Phylogenetic analyses of mtDNA sequences corroborate taxonomic designations based on cuticular hydrocarbons in subterranean termites

Cuticular hydrocarbons (CHCs) are valuable characters for the analysis of cryptic insect species with few discernible morphological characters. Yet, their use in insect systematics, specifically in subterranean termites in the genus Reticulitermes (Isoptera: Rhinotermitidae), remains controversial. In this paper, we show that taxonomic designations in Reticulitermes from California (USA) suggested in light of differences among CHC phenotypes are corroborated by phylogenetic analyses using mtDNA sequences. Analyses based on CHC phenotypes and supported, in part, by behavioral and ecological differences have suggested the presence of more species than the two currently recognized: R. hesperus Banks and R. tibialis Banks. We analyze a 680 base pair fragment of the mitochondrial DNA cytochrome oxidase (COII) gene from 45 new (21 collection localities) and two previously recorded samples of Reticulitermes from California using parsimony and maximum likelihood methods. Both methods result in trees with highly similar topologies. Bootstrapping indicates support for six clades of Reticulitermes, and corroborates groupings based on cuticular hydrocarbons. One of the clades, R. hesperus, is already recognized in California, while four clades appear to be previously undescribed taxa. Although identification of the final clade is inconclusive, it includes a sample putatively identified as R. tibialis. Therefore, using phylogenetic analyses we corroborate chemical characters used to identify taxa, associate a chemical phenotype with a previously described species, and provide additional support for undescribed taxa of Reticulitermes.     

Study of a new group of Enterobacteriacea (group H1) related to Enterobacter cloacae strain]

A DNA-DNA hybridization study was carried out on a new group of enterobacteria (group H1) previously studied by numerical taxonomy work on the genus Enterobacter. This group showed a very high genetic homogeneity since the average relative binding ratio of nine analysed strains is equal to 91%. The taxonomic position of this group into the family of enterobacteria is discussed with the species E. cloacae (37 to 61%), K. pneumoniae (44 to 60%), K. oxytoca (57-58%), L. malonatica (syn. Citrobacter intermedius, a:46 to 54%), L. amalonatica (syn. C. intermedius, b: 51%), and the group H3 (52-61%). The group H1 is defined on phenotypic and genetic data.     

Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective

The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286 bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity.     

A contribution to the taxonomy of the genus Rinodina (Physciaceae, lichenized Ascomycotina) using combined ITS and mtSSU rDNA data

To test the phylogenetic position of phenotypically peculiar species in the Physciaceae we generated 47 new sequences (26 of nrITS region and 21 of mtSSU rDNA) from 19 crustose taxa of Physciaceae mainly from the genus Rinodina. Phylogenetic analysis confirmed the Buellia and Physcia groups. The analysis revealed a considerable variability of characters traditionally used for classification, especially in the delimitation of the genera Buellia and Rinodina. While ascus types agree well with the distinction of the Buellia and Physcia groups, none of the other traditional characters, including excipulum type and ascospore thickening, were consistent within subclades of the Physcia group. We suggest that both excipulum type and ascospore characters are rather dynamic in the evolution of Rinodina species and only appear consistent in morphologically more complex foliose and fruticose groups, which are characterized by thallus characters not present in the crustose groups. Two recent taxonomic changes are supported by molecular characters: Endohyalina insularis (syn. 'Rinodina' insularis) and Rinodina lindingeri (syn. 'Buellia' lindingeri). In addition Rinodina parvula (syn. 'Buellia' parvula) is reinstated. New records for Endohyalina brandii, E. diederichii, E. insularis and Rinodina albana are presented.     

Revision of the endemic Taiwanese millipede genus Aponedyopus Verhoeff, 1939, with descriptions of two new species (Diplopoda, Polydesmida, Paradoxosomatidae). Advances in the systematica of Diplopoda III

The millipede genus Aponedyopus is endemic to Taiwan and contains three species. All previously described nominal species are considered to represent one species: Aponedyopus montanus Verhoeff, 1939 (the type species), including Aponedyopus reesi (Wang, 1957) and Aponedyopus maculatus Takakuwa, 1942, syn. n. Two further species are described as new: Aponedyopus similissp. n. and Aponedyopus latilobatussp. n. The genus is re-diagnosed, all of its three species are keyed, and their distributions mapped.     

