Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects

<p>Abstract</p> <p>Background</p> <p>Published molecular phylogenies are usually based on data whose quality has not been explored prior to tree inference. This leads to errors because trees obtained with conventional methods suppress conflicting evidence, and because support values may be high even if there is no distinct phylogenetic signal. Tools that allow an a priori examination of data quality are rarely applied.</p> <p>Results</p> <p>Using data from published molecular analyses on the phylogeny of crustaceans it is shown that tree topologies and popular support values do not show existing differences in data quality. To visualize variations in signal distinctness, we use network analyses based on split decomposition and split support spectra. Both methods show the same differences in data quality and the same clade-supporting patterns. Both methods are useful to discover long-branch effects.</p> <p>We discern three classes of long branch effects. Class I effects consist of attraction of terminal taxa caused by symplesiomorphies, which results in a false monophyly of paraphyletic groups. Addition of carefully selected taxa can fix this effect. Class II effects are caused by drastic signal erosion. Long branches affected by this phenomenon usually slip down the tree to form false clades that in reality are polyphyletic. To recover the correct phylogeny, more conservative genes must be used. Class III effects consist of attraction due to accumulated chance similarities or convergent character states. This sort of noise can be reduced by selecting less variable portions of the data set, avoiding biases, and adding slower genes.</p> <p>Conclusion</p> <p>To increase confidence in molecular phylogenies an exploratory analysis of the signal to noise ratio can be conducted with split decomposition methods. If long-branch effects are detected, it is necessary to discern between three classes of effects to find the best approach for an improvement of the raw data.</p

The taxonomist - an endangered race : a practical proposal for its survival

Background: Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based. Discussion: Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance. Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISISM. Summary: The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty. Keywords: Taxonomy crisis; taxonomic impediment; impact factor; original species description; citation index; systematic

Cryptic speciation in a benthic isopod from Patagonian and Falkland Island waters and the impact of glaciations on its population structure

<p>Abstract</p> <p>Background</p> <p>The Falkland Islands and Patagonia are traditionally assigned to the Magellan Biogeographic Province. Most marine species in Falkland waters are also reported from southern Patagonia. It remains unclear if relatively immobile, marine benthic, shallow-water species maintain gene flow, and by what mechanism. Recurrent fluctuations in sea level during glacial cycles are regarded as a possible mechanism that might have allowed genetic exchange between the regions. However, the realized genetic exchange between the Falkland Islands and Patagonia has never been estimated.</p> <p>Results</p> <p>This study analyses the genetic structure of three populations of the marine shallow-water isopod <it>Serolis paradoxa </it>(Fabricius, 1775) from the Falkland Islands and southern Patagonia (central Strait of Magellan and the Atlantic opening) applying seven nuclear microsatellites and a fragment of the mitochondrial 16S rRNA gene. Both marker systems report highest genetic diversity for the population from the central Strait of Magellan and lowest for the Falkland Islands. The estimated effective population sizes were large for all populations studied. Significant differentiation was observed among all three populations. The magnitude of differentiation between Patagonia and the Falkland Islands (16S: uncorrected p-distance 2.1%; microsatellites: standardized F'_ST> 0.86) was an order of magnitude higher than between populations from within Patagonia. This indicates that there is currently no effective gene flow for nominal <it>S. paradoxa </it>between these two regions and it has been absent for time exceeding the last glacial maximum. We argue that specimens from the Strait of Magellan and the Falkland Islands very likely represent two distinct species that separated in the mid-Pleistocene (about 1 MY BP).</p> <p>Conclusion</p> <p>The results of this study indicate limited gene flow between distant populations of the brooding isopod <it>Serolis paradoxa</it>. The patterns of genetic diversity suggest that the only recently inundated Strait of Magellan was colonized by different source populations, most likely from Atlantic and Pacific coastal waters. Our results demonstrate that more systematic testing of shared faunal inventory and realized genetic exchange between Patagonia and the Falkland Islands is needed before a consensus concerning the position of the Falkland Islands relative to the Magellan zoogeographic province can be reached.</p

Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes

<p>Abstract</p> <p>Background</p> <p>The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome <it>c </it>oxidase I (COI) gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous.</p> <p>Results</p> <p>We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97%) of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95%) of the studied Carabidae.</p> <p>Conclusion</p> <p>Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.</p

Can comprehensive background knowledge be incorporated into substitution models to improve phylogenetic analyses? A case study on major arthropod relationships

<p>Abstract</p> <p>Background</p> <p>Whenever different data sets arrive at conflicting phylogenetic hypotheses, only testable causal explanations of sources of errors in at least one of the data sets allow us to critically choose among the conflicting hypotheses of relationships. The large (28S) and small (18S) subunit rRNAs are among the most popular markers for studies of deep phylogenies. However, some nodes supported by this data are suspected of being artifacts caused by peculiarities of the evolution of these molecules. Arthropod phylogeny is an especially controversial subject dotted with conflicting hypotheses which are dependent on data set and method of reconstruction. We assume that phylogenetic analyses based on these genes can be improved further i) by enlarging the taxon sample and ii) employing more realistic models of sequence evolution incorporating non-stationary substitution processes and iii) considering covariation and pairing of sites in rRNA-genes.</p> <p>Results</p> <p>We analyzed a large set of arthropod sequences, applied new tools for quality control of data prior to tree reconstruction, and increased the biological realism of substitution models. Although the split-decomposition network indicated a high noise content in the data set, our measures were able to both improve the analyses and give causal explanations for some incongruities mentioned from analyses of rRNA sequences. However, misleading effects did not completely disappear.</p> <p>Conclusion</p> <p>Analyses of data sets that result in ambiguous phylogenetic hypotheses demand for methods, which do not only filter stochastic noise, but likewise allow to differentiate phylogenetic signal from systematic biases. Such methods can only rely on our findings regarding the evolution of the analyzed data. Analyses on independent data sets then are crucial to test the plausibility of the results. Our approach can easily be extended to genomic data, as well, whereby layers of quality assessment are set up applicable to phylogenetic reconstructions in general.</p

