Cryptic Species of the Anastrepha fraterculus Complex (Diptera: Tephritidae): A Multivariate Approach for the Recognition of South American Morphotypes

Although a large amount of data have been published in past years on the taxonomic status of the Anastrepha fraterculus (Wiedemann) species complex, there is still a need to know how many species this complex comprises, the distribution of each one, and their distinguishing features. In this study, we assessed the morphometric variability of 32 populations from the A. fraterculus complex, located in major biogeographical areas from the Neotropics. Multivariate techniques for analysis were applied to the measurements of 21 variables referring to the mesonotum, aculeus, and wing. For the first time, our results identified the presence of seven distinct morphotypes within this species complex. According to the biogeographical areas, populations occurring in the Mesoamerican dominion (Mexico, Guatemala, and Panama) were clustered within a single natural entity labeled as the "Mexican" morphotype; whereas in the northwestern South American dominion, samples fell into three distinct groups: the "Venezuelan" morphotype with a single population from the Caribbean lowlands of Venezuela, the "Andean" morphotype from the highlands of Venezuela and Colombia, and the third group or "Peruvian" morphotype comprised the samples from the Pacific coastal lowlands of Ecuador and Peru. Three additional groups were identified from the Chacoan and Paranaense sub-regions: the morphotype "Brazilian-1" was recognized as including the Argentinean samples with most pertaining to Brazil, and widely distributed in these biogeographical areas; the morphotype "Brazilian-2" was recognized as including two samples from the state of Sao Paulo (Ilha-Bela and Sao Sebastiao); whereas the morphotype "Brazilian-3" included a single population from Botucatu (state of Sao Paulo). Based on data published by previous authors showing genetic and karyotypic differentiation, as well as reproductive isolation, we have concluded that such morphotypes indeed represent natural groups and distinct taxonomic entities.

How far can we go in simplifying biomonitoring assessments? An integrated analysis of taxonomic surrogacy, taxonomic sufficiency and numerical resolution in a megadiverse region

The need for biodiversity conservation is increasing at a rate much faster than the acquisition of knowledge of biodiversity, such as descriptions of new species and mapping species distributions. As global changes are winning the race against the acquisition of knowledge, many researchers resort to the use of surrogate groups to aid in conservation decisions. Reductions in taxonomic and numerical resolution are also desirable, because they could allow more rapid the acquisition of knowledge while requiring less effort, if little important information is lost. In this study, we evaluated the congruence among 22 taxonomic groups sampled in a tropical forest in the Amazon basin. Our aim was to evaluate if any of these groups could be used as surrogates for the others in monitoring programs. We also evaluated if the taxonomic or numerical resolution of possible surrogates could be reduced without greatly reducing the overall congruence. Congruence among plant groups was high, whereas the congruence among most animal groups was very low, except for anurans in which congruence values were only slightly lower than for plants. Liana (Bignoniaceae) was the group with highest congruence, even using genera presence-absence data. The congruence among groups was related to environmental factors, specifically the clay and phosphorous contents of soil. Several groups showed strong spatial clumping, but this was unrelated to the congruence among groups. The high degree of congruence of lianas with the other groups suggests that it may be a reasonable surrogate group, mainly for the other plant groups analyzed, if soil data are not available. Although lianas are difficult to count and identify, the number of studies on the ecology of lianas is increasing. Most of these studies have concluded that lianas are increasing in abundance in tropical forests. In addition to the high congruence, lianas are worth monitoring in their own right because they are sensitive to global warming and the increasing frequency and severity of droughts in tropical regions. Our findings suggest that the use of data on surrogate groups with relatively low taxonomic and numerical resolutions can be a reliable shortcut for biodiversity assessments, especially in megadiverse areas with high rates of habitat conversion, where the lack of biodiversity knowledge is pervasive. (c) 2012 Elsevier Ltd. All rights reserved.

Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications

Madrepora is one of the most ecologically important genera of reef-building scleractinians in the deep sea, occurring from tropical to high-latitude regions. Despite this, the taxonomic affinities and relationships within the genus Madrepora remain unclear. To clarify these issues, we sequenced the mitochondrial (mt) genome of the most widespread Madrepora species, M. oculata, and compared this with data for other scleractinians. The architecture of the M. oculara mt genome was very similar to that of other scleractinians, except for a novel gene rearrangement affecting only cox2 and cox3. This pattern of gene organization was common to four geographically distinct M. oculata individuals as well as the congeneric species M. minutiseptum, but was not shared by other genera that are closely related on the basis of cox1 sequence analysis nor other oculinids, suggesting that it might be unique to Madrepora. (C) 2012 Elsevier Inc. All rights reserved.