Hiding deep in the trees: discovery of divergent mitochondrial lineages in Malagasy chameleons of the Calumma nasutum group

WE CONDUCTED A COMPREHENSIVE MOLECULAR PHYLOGENETIC STUDY FOR A GROUP OF CHAMELEONS FROM MADAGASCAR (CHAMAELEONIDAE: Calumma nasutum group, comprising seven nominal species) to examine the genetic and species diversity in this widespread genus. Based on DNA sequences of the mitochondrial gene (ND2) from 215 specimens, we reconstructed the phylogeny using a Bayesian approach. Our results show deep divergences among several unnamed mitochondrial lineages that are difficult to identify morphologically. We evaluated lineage diversification using a number of statistical phylogenetic methods (general mixed Yule-coalescent model; SpeciesIdentifier; net p-distances) to objectively delimit lineages that we here consider as operational taxonomic units (OTUs), and for which the taxonomic status remains largely unknown. In addition, we compared molecular and morphological differentiation in detail for one particularly diverse clade (the C. boettgeri complex) from northern Madagascar. To assess the species boundaries within this group we used an integrative taxonomic approach, combining evidence from two independent molecular markers (ND2 and CMOS), together with genital and other external morphological characters, and conclude that some of the newly discovered OTUs are separate species (confirmed candidate species, CCS), while others should best be considered as deep conspecific lineages (DCLs). Our analysis supports a total of 33 OTUs, of which seven correspond to described species, suggesting that the taxonomy of the C. nasutum group is in need of revision.     

DNA barcodes as a tool in biodiversity research: testing pre-existing taxonomic hypotheses in Delphic Apollo butterflies (Lepidoptera,Papilionidae)

Numerous studies have demonstrated that DNA barcoding is an effective tool for detecting DNA clusters, which can be viewed as operational taxonomic units (OTUs), useful for biodiversity research. Frequently, the OTUs in these studies remained unnamed, not connected with pre-existing taxonomic hypotheses, and thus did not really contribute to feasible estimation of species number and adjustment of species boundaries. For the majority of organisms, taxonomy is very complicated with numerous, often contradictory interpretations of the same characters, which may result in several competing checklists using different specific and subspecific names to describe the same sets of populations. The highly species-rich genus Parnassius (Lepidoptera: Papilionidae) is but one example, such as several mutually exclusive taxonomic systems have been suggested to describe the phenotypic diversity found among its populations. Here we provide an explicit flow chart describing how the DNA barcodes can be combined with the existing knowledge of morphology-based taxonomy and geography (sympatry versus allopatry) of the studied populations in order to support, reject or modify the pre-existing taxonomic hypotheses. We then apply this flow chart to reorganize the taxa within the Parnassius delphius species group, solving long-standing taxonomic problems.     

Taxonomy of Mechanitis (F.) (Lepidoptera: Nymphalidae) from the West Colombian Andes: an Integrative Approach

Species identification in the butterfly genus Mechanitis (F.) (Lepidoptera: Nymphalidae) becomes difficult when it is based only on wing color patterns, a common practice in butterfly taxonomy. Difficulties in Mechanitis taxonomy are related to the widespread mimicry and polymorphism among species belonging to this genus. Species recognition and inventories of Mechanitis genus in geographic areas as the Andean region of Colombia are of particular interest and the use of more than one character for taxonomic identification is desirable. In this study, we included morphological, ecological, and mitochondrial DNA data to identify the occurring species in this region. Species of Mechanitis were studied from ecological, morphological, and molecular perspectives considering host plant identification, oviposition behavior, and life cycles under laboratory conditions. Immature morphology, patterns of wing color, and genital structures of adults were also studied. The genetic barcoding region of the cytochrome oxidase I mitochondrial gene was sequenced and used to verify the limits between species previously defined by the other characters and to validate its usefulness for species delimitation in this particular genus. The integrative approach combining independent datasets successfully allowed species identification as compared to the approach based on a single dataset. Three well-differentiated species were found in the studied region, Mechanitis menapis (Hewitson), Mechanitis polymnia (Linnaeus), and Mechanitis lysimnia (Fabricius). New valuable characters that could improve taxonomic identification in this genus are considered.     

