Surrogates in marine benthic investigations ‐ which taxonomic unit to target?

Although the identification of organisms to the levelof species is the ideal in studies of marinemacrobenthos, there are situations where such a finelevel of taxonomic discrimination may be eitherimpossible or unwarranted, for example when much thefauna is undescribed, or if the task for which samplesare collected does not require them to be identifiedto the species level. The idea that abundances ofhigher taxa, or particular groups of organisms, may beused as surrogates for the total fauna in such studiesis explored in this paper using data from theNorwegian sector of the North Sea. The generalconclusion is that, in surveys of soft sedimentmacrofauna in disturbed areas of the North Sea wherepollution imposes simple spatial gradients on thebenthic communities, little information aboutinter-sample relationships is lost using data based onfamily, polychaete species, or polychaete familyabundances, rather than species abundances. In morepristine areas where spatial patterns are determinedby a number of processes, correlations betweencalculated diversity indices and similarity in faunalpatterns between species and family abundances arestill very high, but less so for polychaete species orpolychaete family abundances. This suggests thatidentification to the level of family may besatisfactory in many routine monitoring surveys,andidentification of only the polychaetes, either to thelevel of species or family, may also be a possiblealternative if there are clear disturbance gradientsin the survey area. Polychaetes are of importance indisturbed areas because the group contains tolerantand intolerant species, and in undisturbed areasbecause within the taxon species have a greater rangeof trophic and reproductive strategies than withinother taxa. Ultimately it is the distribution ofspecies, their identities, and their interactions witheach other and with the environment, that are ofinterest. The use of surrogates is likely to be mostadvantageous if it is only the extent of pollutioneffects from a discrete source that matters, andspecies level baseline studies have already beencompleted.     

蚁蛉亚科电子图文链接式分族检索表

介绍一种电子图文链接式分类检索表 ,这种检索表有以下优点 :( 1 )检索表中所用的特征超级链接图像 ,有利于使用者对鉴别特征的正确理解 ;( 2 )图像可放大缩小任意拉动 ,清晰展示所有细节 ;( 3 )检索表文字保持连贯 ;( 4 )检索表容量基本不受分类单元数量的限制 ;( 5 )制作方法简单。文章阐述了制作这种检索表的意义和方法 ,并展示用这种检索表形式制作的蚁蛉亚科分族检索表     

From taxonomic literature to cybertaxonomic content

In the ubiquitin-proteasome system, a subset of ubiquitylated proteins requires the AAA+ ATPase p97 (also known as VCP or Cdc48) for extraction from membranes or protein complexes before delivery to the proteasome for degradation. Diverse ubiquitin adapters are known to link p97 to its client proteins, but two recent papers on the adapter protein UBXD7, including one by Bandau et al. in BMC Biology, suggest that rather than simply linking p97 to ubiquitylated proteins, this adapter may be essential to coordinate ubiquitylation and p97-mediated extraction of the proteasome substrate. These findings add to growing indications of richly diverse roles of adapters in p97-mediated signaling functions. See research article: http://www.biomedcentral.com/1741-7007/10/36     

A taxonomic distance applicable to paleontology

A general Hausdorff-like metric on sets is presented with applications to paleontological “dissimilarity measures.” The distances between taxa represented by living organisms and/or fossil material are obtainable simply and independently of the nature of the characteristics used to define the taxonomic units. In particular, linear independence of the measured anatomical characters is not required.     

Sensitivity of phylogeny estimation to taxonomic sampling

Recent studies have shown that addition or deletion of taxa from a data matrix can change the estimate of phylogeny. I used 29 data sets from the literature to examine the effect of taxon sampling on phylogeny estimation within data sets. I then used multiple regression to assess the effect of number of taxa, number of characters, homoplasy, strength of support, and tree symmetry on the sensitivity of data sets to taxonomic sampling. Sensitivity to sampling was measured by mapping characters from a matrix of culled taxa onto optimal trees for that reduced matrix and onto the pruned optimal tree for the entire matrix, then comparing the length of the reduced tree to the length of the pruned complete tree. Within-data-set patterns can be described by a second-order equation relating fraction of taxa sampled to sensitivity to sampling. Multiple regression analyses found number of taxa to be a significant predictor of sensitivity to sampling; retention index, number of informative characters, total support index, and tree symmetry were nonsignificant predictors. I derived a predictive regression equation relating fraction of taxa sampled and number of taxa potentially sampled to sensitivity to taxonomic sampling and calculated values for this equation within the bounds of the variables examined. The length difference between the complete tree and a subsampled tree was generally small (average difference of 0-2.9 steps), indicating that subsampling taxa is probably not an important problem for most phylogenetic analyses using up to 20 taxa.     