Taxonomic sufficiency of polychaete taxocenes for estuary monitoring

The polychaetes assemblage structure was used in order to investigate taxonomic sufficiency in a heavily polluted tropical bay. Species abundance was aggregated into progressively higher taxa matrices (genus, family, order) and was analyzed using univariate and multivariate techniques. Polychaetes distribution in Guanabara Bay (GB) was in accordance with a pollution gradient, probably ruled by the organic enrichment, consequent effects of hypoxia and altered redox conditions coupled with prevailing patterns of circulation. Within the sectors of GB, an increasing gradient in species richness and occurrence was observed, ranging from the azoic and impoverished stations in the inner sector to a well-structured community in terms of species composition and abundance inhabiting the outer sector. Multivariate statistical analysis showed similar results when species were aggregated into genera and families, while greater difference occurred at coarser taxonomic identification (order). The literature about taxonomic sufficiency has demonstrated that faunal patterns at different taxonomic levels tend to become similar with increased pollution. In GB, an analysis carried out solely at family level is perfectly adequate to describe the environmental gradient, considered a useful tool for a quick environmental assessment. (C) 2011 Elsevier Ltd. All rights reserved.

Phylogenetic analysis of Codium species from Brazil, with the description of the new species C. pernambucensis (Bryopsidales, Chlorophyta)

The genus Codium comprises c. 125 species widely distributed in marine coastal environments throughout the world. Due to morphological plasticity, the taxonomic delimitation of Codium species can be difficult. Sequences of the first exon of the large subunit of RUBISCO (rbcL) have been used in the molecular delimitation of species and for phylogenetic purposes. In the present study, we complement previous morphological work on Brazilian Codium species with molecular systematics. Based on the partial rbcL sequences, seven species are recognized along the Brazilian coast: C. decorticatum, C. intertextum, C. isthmocladum, C. profundum, C. spongiosum, C. taylorii and the new species Codium pernambucensis. Ten unique sequences were obtained among the samples examined, which we used in combination with previously published sequences to infer molecular phylogenies using various methods. The resulting trees showed three principal monophyletic groupings: Clade A with species having a prostrate habit, not branched, and mostly with small, grouped utricles; Clade B primarily consisting of upright species with cylindrical branches and large individual utricles; and Clade C composed of upright species with cylindrical branches that are slightly flattened, and have intermediate-sized individual utricles. The Brazilian species grouped with morphologically similar taxa from other geographic localities, and are present in all three main clades. A new sprawling species, Codium pernambucensis is described based on morphology and molecular analyses.

Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

Abstract Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

Rapid assessment survey for exotic benthic species in the São Sebastião Channel, Brazil

The study of biological invasions can be roughly divided into three parts: detection, monitoring, mitigation. Here, our objectives were to describe the marine fauna of the area of the port of São Sebastião (on the northern coast of the state of São Paulo, in the São Sebastião Channel, SSC) to detect introduced species. Descriptions of the faunal community of the SSC with respect to native and allochthonous (invasive or potentially so) diversity are lacking for all invertebrate groups. Sampling was carried out by specialists within each taxonomic group, in December 2009, following the protocol of the Rapid Assessment Survey (RAS) in three areas with artificial structures as substrates. A total of 142 species were identified (61 native, 15 introduced, 62 cryptogenic, 4 not classified), of which 17 were Polychaeta (12, 1, 1, 3), 24 Ascidiacea (3, 6, 15, 0), 36 Bryozoa (17, 0, 18, 1), 27 Cmdana (2, 1, 24, 0), 20 Crustacea (11, 4, 5, 0), 2 Entoprocta (native), 16 Mollusca (13, 3, 0, 0). Twelve species are new occurrences for the SSC. Among the introduced taxa, two are new for coastal Brazil. Estimates of introduced taxa are conservative as the results of molecular studies suggest that some species previously considered cryptogenic are indeed introduced. We emphasize that the large number of cryptogenic species illustrates the need for a long-term monitoring program, especially in areas most susceptible to bioinvasion. We conclude that rapid assessment studies, even in relatively well-known regions, can be very useful for the detection of introduced species and we recommend that they be carried out on a larger scale in all ports with heavy ship traffic.