Phylogeny and taxonomy of Potamotrygonocotyle Mayes, Brooks & Thorson, 1981 (Monogenoidea: Monocotylidae) with a description of four new species

The marine-derived stingrays of Potamotrygonidae, endemic to South American river systems, host an interesting parasite fauna equally related to marine lineages. Among those lineages, the diversity and phylogenetic relationships within Potamotrygonocotyle - a monocotylid monogenoidean specific to potamotrygonids - are poorly known, since 9 of 10 species attributed to this genus have been described in the past 3 years. Here, we readdress the diversity of Potamotrygonocotyle after examining the gills of 436 potamotrygonid individuals representing 12 described and 14 potentially undescribed species of freshwater stingrays from 19 major river systems of South America (i.e. sub-basins). We recognized 12 valid species within the parasite genus, of which four are described in this study. Our taxonomic decisions were based on the phylogenetic analysis of 14 ingroup terminal taxa and 12 morphological characters, which resulted in the following hypothesis of sister-group relationships: ((P. dromedarius, P. tatianae sp. nov.), (P. rionegrense, P. auriculocotyle sp. nov., ((P. quadracotyle, P. umbella), (P. septemcotyle sp. nov., (P. chisholmae, P. uruguayense)), (P. tsalickisi, P. eurypotamoxenus, P. rarum, (P. tocantinsense sp. nov., P. aramasae))))). According to our hypothesis, the absence of autapomorphic features for some nominal species, and the re-evaluation of morphological variation among populations, led us to consider P. eurypotamoxenus and P. uruguayense as junior synonymys of P. tsalicksi and P. chisholmae, respectively. Finally, we address the importance of biogeographic and host representation, in order to fully understand the patterns of morphological variation and host specificity within this group. We found that hypotheses of species delimitation depend greatly on efforts to sample specimens throughout its distributional range and that host specificity within this genus varies dramatically among lineages.     

INFERRING TAXONOMIC POSITIONS AND TESTING GENUS LEVEL ASSIGNMENTS IN COCCOID GREEN LICHEN ALGAE: A PHYLOGENETIC ANALYSIS OF 18S RIBOSOMAL RNA SEQUENCES FROM DICTYOCHLOROPSIS RETICULATA AND FROM MEMBERS OF THE GENUS MYRMECIA (CHLOROPHYTA, TREBOUXIOPHYCEAE CL. NOV.)1

Complete nuclear-encoded small-subunit ribosomal RNA (18S rRNA) coding sequences were determined for the coccoid green algae Dictyochloropsis reticulata (Tschermak-Woess) Tschermak-Woess , Myrmecia astigmatica Vinatzer, and M. bisecta Reisigl, to investigate the taxonomic position of Dictyochloropsis Geitler and of the genus Myrmecia Printz. Phylogenies inferred from these data revealed a sister-group relationship between D. reticulata and certain coccoid green algae that lack motile stages (autosporic coccoids) within the order Microthamniales. The monophyletic origin of the Microthamniales, including autosporic coccoids previously classified in the Chlorophyceae, is clearly resolved by the rRNA sequence data. This finding. shows the considerable taxonomic breadth of that order, whose taxonomic position has been unclear so far. A new class, Trebouxiophyceae, is proposed for this group of green algae. Phylogenetic inferences from the rRNA sequences show paraphyly of the genus Myrmecia. The 18S rRNA sequence data suggest that, among taxa that share similar vegetative cell morphologies, the zoospore characters resolve better the actual genus and species boundaries. Within identical zoospore types, the rRNA data allow further resolution of taxonomic relationships. On the basis of the.se findings, I propose that the genus Friedmannia Chantanachat ± Bold be merged into Myrmecia and that only those species be left in the genus Myrmecia that are identical in particular zoospore characters (i.e. those described in detail for M. israeliensis ( Chantanachat ± Bold) comb, nov.), namely M. astigmatica, M. biatorellae (Tschermak-Woess ± Ptesst) Petersen, and M. israeliensis. Myrmecia bisecta has to be excluded from Myrmecia; its taxonomic position within the Trebouxiophyceae is unclear .     

