Systematics (Taxonomy)

16s rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three
psychrophilic strains: Bacillus globisporus W25* (T = type strain) and Bacillus psychrophilus W16AT, and W5.
These strains exhibited more than 99.5 % sequence identity and within experimental uncertainty could be
regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities.
In contrast, previously published DNA-DNA hybridization results have convincingly established that these
strains do not belong to the same species if current standards are used. These results emphasize the important
point that effective identity of 16s rRNA sequences is not necessarily a sufficient criterion to guarantee species
identity. Thus, although 16s rRNA sequences can be used routinely to distinguish and establish relationships
between genera and well-resolved species, very recently diverged species may not be recognizable.

A peer-reviewed open-access journal D. Johan Kotze et al. / ZooKeys 100: 55-148 (2011) 56 abstract 'Carabidologists do it all' (Niemelä 1996a) is a phrase with which most European carabidologists are familiar. Indeed, during the last half a century, professional and amateur entomologists have contributed enormously to our understanding of the basic biology of carabid beetles. The success of the field is in no small part due to regular European Carabidologists' Meetings, which started in 1969 in Wijster, the Netherlands, with the 14 th meeting again held in the Netherlands in 2009, celebrating the 40 th anniversary of the first meeting and 50 years of long-term research in the Dwingelderveld. This paper offers a subjective summary of some of the major developments in carabidology since the 1960s. Taxonomy of the family Carabidae is now reasonably established, and the application of modern taxonomic tools has brought up several surprises like elsewhere in the animal kingdom. Progress has been made on the ultimate and proximate factors of seasonality and timing of reproduction, which only exceptionally show non-seasonality. Triggers can be linked to evolutionary events and plausibly explained by the "taxon cycle" theory. Fairly little is still known about certain feeding preferences, including granivory and ants, as well as unique life history strategies, such as ectoparasitism and predation on higher taxa. The study of carabids has been instrumental in developing metapopulation theory (even if it was termed differently). Dispersal is one of the areas intensively studied, and results show an intricate interaction between walking and flying as the major mechanisms. The ecological study of carabids is still hampered by some unresolved questions about sampling and data evaluation. It is recognised that knowledge is uneven, especially concerning larvae and species in tropical areas. By their abundance and wide distribution, carabid beetles can be useful in population studies, bioindication, conservation biology and landscape ecology. Indeed, 40 years of carabidological research have provided so much data and insights, that among insects -and arguably most other terrestrial organisms -carabid beetles are one of the most worthwhile model groups for biological studies.

This nomenclator provides details on all published names in the family-, genus-, and species-group, as well as for a few infrasubspecific names introduced for, or attributed to, the family Melanopsidae. It includes nomenclaturally valid names, as well as junior homonyms, junior objective synonyms, nomina nuda, common incorrect subsequent spellings, and as far as possible discussion on the current status in taxonomy. The catalogue encompasses three family-group names, 79 genus-group names, and 1381 species-group names. All of them are given in their original combination and spelling (except mandatory corrections requested by the Code), along with their original source. For each family- and genus-group name, the original classification and the type genus and type species, respectively, are given. Data provided for species-group taxa are type locality, type horizon (for fossil taxa), and type specimens, as far as available.

The freshwater crayfishes are a group of decapod crustaceans that have played a critical role in a diversity of biological studies, from physiology, to ecology, neurobiology, conservation , and evolution. Central to many of these fields of study is the dependence on a robust taxonomic framework for accurate communication relating to species diversity and associated attributes. Despite a huge body of taxonomic work since Linnaeus, there has never been a single, comprehensive taxonomic summary of all the species of crayfish of the world. There has also been an abundance of recent taxonomic work in terms of new species descriptions and taxonomic insights gained from a variety of phylogenetic studies. Here we gather diverse taxonomic and phylogenetic information into a single resource. We develop an updated classification system that includes all the crayfishes worldwide and taxonomic changes to better reflect the current phylogenetic knowledge of the group. We also include all the fossil crayfish taxa for a complete classification of extant and extinct crayfishes. Our classification results in two superfamilies (Astacoidea and Parastacoidea), five families, 38 genera, and 669 species (692 including distinct subspecies). We provide a checklist of all species and include validated taxonomic authorities, type localities, figure references, and synonyms. We also provide arguments for our revised classification. The updated and complete classification aims to provide a robust framework for future studies of the freshwater crayfishes of the world.