Cradoscrupocellaria, a new bryozoan genus for Scrupocellaria bertholletii (Audouin) and related species (Cheilostomata, Candidae): taxonomy, biodiversity and distribution

A new genus, Cradoscrupocellaria n. gen., is erected for Scrupocellaria bertholletii Audouin, 1826), reported as widespread in tropical and subtropical waters. Here we select a neotype of this species in order to establish its identity and distinguish it from morphologically similar species. We include redescriptions and figures of additional species now assigned to this new genus: Cradoscrupocellaria curacaoensis (Fransen, 1986) n. comb., Cradoscrupocellaria hirsuta (Jullien & Calvet, 1903) n. comb., and Cradoscrupocellaria macrorhyncha (Gautier, 1962) n. comb. Five additional species are assigned to the genus: Cradoscrupocellaria ellisi (Vieira & Spencer Jones, 2012) n. comb., Cradoscrupocellaria nanshaensis (Liu, 1991) n. comb., Cradoscrupocellaria reptans (Linnaeus, 1758) n. comb., Cradoscrupocellaria serrata (Waters, 1909) n. comb., and Cradoscrupocellaria tenuirostris (Osburn, 1950) n. comb. Eighteen new species are described: Cradoscrupocellaria aegyptiana n. sp., Cradoscrupocellaria arisaigensis n. sp., Cradoscrupocellaria atlantica n. sp., Cradoscrupocellaria calypso n. sp., Cradoscrupocellaria floridana n. sp., Cradoscrupocellaria galapagensis n. sp., Cradoscrupocellaria gautieri n. sp., Cradoscrupocellaria gorgonensis n. sp., Cradoscrupocellaria hastingsae n. sp., Cradoscrupocellaria insularis n. sp., Cradoscrupocellaria jamaicensis n. sp., Cradoscrupocellaria lagaaiji n. sp., Cradoscrupocellaria macrorhynchoides n. sp., Cradoscrupocellaria makua n. sp., Cradoscrupocellaria marcusorum n. sp., Cradoscrupocellaria normani n. sp., Cradoscrupocellaria odonoghuei n. sp., and Cradoscrupocellaria osburni n. sp.

Species identification, distributioin and reproductive interactions of common smoot-hound and blackspotted smooth-hound shark (Genus mustelus) in the Adriatic Sea

Longstanding taxonomic ambiguity and uncertainty exist in the identification of the common (M. mustelus) and blackspotted (M. punctulatus) smooth-hound in the Adriatic Sea. The lack of a clear and accurate method of morphological identification, leading to frequent misidentification, prevents the collation of species-specific landings and survey data for these fishes and hampers the delineation of the distribution ranges and stock boundaries of the species. In this context, adequate species-specific conservation and management strategies can not be applied without risks of population declining and local extinction. In this thesis work I investigated the molecular ecology of the two smooth-hound sharks which are abundant in the demersal trawl surveys carried out in the NC Adriatic Sea to monitor and assess the fishery resources. Ecological and evolutionary relationships were assessed by two molecular tests: a DNA barcoding analysis to improve species identification (and consequently the knowledge of their spatial ecology and taxonomy) and a hybridization assay based on the nuclear codominant marker ITS2 to evaluate reproductive interactions (hybridization or gene introgression). The smooth-hound sharks (N=208) were collected during the MEDITS 2008 and 2010 campaigns along the Italian and Croatian coasts of the Adriatic Sea, in the Sicilian Channel and in the Algerian fisheries. Since the identification based on morphological characters is not strongly reliable, I performed a molecular identification of the specimens producing for each one the cytochrome oxidase subunit 1 (COI) gene sequence (ca. 640 bp long) and compared them with reference sequences from different databases (GenBank and BOLD). From these molecular ID data I inferred the distribution of the two target species in the NC Adriatic Sea. In almost the totality of the MEDITS hauls I found no evidence of species sympatry. The data collected during the MEDITS survey showed an almost different distribution of M. mustelus (confined along the Italian coasts) and M. punctulatus (confined along the Croatian coasts); just one sample (Gulf of Venice, where probably the ranges of the species overlap) was found to have catches of both the species. Despite these data results suggested no interaction occurred between my two target species at least during the summertime (the period in which MEDITS survey is carried out), I still wanted to know if there were inter-species reproductive interactions so I developed a simple molecular genetic method to detect hybridization. This method is based on DNA sequence polymorphism among species in the nuclear ribosomal Internal Transcribed Spacer 2 locus (ITS2). Its application to the 208 specimens collected raised important questions regarding the ecology of this two species in the Adriatic Sea. In fact results showed signs of hybridization and/or gene introgression in two sharks collected during the trawl survey of 2008 and one collected during the 2010 one along the Italian and Croatian coasts. In the case that it will be confirmed the hybrid nature of these individuals, a spatiotemporal overlapping of the mating behaviour and ecology must occur. At the spatial level, the northern part of the Adriatic Sea (an area where the two species occur with high frequency of immature individuals) could likely play the role of a common nursery area for both species.