Species boundaries, specialization, and the radiation of sponge-dwelling alpheid shrimp

Microevolutionary studies and natural history suggest that host-specialization has promoted the high diversity of tropical sponge-dwelling snapping shrimps (Decapoda, Alpheidae, Synalpheus ). Yet the taxonomic difficulty of this genus has precluded rigorous tests of this hypothesis. S. rathbunae Coutiére is among the most abundant invertebrates inhabiting the framework of sponges and dead coral that forms the floor of Caribbean coral reefs. Even within a small area S. rathbunae exhibits the apparently wide variation in size, color, and morphology that has long frustrated efforts to identify and define species boundaries within this large (> 100 described species) genus. Here I show that sympatric populations of this nominal species occupying different sponge hosts display clear, concordant differences in allozyme genotypes and in multivariate morphometries, confirming that the populations represent three distinct biological species. Moreover, careful field sampling revealed that the three S. rathbunce taxa and the closely related S. filidigitus Armstrong showed almost no overlap in the species of hosts occupied. Interestingly, while there was significant differentiation between Belizean and Panamanian populations of the one taxon that occurred at both sites (∼1500 km apart), these populations were recognizable as conspecific using both genetic and morphological characters. These results show that (1) diversity of Synalpheus , which is already among the most species-rich crustacean genera, is probably several times higher than currendy recognized, and (2) species of sponge-dwelling Synalpheus are highly host-specific, with related species distinctly segregated among hosts. Together with previous evidence of host race differentiation within shrimp species, these results suggest a primary role for resource specialization in the origin and/or maintenance of this group's characteristically high diversity.     

Phylogenetic investigation of the genus Raoiella (Prostigmata: Tenuipalpidae): diversity, distribution, and world invasions

The genus Raoiella is best known because of the red palm mite, R. indica, a major pest of palms spreading aggressively throughout the Americas. Not much was known about the biology, geographic origins, or evolutionary history of the genus when R. indica emerged as a major invasive pest. This paper attempts to address some of the basic historical questions regarding the palm mite as well as the genus. Molecular characters from COI and 28S regions were used to produce a phylogenetic hypothesis for the genus in an effort to understand its geographic origin. It also uses COI barcode data to delimit several potentially new species discovered by the authors in Australia. Results show a basal split between R. indica and all other Raoiella species, which indicates Africa or the Middle East as the most probable origin of the genus. Additionally, COI data suggests that at least eight new species are represented among the 20 Australian populations included in this study.     

Increased molecular divergence of two endemic Trachelipus (Isopoda,Oniscidea) species from Greece reveals patterns not congruent with current taxonomy

In the present study, we employed three mitochondrial DNA genetic markers in a phylogenetic analysis aiming at the delineation of the relationships amongst nominal Trachelipus kytherensis populations, as well as between populations of this species and of Trachelipus aegaeus and a new form, occurring syntopically with the latter. Both the phylogenetic analysis and the genetic distances separating populations, show the presence of several distinct and well differentiated clades that undermine the monophyly of T. kytherensis. On the other hand, despite the insular distribution of T. aegaeus populations, their divergence is low and the monophyly of this taxon can be rescued by the inclusion of two more insular populations previously assigned to T. kytherensis. The patterns of genetic divergence among clades are only partially congruent with the geographic distribution of populations. The validity of taxonomic characters used so far in the genus appears to be questionable; therefore, a more comprehensive phylogenetic study at a population level is deemed necessary for understanding the divergence of Trachelipus lineages. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 361–370.     