A formal classification of the land plants that is compatible with the APG III classification is proposed. Previous classifications inflated taxonomic ranks, particularly of the angiosperms. If the major clades of green algae are recognized as classes, then all land plants, the embryophytes, should be included in a single class, here recognized as Equisitopsida. Accordingly, the 16 major clades of land plants, including the angiosperms, should all be recognized as subclasses, the angiosperms as Magnoliidae. Major clades within the angiosperms are then recognized as superorders. This classification still uses a few informal categories (e.g. eudicots, lamiids, etc.) within the angiosperms because this is convenient. Two new names are established: Amborellanae and Austrobaileyanae.

Three strains of a spore-forming, Gram-positive, motile, rod-shaped and boron-tolerant bacterium were isolated from soil. The strains, designated 10aT, 11c and 12B, can tolerate 5% (w/v) NaCl and up to 150 mM boron, but optimal growth was observed without addition of boron or NaCl in Luria–Bertani agar medium. The optimum temperature for growth was 37 6C (range 16–45 6C) and the optimum pH was 7.0–8.0 (range pH 5.5–9.5). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strains were closely related to Bacillus fusiformis DSM 2898T (97.2% similarity) and Bacillus sphaericus DSM 28T (96.9 %). DNA–DNA relatedness was greater than 97% among the isolated strains and 61.1% with B. fusiformis DSM 2898T and 43.2% with B. sphaericus IAM 13420T. The phylogenetic and phenotypic analyses and DNA–DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5–37.9 mol%, MK-7 as the predominant menaquinone system and iso-C15 : 0 (32% of the total) as a major cellular fatty acid. In contrast to the type species of the genus Bacillus, the strains contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid. Based on the distinctive peptidoglycan composition, phylogenetic analyses and physiology, the strains are assigned to a novel species within a new genus, for which the name Lysinibacillus boronitolerans gen. nov., sp. nov. is proposed. The type strain of Lysinibacillus boronitolerans is strain 10aT (=DSM 17140T=IAM 15262T=ATCC BAA-1146T). It is also proposed that Bacillus fusiformis and Bacillus sphaericus be transferred to this genus as Lysinibacillus fusiformis comb. nov. and Lysinibacillus sphaericus comb. nov., respectively.

While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes—chelicerates, myriapods, crustaceans and hexapods—are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the close relationship of euarthropods to tardigrades and onychophorans. Morphology predicts that myriapods, insects and crustaceans form a monophyletic group, the Mandibulata, which has been contradicted by many molecular studies that support an alternative Myriochelata hypothesis (Myriapoda plus Chelicerata). Because of the conflicting insights from published molecular datasets, evidence from nuclear-coding genes needs corroboration from independent data to define the relationships among major nodes in the euarthropod tree. Here, we address this issue by analysing two independent molecular datasets: a phylogenomic dataset of 198 protein-coding genes including new sequences for myriapods, and novel microRNA complements sampled from all major arthropod lineages. Our phylogenomic analyses strongly support Mandibulata, and show that Myriochelata is a tree-reconstruction artefact caused by saturation and long-branch attraction. The analysis of the microRNA dataset corroborates the Mandibulata, showing that the microRNAs miR-965 and miR-282 are present and expressed in all mandibulate species sampled, but not in the chelicerates. Mandibulata is further supported by the phylogenetic analysis of a comprehensive morphological dataset covering living and fossil arthropods, and including recently proposed, putative apomorphies of Myriochelata. Our phylogenomic analyses also provide strong support for the inclusion of pycnogonids in a monophyletic Chelicerata, a paraphyletic Cycloneuralia, and a common origin of Arthropoda (tardigrades, onychophorans and arthropods), suggesting that previous phylogenies grouping tardigrades and nematodes may also have been subject to tree-reconstruction artefacts.

