. Methodology In order to better understand the origin and the diversification of B3 domains in plants, we combined comparative phylogenetic analysis with exon/intron structure and duplication events. In addition, we investigated the conservation and divergence of the B3 domain during the origin and evolution of each family. Conclusions Our data indicate that showed that the B3 containing genes have undergone extensive duplication events, and that the REM family B3 domain has a highly diverged DNA binding. Our results also indicate that the founding member of the B3 gene family is likely to be similar to the ABI3/HSI genes found in C. reinhardtii and V. carteri. Among the B3 families, ABI3, HSI, RAV and ARF are most structurally conserved, whereas the REM family has experienced a rapid divergence. These results are discussed in light of their functional and evolutionary roles in plant development.

Molecular phylogeny of Triatomini (Hemiptera: Reduviidae: Triatominae)

BackgroundThe Triatomini and Rhodniini (Hemiptera: Reduviidae) tribes include the most diverse Chagas disease vectors; however, the phylogenetic relationships within the tribes remain obscure. This study provides the most comprehensive phylogeny of Triatomini reported to date.MethodsThe relationships between all of the Triatomini genera and representatives of the three Rhodniini species groups were examined in a novel molecular phylogenetic analysis based on the following six molecular markers: the mitochondrial 16S; Cytochrome Oxidase I and II (COI and COII) and Cytochrome B (Cyt B); and the nuclear 18S and 28S.ResultsOur results show that the Rhodnius prolixus and R. pictipes groups are more closely related to each other than to the R. pallescens group. For Triatomini, we demonstrate that the large complexes within the paraphyletic Triatoma genus are closely associated with their geographical distribution. Additionally, we observe that the divergence within the spinolai and flavida complex clades are higher than in the other Triatoma complexes.ConclusionsWe propose that the spinolai and flavida complexes should be ranked under the genera Mepraia and Nesotriatoma. Finally, we conclude that a thorough morphological investigation of the paraphyletic genera Triatoma and Panstrongylus is required to accurately assign queries to natural genera.

Population structure and genetic variation in two tropical sea anemones (Cnidaria, Actinidae) with different reproductive strategies

Genetic variation and population structure of two tropical sea anemones, Bunodosoma caissarum Correa and Actinia bermudensis McMurrich were related to their different dispersal capabilities and reproductive modes. B. caissarum reproduces sexually and has a long-lived planktotrophic larva; A. bermudensis can reproduce both sexually and asexually, supposedly with short-range dispersal. Both species were sampled along 1150 km of Brazilian coastline between 1990 and 1991 and analyzed by horizontal starch gel electrophoresis for 16 enzyme loci in B. caissarum and 19 in A. bermudensis. B. caissarum had higher levels of heterozygosity (H=0.35) and lower levels of population structuring (FST=0.042) than A. bermudensis (H=0.17; FST=0.262). At one locality large genetic differences between two sympatric colour morphs of A. bermudensis provide evidence of possible cryptic speciation. Overall levels of genetic variation and heterozygosity in the two species are compatible with their known modes of reproduction.

A Paleogene origin for crown passerines and the diversification of the Oscines in the New World.

In this study, we present a detailed family-level phylogenetic hypothesis for the largest avian order (Aves: Passeriformes) and an unmatched multi-calibrated, relaxed clock inference for the diversification of crown passerines. Extended taxon sampling allowed the recovery of many challenging clades and elucidated their position in the tree. Acanthisittia appear to have diverged from all other passerines at the early Paleogene, which is considerably later than previously suggested. Thus, Passeriformes may be younger and represent an even more intense adaptive radiation compared to the remaining avian orders. Based on our divergence time estimates, a novel hypothesis for the diversification of modern Suboscines is proposed. According to this hypothesis, the first split between New and Old World lineages would be related to the severing of the Africa-South America biotic connection during the mid-late Eocene, implying an African origin for modern Eurylaimides. The monophyletic status of groups not recovered by any subsequent study since their circumscription, viz. Sylvioidea including Paridae, Remizidae, Hyliotidae, and Stenostiridae; and Muscicapoidea including the waxwing assemblage (Bombycilloidea) were notable topological findings. We also propose possible ecological interactions that may have shaped the distinct Oscine distribution patterns in the New World. The insectivorous endemic Oscines of the Americas, Vireonidae (Corvoidea), Mimidae, and Troglodytidae (Muscicapoidea), probably interfered with autochthonous Suboscines through direct competition. Thus, the Early Miocene arrival of these lineages before any other Oscines may have occupied the few available niches left by Tyrannides, constraining the diversification of insectivorous Oscines that arrived in the Americas later. The predominantly frugivorous-nectarivorous members of Passeroidea, which account for most of the diversity of New World-endemic Oscines, may not have been subjected to competition with Tyrannides. In fact, the vast availability of frugivory niches combined with weak competition with the autochthonous passerine fauna may have been crucial for passeroids to thrive in the New World.