Sensitivity of the relative-rate test to taxonomic sampling

Relative-rate tests may be used to compare substitution rates between more than two sequences, which yields two main questions: What influence does the number of sequences have on relative-rate tests and what is the influence of the sampling strategy as characterized by the phylogenetic relationships between sequences? Using both simulations and analysis of real data from murids (APRT and LCAT nuclear genes), we show that comparing large numbers of species significantly improves the power of the test. This effect is stronger if species are more distantly related. On the other hand, it appears to be less rewarding to increase outgroup sampling than to use the single nearest outgroup sequence. Rates may be compared between paraphyletic ingroups and using paraphyletic outgroups, but unbalanced taxonomic sampling can bias the test. We present a simple phylogenetic weighting scheme which takes taxonomic sampling into account and significantly improves the relative- rate test in cases of unbalanced sampling. The answers are thus: (1) large taxonomic sampling of compared groups improves relative-rate tests, (2) sampling many outgroups does not bring significant improvement, (3) the only constraint on sampling strategy is that the outgroup be valid, and (4) results are more accurate when phylogenetic relationships between the investigated sequences are taken into account. Given current limitations of the maximum-likelihood and nonparametric approaches, the relative-rate test generalized to any number of species with phylogenetic weighting appears to be the most general test available to compare rates between lineages.      

Where to draw the nonprimate-primate taxonomic boundary.

The known Cretaceous and Paleocene primates, the Paromomyiformes, although lacking a fully developed postorbital bar, are nevertheless, both cladistically and phenetically, closest to the common ancestor of the living primates. Not only their undisputed phylogenetic ties but also their early experiments inthe arboreal milieu necessitate their balanced evolutionary classification within the order Primates.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

Should universal guidelines be applied to taxonomic research?

In an attempt to facilitate the integration of various methods of species delimitation, Dayrat (2005 ) recommends a set of nomenclatorial guidelines. He proposes to restrict the application of new specific epithets where a recent taxonomic revision has not dealt with the totality of names and variation in the group, where specimens are not well-represented in collections, where DNA extraction from type specimens is not possible, and where putative novel species are supported only by a single type of data (e.g. morphological). Dayrat further recommends that putative novel species for which only one type of data exists be described with the abbreviation 'sp.', so as to avoid the permanent establishment of a specific epithet, as required by the current codes of nomenclature. Contradicting himself, Dayrat implies that putative novel species supported only by DNA sequences should be named as valid species. If adopted, Dayrat's guidelines would impede taxonomic progress, diminish the utility of taxonomy to its users (e.g. conservation biologists and biogeographers), and prevent the integration of methods of species delimitation.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 761–764.     

Conserving taxonomic complexity

Traditional species-based conservation programmes are appropriate in situations where species are readily identifiable. However, in certain taxonomically complex groups of organisms, generally characterized by the presence of uniparental lineages and reticulate evolution, it is not possible to classify biodiversity into discrete and unambiguous species. Attempts to impose species-based conservation on such taxonomically complex groups are proving untenable, and threaten to divert scarce resources and taxonomic expertise from the conservation of other priority groups. We argue here that a new approach should be adopted for taxonomically complex groups. We advocate the conservation of evolutionary processes that generate taxonomic biodiversity, rather than the preservation of a limited number of poorly defined taxa arising from this evolution.     

Classical plant taxonomic ambiguities extend to the molecular level

Summary The molecular evolution of cytochrome c from angiosperms is compared to that from vertebrates. On the basis of a cladistic analysis from 26 plant species, compared to that from 27 vertebrate species, we find that although the vertebrate sequences yield reasonably well-defined minimal trees that are congruent with the biological tree, the plant sequences yield multiple minimal trees that are not only highly incongruent with each other, but none of which is congruent with any reasonably biological tree. That is, the plant sequence set is much more homoplastic than that of the animal. However, as judged by the relative rate test, the extent of divergence, and degree of functional constraint, cytochrome c evolution in plants does not appear to differ from that of vertebrates.     

A novel multiple-site extension to pairwise partitioned taxonomic beta diversity

Our understanding of the causes of variation in taxonomic composition, or beta diversity, is progressing rapidly, thanks in part to recent methodological advances. For example, methods for partitioning beta diversity into its “replacement” and “richness” components have helped reveal patterns that had been undetected by traditional analyses. These partitioning methods are derived from pairwise dissimilarity measures, and are thus well suited to many conventional beta diversity analyses, including “distance decay” relationships. However, pairwise beta diversity measures have limitations, including their lack of information about taxa that are shared among three or more sites. Recently, a new suite of multiple-site counterparts to the pairwise partitioning measures of beta diversity was proposed, but the pairwise analogs upon which these were based were subsequently criticized, and compelling arguments were presented in favor of other partitioning approaches. Here, we introduce multiple-site partitioning measures that address these shortcomings, and illustrate their desirable properties using numerical simulations. We also provide an empirical example of their utility by analyzing the temporal beta diversity of breeding birds within the conterminous USA. We show that temporal beta diversity is predominantly driven by replacement rather than richness differences, and correspondingly, that correlations between temporal beta diversity and productivity and elevation are driven primarily by the replacement component. Furthermore, in contrast to existing multiple-site measures, we show that richness differences do play an important part in driving overall beta diversity patterns. Our new multiple-site measures therefore complement existing methods for analyzing beta diversity, and are especially suitable when compositional heterogeneity is the response of interest.