Species distributed across vast continental areas and across major biomes provide unique model systems for studies of
biotic diversification, yet also constitute daunting financial, logistic and political challenges for data collection across such
regions. The tree frog Dendropsophus minutus (Anura: Hylidae) is a nominal species, continentally distributed in South
America, that may represent a complex of multiple species, each with a more limited distribution. To understand the spatial
pattern of molecular diversity throughout the range of this species complex, we obtained DNA sequence data from two
mitochondrial genes, cytochrome oxidase I (COI) and the 16S rhibosomal gene (16S) for 407 samples of D. minutus and
closely related species distributed across eleven countries, effectively comprising the entire range of the group. We
performed phylogenetic and spatially explicit phylogeographic analyses to assess the genetic structure of lineages and infer
ancestral areas. We found 43 statistically supported, deep mitochondrial lineages, several of which may represent currently
unrecognized distinct species. One major clade, containing 25 divergent lineages, includes samples from the type locality of
D. minutus. We defined that clade as the D. minutus complex. The remaining lineages together with the D. minutus complex
constitute the D. minutus species group. Historical analyses support an Amazonian origin for the D. minutus species group
with a subsequent dispersal to eastern Brazil where the D. minutus complex originated. According to our dataset, a total of
eight mtDNA lineages have ranges .100,000 km 2 . One of them occupies an area of almost one million km 2 encompassing
multiple biomes. Our results, at a spatial scale and resolution unprecedented for a Neotropical vertebrate, confirm that
widespread amphibian species occur in lowland South America, yet at the same time a large proportion of cryptic diversity still remains to be discovered.

The systematic relationships of taxa traditionally referred to as ‘basal ornithopods’ or ‘hypsilophodontids’ remain poorly resolved since it was discovered that these taxa are not a monophyletic group, but rather a paraphyletic set of neornithischian taxa. Thus, even as the known diversity of these taxa has dramatically increased over the past two decades, our knowledge of their placement relative to each other and the major ornithischian subclades remained incomplete. This study employs the largest phylogenetic dataset yet compiled to assess basal ornithischian relationships (255 characters for 65 species level terminal taxa). The resulting strict consensus tree is the most well-resolved, stratigraphically consistent hypothesis of basal ornithischian relationships yet hypothesized. The only non-iguanodontian ornithopod (= basal ornithopod) recovered in this analysis is Hypsilophodon foxii. The majority of former ‘hypsilophodontid’ taxa are recovered within a single clade (Parksosauridae) that is situated as the sister-taxon to Cerapoda. The Parksosauridae is divided between two subclades, the Orodrominae and the Thescelosaurinae. This study does not recover a clade consisting of the Asian taxa Changchunsaurus, Haya, and Jeholosaurus (=Jeholosauridae). Rather, the former two taxa are recovered as basal members of Thescelosaurinae, while the latter taxon is recovered in a clade with Yueosaurus near the base of Neornithischia. The endemic South American clade Elasmaria is recovered within the Thescelosaurinae as the sister taxon to Thescelosaurus.

This study supports the origination of Dinosauria and the early diversification of Ornithischia within Gondwana. Neornithischia first arose in Africa by the Early Jurassic before dispersing to Asia before the late Middle Jurassic, where much of the diversification among non-cerapodan neornithischians occurred. Under the simplest scenario the Parksosauridae originated in North America, with at least two later dispersals to Asia and one to South America. However, when ghost lineages are considered an alternate dispersal hypothesis has thescelosaurines dispersing from Asia into South America (via North America) during the Early Cretaceous, then back into North America in the latest Cretaceous. The latter hypothesis may explain the dominance of orodromine taxa prior to the Maastrichtian in North America and the sudden appearance and wide distribution of thescelosaurines in North America beginning in the early Maastrichtian. While the diversity of parksosaurids has greatly increased over the last fifteen years, a ghost lineage of over 40 myr is present between the base of Parksosauridae and Cerapoda, indicating that much of the early history and diversity of this clade is yet to be discovered. This new phylogenetic hypothesis provides a comprehensive framework for testing further hypotheses regarding evolutionary patterns and processes within Ornithischia.

Describing biological diversity is a challenging endeavour, especially for the small, cryptic animals that make up the meiofauna. The field of DNA taxonomy, i.e., the use of DNA to delineate species boundaries, is rapidly growing and changing; herein we review the recent advances in the acquisition of DNA sequence data and the analytical tools for DNA-based species delimitation, with a focus on applications to the meiofauna. After providing general guidelines on the data collection and anal- ysis steps (sampling design, sequencing, phasing of nuclear markers, and sequence alignment), we explain the rationale and usage of several widely used or promising methods developed for delineating species from single-locus data sets (distance-based DNA barcoding, automated barcode gap discovery, K/θ, general- ized mixed Yule–coalescent models, Poisson tree process model, and haplowebs). As it is increasingly recognised that several loci are required to delineate species accurately,we then briefly outline multilocus species delimitation approaches (Structure, Structurama, Bayesian phylogenetics & phylogeography, SpedeSTEM, O’Meara’s heuristic search, and several newly pub- lished Bayesian approaches based on the multispecies coalescent).