Phylogeny and genetic diversity of Italian species of hares (genus Lepus)

In this study we have analysed the genetic variability in ca. 700 samples belonging to six species of genus Lepus using maternal and biparental molecular markers (mitochondrial DNA, microsatellites, Single Nucleotide Polimorphisms). We aimed to reconstruct the phylogenetic relationships of species of hares living in Europe, and assess the occurrence of hybridization between the European hare Lepus europaeus and the Italian hare Lepus corsicanus. Results showed a deep genetic differentiation and absence of hybridization between L. corsicanus and L. europaeus, confirming that they are distinct and distantly related biological species. In contrast, we showed small genetic distances and a close phylogenetic relationship between the Italian hare and Cantabrian hare L. castroviejoi, which suggest a deeper evaluation of their taxonomic status. Populations of L. corsicanus are geographically differentiated. In particular, the peninsular and Sicilian populations of Italian hares are sharply genetically distinct, which calls for avoiding any translocation between Italy and Sicily. Information on genetic variability and population structure is being used to implement the Italian Action Plan for L. corsicanus.

Species Richness-Environment Relationships of European Arthropods at Two Spatial Grains: Habitats and Countries

We study how species richness of arthropods relates to theories concerning net primary productivity, ambient energy, water-energy dynamics and spatial environmental heterogeneity. We use two datasets of arthropod richness with similar spatial extents (Scandinavia to Mediterranean), but contrasting spatial grain (local habitat and country). Samples of ground-dwelling spiders, beetles, bugs and ants were collected from 32 paired habitats at 16 locations across Europe. Species richness of these taxonomic groups was also determined for 25 European countries based on the Fauna Europaea database. We tested effects of net primary productivity (NPP), annual mean temperature (T), annual rainfall (R) and potential evapotranspiration of the coldest month (PETmin) on species richness and turnover. Spatial environmental heterogeneity within countries was considered by including the ranges of NPP, T, R and PETmin. At the local habitat grain, relationships between species richness and environmental variables differed strongly between taxa and trophic groups. However, species turnover across locations was strongly correlated with differences in T. At the country grain, species richness was significantly correlated with environmental variables from all four theories. In particular, species richness within countries increased strongly with spatial heterogeneity in T. The importance of spatial heterogeneity in T for both species turnover across locations and for species richness within countries suggests that the temperature niche is an important determinant of arthropod diversity. We suggest that, unless climatic heterogeneity is constant across sampling units, coarse-grained studies should always account for environmental heterogeneity as a predictor of arthropod species richness, just as studies with variable area of sampling units routinely consider area.

Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries

The taxonomic and phylogenetic status of Echinococcus granulosus strains are still controversial and under discussion. In the present study, we investigated the genetic polymorphism of E. granulosus isolates originating from three countries of Africa, including a region of Algeria, where the common G1 sheep and the camel G6 strains coexist sympatrically. Seventy-one hydatid cysts were collected from sheep, cattle, camels, and humans. Two mitochondrial markers (cox1 and nad1) were used for strain identification. Two nuclear markers (actII and hbx2) were used to study the possible occurrence of cross-fertilization. Despite the heterogeneity observed among the G1 isolates, they were all localized within one robust cluster. A second strong cluster was also observed containing all of the G6 isolates. Both strains appeared as two distinct groups, and no cases of interbreeding were found. Thus, the attribution of a species rank can be suggested. We also found the Tasmanian sheep G2 strain for the first time in Africa. Because of the slight variations observed between the common sheep and the Tasmanian sheep strains, further studies should be carried out to elucidate the epidemiological relevance of this genetic discrimination.

