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

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

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

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

<p>Abstract</p> <p>Background</p> <p>Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of <it>a priori </it>rating of parameter space and therefore more objective.</p> <p>Results</p> <p>ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict.</p> <p>Conclusions</p> <p>Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.</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

Testing a Short Nuclear Marker for Inferring Staphylinid Beetle Diversity in an African Tropical Rain Forest

The use of DNA based methods for assessing biodiversity has become increasingly common during the last years. Especially in speciose biomes as tropical rain forests and/or in hyperdiverse or understudied taxa they may efficiently complement morphological approaches. The most successful molecular approach in this field is DNA barcoding based on cytochrome c oxidase I (COI) marker, but other markers are used as well. Whereas most studies aim at identifying or describing species, there are only few attempts to use DNA markers for inventorying all animal species found in environmental samples to describe variations of biodiversity patterns.In this study, an analysis of the nuclear D3 region of the 28S rRNA gene to delimit species-like units is compared to results based on distinction of morphospecies. Data derived from both approaches are used to assess diversity and composition of staphylinid beetle communities of a Guineo-Congolian rain forest in Kenya. Beetles were collected with a standardized sampling design across six transects in primary and secondary forests using pitfall traps. Sequences could be obtained of 99% of all individuals. In total, 76 molecular operational taxonomic units (MOTUs) were found in contrast to 70 discernible morphospecies. Despite this difference both approaches revealed highly similar biodiversity patterns, with species richness being equal in primary and secondary forests, but with divergent species communities in different habitats. The D3-MOTU approach proved to be an efficient tool for biodiversity analyses.Our data illustrate that the use of MOTUs as a proxy for species can provide an alternative to morphospecies identification for the analysis of changes in community structure of hyperdiverse insect taxa. The efficient amplification of the D3-marker and the ability of the D3-MOTUs to reveal similar biodiversity patterns as analyses of morphospecies recommend its use in future molecular studies on biodiversity

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

Les mille-pattes géants de Madagascar : révision du genre &lt;i&gt;Zoosphaerium&lt;/i&gt; (Myriapoda, Diplopoda, Sphaerotheriida)

Tout le matériel disponible du genre Zoosphaerium Pocock, 1895, qui contient 27 des 37 espèces décrites, a été examiné. Sept nouvelles synonymies sont établies : Z. stridulator (de Saussure &amp; Zehntner, 1902) synonyme plus récent de Z. blandum (de Saussure &amp; Zehntner, 1902) ; Z. digitale (de Saussure &amp; Zehntner, 1897) et Z. pygidiale (de Saussure &amp; Zehntner, 1897) synonymes plus récents de Z. neptunus (Butler, 1872) ; Z. imbecillum (de Saussure &amp; Zehntner, 1897) et Z. globulus (de Saussure &amp; Zehntner, 1902) synonymes plus récents de Z. voeltzkowianum (de Saussure &amp; Zehntner, 1897) ; Z. amittum Chamberlin, 1921 et Heligmasoma errans Chamberlin, 1921 synonymes plus récents de Z. coquerelianum (de Saussure &amp; Zehntner, 1897). Le genre Heligmasoma Chamberlin, 1921 et le sous-genre Globotherium Brolemann, 1922 sont tous les deux des synonymes plus récents de Zoosphaerium Pocock, 1895. Les types de neuf espèces (Zoosphaerium actaeon, Z. reflexum, Z. elegans, Z. crassum, Z. stigmaticum, Z. glabrum, Z. latum, Z. lamprinum et Z. testaceum) n’ont pu être localisés dans les collections. Nous proposons donc de traiter ces noms comme nomina dubia. Dix-huit espèces malgaches sont redécrites, avec des dessins de toutes les structures d’importance taxonomique et micrographies MEB présentés ici pour la première fois. Le matériel type est comparé à celui des mille-pattes géants ramassé pendant les inventaires généraux conduits pendant les années 1990 et en 2003 par diverses institutions, comprenant en tout plus de 70 morphospecies, parmi lesquelles huit peuvent être assignées à un nom d’espèce. Une clé de détermination des Sphaerotheriida malgaches est présentée et le statut du genre Zoosphaerium est discuté. Une partie des espèces sont placées dans des groupes d’espèces préliminaires.All available type material of the genus Zoosphaerium Pocock, 1895, which includes 27 of 37 described species, is revised. Seven new synonyms are established: Z. stridulator (de Saussure &amp; Zehntner, 1902) junior synonym of Z. blandum (de Saussure &amp; Zehntner, 1902); Z. digitale (de Saussure &amp; Zehntner, 1897) and Z. pygidiale (de Saussure &amp; Zehntner, 1897) junior synonyms of Z. neptunus (Butler, 1872); Z. imbecillum (de Saussure &amp; Zehntner, 1897) and Z. globulus (de Saussure &amp; Zehntner, 1902) junior synonyms of Z. voeltzkowianum (de Saussure &amp; Zehntner, 1897); Z. amittum Chamberlin, 1921 and Heligmasoma errans Chamberlin, 1921 junior synonyms of Z. coquerelianum (de Saussure &amp; Zehntner, 1897). The genus Heligmasoma Chamberlin, 1921 and the subgenus Globotherium Brolemann, 1922 are both junior synonyms of Zoosphaerium Pocock, 1895. For nine species (Zoosphaerium actaeon, Z. reflexum, Z. elegans, Z. crassum, Z. stigmaticum, Z. glabrum, Z. latum, Z. lamprinum and Z. testaceum), no types could be detected in collections, so these names are to be nomina dubia. Eighteen Malagasy species are redescribed, with drawings of all structures of taxonomic importance and SEM micrographs presented here for the first time. The type material is compared with giant pill-millipede material collected during general species inventories on Madagascar conducted during the 1990s and in 2003 by different institutions, altogether comprising more than 70 morphospecies, from which eight species could be assigned to a species name. A key to Malagasy Sphaerotheriida is presented. The status of the genus Zoosphaerium is discussed. Some of the species can already be placed in preliminarily outlined species-groups.</p