Teleosauroidea was a clade of ancient crocodylomorphs that were a key element of coastal marine environments during the Jurassic. Despite a 300-year research history and a recent renaissance in the study of their morphology and taxonomy, macroevolutionary studies of teleosauroids are currently limited by our poor understanding of their phylogenetic interrelationships. One major problem is the genus Steneosaurus, a wastebasket taxon recovered as paraphyletic or polyphyletic in phylogenetic analyses. We constructed a newly updated phylogenetic data matrix containing 153 taxa (27 teleosauroids, eight of which were newly added) and 502 characters, which we analysed under maximum parsimony using TNT 1.5 (weighted and unweighted analyses) and Bayesian inference using MrBayes v3.2.6 (standard, gamma and variation). The resulting topologies were then analysed to generate comprehensive higher-level phylogenetic hypotheses of teleosauroids and shed light on species-level interrelationships within the clade. The results from our parsimony and Bayesian analyses are largely consistent. Two large subclades within Teleosauroidea are recovered, and they are morphologically, ecologically and biogeographically distinct from one another. Based on comparative anatomical and phylogenetic results, we propose the following major taxonomic revisions to Teleosauroidea: (1) redefining Teleosauridae; (2) introducing one new family and three new subfamilies; (3) the resurrection of three historical genera; and (4) erecting seven new generic names and one new species name. The phylogeny infers that the Laurasian subclade was more phenotypically plastic overall than the Sub-Boreal-Gondwanan subclade. The proposed phylogeny shows that teleosauroids were more diverse than previously thought, in terms of morphology, ecology, dispersal and abundance, and that they represented some of the most successful crocodylomorphs during the Jurassic.

Parataxonomic sorting of samples to recognizable taxonomic units (RTUs, morphospecies, morphotypes or, as proposed here: parataxonomic units [PUs]) is generally considered to be a sufficiently reliable and conservative approach in ecological biodiversity studies or conservation biology. It is obviously time-saving because it avoids the burdens of taxonomy. However, evaluations of parataxonomic sorting by taxonomic resorting show many overestimations of species numbers. Hence, RTU sorting is not necessarily conservative. Sorting errors can be more than 100% (median in the present compilation: 22%). Even if the cumulative results for diverse groups like beetles have a very low overall error, the error rate in the single families is generally much higher. This pattern is likely to cause severe problems in multivariate analyses. The presumable error rate in sorting does not depend only on the group to be sorted, but also on the sorter and the sample. Therefore, the sorting error is not predictable. Since PUs are generally neither described nor assigned to existing names, the sorting results are difficult to check and it is mostly not revealed why the samples are sorted as they are. Since parataxonomy does not use existing biological knowledge, creates typological units and does not disclose its sorting criteria, inter-subjective testability and falsifiability of the sorting results are more difficult than of taxonomic identifications (or are even impossible). Parataxonomy does not fulfil the criteria of a scientific method, but is propedeutic and can be a heuristically valuable tool to find out patterns in taxonomically neglected groups. However, it is only the first step in sorting and identifying samples in biodiversity studies. PUs are useless for inventories and area selection in conservation evaluation, biogeographical and autecological studies; they provide only uncertain data for studies in species turnover and overlap, but they can be used quite reliably for global comparisons of gross species richness, non-comparative descriptions of species richness of single sites or for comparisons of sites without species overlap. If results of parataxonomic sorting show clear and biologically meaningful patterns, the sorting is likely to be reliable. Weak or no detectable patterns may easily be caused by erroneous sorting.