O caramujo exótico invasor Achatina fulica (Stylommatophora, Mollusca) no Estado do Rio de Janeiro (Brasil): situação atual

The invasive African snail Achatina fulica was introduced in Brazil through South and Southeast States in at least three separate occasions. A. fulica is currently present in 24 out of 26 Brazilian States and in the Federal District. Dense populations of A. fulica are nuisance to human populations and pest to gardens and small crops. Such populations also act in the transmission of two zoonosis (abdominal angiostrongyliasis and eosinophilic meningitis) as well as other parasitosis of veterinary importance. Here, we report new records of A. fulica and of nematode larvae of medical and veterinary importance found in this snail in the state of Rio de Janeiro (Brazil). A. fulica is present in 26 additional municipalities of the state when compared to the information obtained in 2006, year of the last census. This result represents an increase of 50% in the number of municipalities infested. Only nine out of the 92 municipalities of the state have not yet registered the presence of this invasive species. Nematode larvae of Aelurostrongylus abstrusus, Rhabditis sp. e Strongyluris-like, all of veterinary importance, have been registered in A. fulica individuals from eleven municipalities of the state. The rapid range expansion of A. fulica calls attention for the need of a general and continuous management plan throughout the country in order to effectively control the invasion. The current level of infestation makes a full eradication unlikely.

Birth of a new gene on the Y chromosome of Drosophila melanogaster

Significance Mammalian Y chromosomes are believed to evolve mainly through gene inactivation and loss. Drosophila Y chromosomes seem to not obey this rule, as gene gains are the dominating force in their evolution. Here we describe flagrante delicto Y (FDY), a very young gene that shows how Y-linked genes were acquired. FDY originated 2 million years ago from a duplication of a contiguous autosomal segment of 11 kb containing five genes that inserted into the Y chromosome. Four of these autosome-to-Y gene copies became inactivated (“pseudogenes”), lost part of their sequences, and most likely will disappear in the next few million years. FDY, originally a female-biased gene, acquired testis expression and remained functional. Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.

MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies

UNLABELLED MamMiBase, the mammalian mitochondrial genome database, is a relational database of complete mitochondrial genome sequences of mammalian species. The database is useful for phylogenetic analysis, since it allows a ready retrieval of nucleotide and aminoacid individual alignments, in three different formats (NEXUS for PAUP program, for MEGA program and for PHYLIP program) of the 13 protein coding mitochondrial genes. The user may download the sequences that are useful for him/her based on their parameters values, such as sequence length, p-distances, base content, transition transversion ratio, gamma, which are also given by MamMiBase. A simple phylogenetic tree (neighbor-joining tree with Jukes Cantor distance) is also available for download, useful for parameter calculations and other simple tasks. AVAILABILITY MamMiBase is available at http://www.mammibase.lncc.br

A Molecular Phylogeny for the Order Clathrinida Rekindles and Refines Haeckel’s Taxonomic Proposal for Calcareous Sponges

Most biological groups are still longing for a phylogenetically sound taxonomic organization. In this article, we aimed to verify the consistency of morphological characters in calcarean sponges of the well-known non-monophyletic order Clathrinida using a molecular phylogeny. For this we included 50 species, including six type species, currently assigned to eight different genera. A maximum likelihood topology was generated for the nuclear ITS marker using the General Time Reversible model and the bootstrap reliability test. Our topology indicated 10 clathrinid clades that included species with consistent morphological characters. In the present study, we defined nine of these clades as clathrinid genera, including four newly described and two newly diagnosed genera. Recent studies have indicated that not much phylogenetic information may be found in morphology, but our findings contradict this general assertion. Our study confirms the suitability of skeleton and body anastomosis as valid characters in a phylogenetically sound taxonomy for the order. Interestingly, we have also found that, apart from the Calcinea/Calcaronea split and a few minor details, Haeckels original proposal is remarkably similar to our own, which was based on a molecular phylogeny 140 years later.

Unravelling MADS-box gene family in Eucalyptus spp.: a starting point to an understanding of their developmental role in trees

MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants ranging from root to flower and fruit development. Members of the MADS-box gene family share a highly conserved sequence of approximately 180 nucleotides that encodes a DNA-binding domain. We used bioinformatics tools to investigate the information generated by the Eucalyptus Expressed Sequence Tag (FORESTs) genome project in order to identify and annotate MADS-box genes. The comparative phylogenetic analysis of the Eucalyptus MADS-box genes with Arabidopsis homologues allowed us to group them into one of the well-known subfamilies. Trends in gene expression of these putative Eucalyptus MADS-box genes were investigated by hierarchical clustering analysis. Among 24 MADS-box genes identified by our analysis, 12 are expressed in vegetative organs. Out of these, five are expressed predominately in wood. Understanding of the molecular mechanisms performed by MADS-box proteins underlying Eucalyptus growth, development and stress reactions would provide important insights into tree development and could reveal means by which tree characteristics could be modified for the improvement of industrial properties.