Aspects of the evolution and biogeography of stygobiontic Isopoda (Crustacea: Peracarida)

The evolution of the stygobiontic isopods is discussed correlating the phylogenetic system with biogeography. All stygobiontic isopods probably are derived from remote marine ancestors. The colonization of subterranean aquatic biotopes occurred in two ways: (1) via the coastal groundwater in the case of the Microparasellidae, Gnathostenetroididae, Stenetriidae, and in Cyathura (Stygocyathura), (2) in most families, however, via epigean freshwater ancestors. Ancient freshwater isopods that must already have existed before the Cretaceous and whose stygobiontic phylogenetic lines partly must have existed before the opening of the Atlantic are the Aselloidea, Calabozoida, Phreatoicidea, and probably also the Protojaniridae. In the course of Cretaceous and Tertiary regressions other, more apomorphic taxa “stranded” and adapted to stygobiontic biotopes, such as the “Monolistrini” (Sphaeromatidae)

A new hypogean Cyathura from New Caledonia (Crustacea, Isopoda, Anthuridea)

Cyathuva numeae n.sp. from New Caledonia is the sixth blind species of the genus Cyathura Norman & Stebbing, 1886, found in hypogean habitats. The new species lives in the interstitia of coastal sand or gravel, like C. milloti Chappuis et al., 1956, from Réunion. A close relationship to the other species is not obvious; the specific shape of the appendix masculina can be derived from the carinata-type. In contrast to the slender species, C. curassavica Stork, 1940, and C. specus Bowman, 1965, in the new species the adaptations to hypogean life are limited to the small body size and reduction of the eyes

Especiación críptica en el isópodo gigante antártico Glyptonotus antarcticus (Isopoda, Valvifera, Chaetiliidae).

The genus Glyptonotus is most commonly regarded as monospecific, with Glyptonotus antarcticus Eights 1852 being its only constituent. Two more forms (G. acutus, G. antarcticus var. obtusus) that had been described based on morphological evidence have received little attention in the literature, though no formal attempt to evaluate their taxonomic status has been undertaken. In a survey of within-species genetic diversity, 23 specimens of the benthic Antarctic isopod Glyptonotus antarcticus from three sampling areas around the Antarctic had a high genetic variability in their mitochondrial LSU (16S) gene. Eleven unique mitochondrial haplotypes were found, two at the Antarctic Peninsula (AP), two in the Ross Sea (RS) and seven in the Eastern Weddell Sea (EWS). Average haplotype variation within sampling areas (AP, RS, EWS) was one order of magnitude less than between sampling areas. In the EWS, however, two highly differentiated haplotypes co-exist. These four groups of haplotypes may represent cryptic, but reproductively isolated species rather than a single species.En una investigación sobre diversidad genética intra-específica se registró variabilidad en el gen mitocondrial LSU (16S) de 23 especímenes del isópodo bentónico antártico Glyptonotus antarcticus de tres áreas antárticas. Se encontraron once haplotipos mitocondriales únicos, dos en la Península Antártica (AP), dos en el Mar de Ross (RS) y siete en el Mar de Weddell (EWS). La variación media de los haplotipos dentro de las áreas (AP, RS, EWS) fue un orden de magnitud menor que entre ellas. Sin embargo, en el EWS coexisten dos haplotipos altamente diferenciados. Estos cuatro grupos de haplotipos pueden representar especies crípticas reproductivamente aisladas, más que una única especie como se asumía anteriormente

Morphology and taxonomy of Isopoda Anthuroidea (Crustacea) from Sulawesi with description of six new species

This is a first inventory of Isopoda Anthuroidea from near-shore marine sites in Sulawesi. The material was collected from reefs, sea-grass beds and mangroves of the Minahasa Peninsula in North Sulawesi. Specimens were washed out from benthos samples collected in shallow water. The new species Hyssura reptans sp. nov., Kupellonura indonesica sp. nov., Kupellonura macaroni sp. nov., Pendanthura bangkaensis sp. nov., Expanathura marcoi sp. nov., and Colanthura gerungi sp. nov. are described. We discovered that in Colanthura the mandible is fused to the cephalothorax, a unique feature among isopods. Expanathura collaris (Kensley, 1979) is described from Bangka Island and several differences between other Indo-Pacific populations are discussed

(Table 1) Individual codes, GenBank accession numbers and sampling location for the specimens of Glyptonotus collected during two POLARSTERN expeditions

The genus Glyptonotus is most commonly regarded as monospecific, with Glyptonotus antarcticus Eights 1852 being its only constituent. Two more forms (G. acutus, G. antarcticus var. obtusus) that had been described based on morphological evidence have received little attention in the literature, though no formal attempt to evaluate their taxonomic status has been undertaken. In a survey of within-species genetic diversity, 23 specimens of the benthic Antarctic isopod Glyptonotus antarcticus from three sampling areas around the Antarctic had a high genetic variability in their mitochondrial LSU (16S) gene. Eleven unique mitochondrial haplotypes were found, two at the Antarctic Peninsula (AP), two in the Ross Sea (RS) and seven in the Eastern Weddell Sea (EWS). Average haplotype variation within sampling areas (AP, RS, EWS) was one order of magnitude less than between sampling areas. In the EWS, however, two highly differentiated haplotypes co-exist. These four groups of haplotypes may represent cryptic, but reproductively isolated species rather than a single species