A faunal overview is presented of the molluscan families Amphibulimidae, Megaspiridae, Odontostomidae, Orthalicidae, Simpulopsidae in Bolivia, Ecuador, and Peru. These Central Andean countries are known for their biodiverse malacofauna, of which the superfamily Orthalicoidea takes relatively a large share. In this paper the five families containing 103 (sub)species, for which systematic information (original publication, type locality, type depository, summarizing literature) and distributional records are presented. All species are illustrated by photographs of the type material or, if this could not be located, by a reproduction of the original figure. The following new taxon is introduced: Thaumastus (Thaumastus) sumaqwayqu sp. n. Junior subjective synonyms are established for: Plekocheilus (Sparnotion) Pilsbry, 1944 = Plekocheilus (Eudolichotis) Pilsbry, 1896; Scholvienia (Thomsenia) Strebel, 1910 = Scholvienia Strebel, 1910; Sultana (Trachyorthalicus) Strebel, 1909 = Sultana (Metorthalicus) Pilsbry, 1899; Plekocheilus (Eurytus) conspicuus Pilsbry, 1932 = Thaumastus (Thaumastus) hartwegi (Pfeiffer in Philippi, 1846); Zebra gruneri Strebel, 1909 = Orthalicus maracaibensis (Pfeiffer, 1856); Scholvienia jaspidea minor Strebel, 1910 = Scholvienia alutacea (Reeve, 1850); Bulimus bi-fasciatus unicolor Philippi, 1869 = Scholvienia brephoides (d'Orbigny, 1835). A new status is given to Pleko-cheilus mcgintyi 'Pilsbry' H.B. Baker, 1963 (subspecies of Bulinus piperitus Sowerby I, 1837); Strophocheilus superstriatus var. prodeflexus Pilsbry, 1895 (subspecies of Bulinus piperitus Sowerby I, 1837); Thaumastus (Quechua) salteri maximus Weyrauch, 1967 (subspecies of Thaumastus (Quechua) olmosensis Zilch, 1954);

Speciation in the context of adaptive radiation is regarded as a key process in the creation of biodiversity. While several lacustrine species flocks provide ideal models for elucidating the underlying evolutionary mechanisms, riverine radiations are both rarely known and studied. The Kaek River, a third-order tributary of the Nan River and Chao Praya drainage in central Thailand, harbours an exceptional endemic species assemblage of morphologically distinct, viviparous pachychilid gastropods. Our systematic revision, combining a morphological and molecular genetics approach, reveals the sympatric existence of at least seven species of the genus Brotia that is widespread in rivers of South-east Asia where usually only two species at the most coexist. At eight locations along a 100-kilometre stretch of the Kaek River, we found the syntopic occurrence of two to three species that are separated by specific habitat preferences and exhibit trophic specialization in their radula morphology. Phylogenetic analyses (using MP, NJ, ML and Bayesian inference statistics) of partial COI and 16S sequence data of 17 samples from six species occurring sympatrically and parapatrically, respectively, in the Kaek River drainage (plus the type species B. pagodula as outgroup) indicate monophyly of all these endemic species. Brotia solemiana, which also occurs in the Loei River, a tributary of the Mekong drainage system, was found to be sister to all other Kaek River pachychilids. The distinctive morphotypes, proposed here to represent biospecies, do not show high levels of genetic variation consistent with long periods of reproductive isolation. This suggests a relatively recent origin of this intrariverine radiation and rapid morphological divergence in the Kaek River Brotia. Recent diversification combined with ecological separation and trophic specialization parallels conditions found, albeit on a more specious level, in the lacustrine species flock of the closely related pachychilid genus Tylomelania, which is endemic to ancient lakes on the Indonesian island of Sulawesi. We discuss and compare the allopatric and ecological aspects of speciation in this unique riverine radiation and outline a putative historical biogeography of the Kaek River species, employing the most recent geological and palaeohydrological data for Thailand. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 275–311.

Despite their medical interest, the phylogeny of the snake family Viperidae remains inadequately understood. Previous studies have generally focused either on the pitvipers (Crotalinae) or on the Old World vipers (Viperinae), but there has been no comprehensive molecular study of the Viperidae as a whole, leaving the affinities of key taxa unresolved. Here, we infer the phylogenetic relationships among the extant genera of the Viperidae from the sequences of four mitochondrial genes (cytochrome b, NADH subunit 4, 16S and 12S rRNA). The results confirm Azemiops as the sister group of the Crotalinae, whereas Causus is nested within the Viperinae, and thus not a basal viperid or viperine. Relationships among the major clades of Viperinae remain poorly resolved despite increased sequence information compared to previous studies. Bayesian molecular dating in conjunction with dispersal-vicariance analysis suggests an early Tertiary origin in Asia for the crown group Viperidae, and rejects suggestions of a relatively recent, early to mid-Tertiary origin of the Caenophidia.