Mycoplasma leachii sp. nov. as a new species designation for Mycoplasma sp. bovine group 7 of Leach, and reclassification of Mycoplasma mycoides subsp. mycoides LC as a serovar of Mycoplasma mycoides subsp. capri

The Mycoplasma mycoides cluster consists of six pathogenic mycoplasmas causing disease in ruminants, which share many genotypic and phenotypic traits. The M. mycoides cluster comprises five recognized taxa: Mycoplasma mycoides subsp. mycoides Small Colony (MmmSC), M. mycoides subsp. mycoides Large Colony (MmmLC), M. mycoides subsp. capri (Mmc), Mycoplasma capricolum subsp. capricolum (Mcc) and M. capricolum subsp. capripneumoniae (Mccp). The group of strains known as Mycoplasma sp. bovine group 7 of Leach (MBG7) has remained unassigned, due to conflicting data obtained by different classification methods. In the present paper, all available data, including recent phylogenetic analyses, have been reviewed, resulting in a proposal for an emended taxonomy of this cluster: (i) the MBG7 strains, although related phylogenetically to M. capricolum, hold sufficient characteristic traits to be assigned as a separate species, i.e. Mycoplasma leachii sp. nov. (type strain, PG50(T) = N29(T) = NCTC 10133(T) = DSM 21131(T)); (ii) MmmLC and Mmc, which can only be distinguished by serological methods and are related more distantly to MmmSC, should be combined into a single subspecies, i.e. Mycoplasma mycoides subsp. capri, leaving M. mycoides subsp. mycoides (MmmSC) as the exclusive designation for the agent of contagious bovine pleuropneumonia. A taxonomic description of M. leachii sp. nov. and emended descriptions of M. mycoides subsp. mycoides and M. mycoides subsp. capri are presented. As a result of these emendments, the M. mycoides cluster will hereafter be composed of five taxa comprising three subclusters, which correspond to the M. mycoides subspecies, the M. capricolum subspecies and the novel species M. leachii.

Proposal of Histophilus somni gen. nov., sp. nov. for the three species incertae sedis 'Haemophilus somnus', 'Haemophilus agni' and 'Histophilus ovis'

Earlier investigations have shown that 'Haemophilus somnus', 'Haemophilus agni' and 'Histophilus ovis' represent the same species. In the present investigation, the taxonomic position of this species is explored further by sequencing the 16S rRNA and rpoB genes of strains that were investigated previously by DNA-DNA hybridization. These results clearly support the allocation of this species to a novel genus within the family PASTEURELLACEAE: The phenotypic separation of Histophilus somni gen. nov., sp. nov. from other members of the family can, for most strains, be based on capnophilia, yellowish pigmentation and indole production. However, due to phenotypic variation, the use of a species-specific PCR test based on the 16S rRNA gene is included in the species description. This is justified by the high sequence similarity of the 16S rRNA gene within the species and the fact that the highest sequence similarity to any other taxon within the family is 93.4 %. The type strain, 8025(T)=ATCC 43625(T)=CCUG 36157(T), was isolated in the USA from a bovine brain with lesions of thromboembolic meningoencephalitis.

Phylogenetic relationship of equine Actinobacillus species and distribution of RTX toxin genes among clusters

Equine Actinobacillus species were analysed phylogenetically by 16S rRNA gene (rrs) sequencing focusing on the species Actinobacillus equuli, which has recently been subdivided into the non-haemolytic A. equuli subsp. equuli and the haemolytic A. equuli subsp. haemolyticus. In parallel we determined the profile for RTX toxin genes of the sample of strains by PCR testing for the presence of the A. equuli haemolysin gene aqx, and the toxin genes apxI, apxII, apxIII and apxIV, which are known in porcine pathogens such as Actinobacillus pleuropneumoniae and Actinobacillus suis. The rrs-based phylogenetic analysis revealed two distinct subclusters containing both A. equuli subsp. equuli and A. equuli subsp. haemolyticus distributed through both subclusters with no correlation to taxonomic classification. Within one of the rrs-based subclusters containing the A. equuli subsp. equuli type strain, clustered as well the porcine Actinobacillus suis strains. This latter is known to be also phenotypically closely related to A. equuli. The toxin gene analysis revealed that all A. equuli subsp. haemolyticus strains from both rrs subclusters specifically contained the aqx gene while the A. suis strains harboured the genes apxI and apxII. The aqx gene was found to be specific for A. equuli subsp. haemolyticus, since A. equuli subsp. equuli contained no aqx nor any of the other RTX genes tested. The specificity of aqx for the haemolytic equine A. equuli and ApxI and ApxII for the porcine A. suis indicates a role of these RTX toxins in host species predilection of the two closely related species of bacterial pathogens and allows PCR based diagnostic differentiation of the two.