A phylogenetic perspective on 160 years of troubled taxonomy of Niphargus (Crustacea: Amphipoda)

Niphargus is the largest genus of freshwater amphipods. Its systematics from the species to the family level has always been problematic. This study is the first comprehensive phylogenetic treatment of the chiefly subterranean group in 160 years of its taxonomic history. It includes 103 niphargid species plus outgroups, representing about one‐third of all nominal species. The samples originated mainly from type localities or adjacent sites and covered most of the morphological variability of the genus. Character sampling included nuclear 28S and mitochondrial 12S rDNA sequences, and 122 morphological characters. Quantitative morphological traits were coded using two alternative methods. The first one searches for gaps in the variability range of each character, while the second one uses absolute differences between the standardized raw data as weights. Different data sets yielded alternative topologies. All data support the monophyly of Niphargidae, while Niphargopsis— another niphargid genus — was consistently nested within Niphargus, loosing justification for its separate status. We predict a similar fate for all or most of the remaining six small niphargid genera, which were not yet scrutinized phylogenetically. Different topologies agreed in species composition of five large, well‐supported clades, although the hierarchic relationships between them remain unresolved. These clades reject all previously proposed taxonomic subdivisions of Niphargus, implying a high degree of morphological homoplasy that renders any morphology‐based groups questionable. The clade members are distributed within well‐established zoogeographical regions that do not exceed 1300 km across the longest diagonal. These results provide a framework for future studies on niphargid systematics, the evolution of endemism and cryptic diversity in subterranean environments, the mechanisms leading to exceptional morphological heterogeneity, historical biogeography, and applied ecological issues.     

A new species of <Emphasis Type="Italic">Pustula</Emphasis> (Oomycetes,Albuginales) is the causal agent of sunflower white rust

White blister rust of sunflower is an emerging disease that is among the most important diseases in this crop in South Africa and has recently spread to Europe. For the genus Albugo, it has been demonstrated that species are mostly at least host genus specific and that several previously overlooked species are present on Brassicaceae. It thus seems likely that previously unrecognised species are also present in the genus Pustula. Based on previous phylogenetic reconstruction in combination with differences in oospore ornamentation, it is revealed that Pustula on sunflower, previously attributed to Pustula tragopogonis (syn. Albugo tragopogonis), is distinct from Pustula on Tragopogon. Therefore, this pathogen is described as a new species, Pustula helianthicola. In addition, taxonomic observations revealed that Pustula tragopogonis is an incorrect name and is replaced by the new combination, Pustula obtusata.     

Morphometric divergence in populations of Anastrepha obliqua (Diptera,Tephritidae) from Colombia and some Neotropical locations

The West Indian fruit fly, Anastrepha obliqua, is one of seven species of quarantine importance of its genus and is one of the most economically important fruit fly pests in Colombia. The taxonomic status of this species is a key issue for further implementation of any pest management program. Several molecular studies have shown enough variability within Anastrepha obliqua to suggest its taxonomic status could be revised; however, there are no morphological studies supporting this hypothesis. The aim of this work was to describe the morphological variability of Colombian populations of Anastrepha obliqua, comparing this variability with that of other samples from the Neotropics. Measurements were performed on individuals from 11 populations collected from different geographic Colombian localities and were compared with populations from Mexico (2), Dominica Island (1), Peru (1) and Brazil (2). Linear morphometric analyses were performed using 23 female morphological traits, including seven variables of the aculeus, three of the thorax, and six of the wing; seven ratios among them were also considered. Discriminant function analyses showed significant morphological differentiation among the Colombian populations, separating them into two groups. Furthermore, in the comparisons between Colombian samples with those from other countries, three clusters were observed. The possibility of finding more than one species within the nominal Anastrepha obliqua population is discussed.