In most pan-Eurasiatic species complexes, two phenomena have been traditionally considered key processes of their cladogenesis and biogeography. First, it is hypothesized that the origin and development of the Central Asian Deserts generated a biogeographic barrier that fragmented past continuous distributions in Eastern and Western domains. Second, Pleistocene glaciations have been proposed as the main process driving the regional diversification within each of these domains. The European common toad and its closest relatives provide an interesting opportunity to examine the relative contributions of these paleogeographic and paleoclimatic events to the phylogeny and biogeography of a widespread Eurasiatic group. We investigate this issue by applying a multiproxy approach combining information from molecular phylogenies, a multiple correspondence analysis of allozyme data and species distribution models. Our study includes 304 specimens from 164 populations, covering most of the distributional range of the Bufo bufo species complex in the Western Palearctic. The phylogenies (ML and Bayesian analyses) were based on a total of 1988 bp of mitochondrial DNA encompassing three genes (tRNAval, 16S and ND1). A dataset with 173 species of the family Bufonidae was assembled to estimate the separation of the two pan-Eurasiatic species complexes of Bufo and to date the main biogeographic events within the Bufo bufo species complex. The allozyme study included sixteen protein systems, corresponding to 21 presumptive loci. Finally, the distribution models were based on maximum entropy. Our distribution models show that Eastern and Western species complexes are greatly isolated by the Central Asian Deserts, and our dating estimates place this divergence during the Middle Miocene, a moment in which different sources of evidence document a major upturn of the aridification rate of Central Asia. This climate-driven process likely separated the Eastern and Western species. At the level of the Western Palearctic, our dating estimates place most of the deepest phylogenetic structure before the Pleistocene, indicating that Pleistocene glaciations did not have a major role in splitting the major lineages. At a shallow level, the glacial dynamics contributed unevenly to the genetic structuring of populations, with a strong influence in the European-Caucasian populations, and a more relaxed effect in the Iberian populations.

Debate over the taxonomic status of the Neanderthals has been incessant since the initial discovery of the type specimens, with some arguing they should be included within our species (i.e. Homo sapiens neanderthalensis) and others believing them to be different enough to constitute their own species (Homo neanderthalensis). This synthesis addresses the process of speciation as well as incorporating information on the differences between species and subspecies, and the criteria used for discriminating between the two. It also analyses the evidence for Neanderthal-AMH hybrids, and their relevance to the species debate, before discussing morphological and genetic evidence relevant to the Neanderthal taxonomic debate. The main conclusion is that Neanderthals fulfil all major requirements for species status. The extent of interbreeding between the two populations is still highly debated, and is irrelevant to the issue at hand, as the Biological Species Concept allows for an expected amount of interbreeding between species.

Classification is an important activity that facilitates theory development in many academic disciplines. Scholars in fields such as organizational science, management science and economics and have long recognized that classification offers an approach for ordering and understanding the diversity of organizational taxa (groups of one or more similar organizational entities). However, even the most prominent organizational classifications have limited utility, as they tend to be shaped by a specific research bias, inadequate units of analysis and a standard neoclassical economic view that does not naturally accommodate the disequilibrium dynamics of modern competition. The result is a relatively large number of individual and unconnected organizational classifications, which tend to ignore the processes of change responsible for organizational diversity. Collectively they fail to provide any sort of universal system for ordering, compiling and presenting knowledge on organizational diversity. This paper has two purposes. First, it reviews the general status of the major theoretical approaches to biological and organizational classification and compares the methods and resulting classifications derived from each approach. Definitions of key terms and a discussion on the three principal schools of biological classification (evolutionary systematics, phenetics and cladistics) are included in this review. Second, this paper aims to encourage critical thinking and debate about the use of the cladistic classification approach for inferring and representing the historical relationships underpinning organizational diversity. This involves examining the feasibility of applying the logic of common ancestry to populations of organizations. Consequently, this paper is exploratory and preparatory in style, with illustrations and assertions concerning the study and classification of organizational diversity

An ambitious, yet fundamental goal for comparative biology is to understand the evolutionary relationships for all of life. Yet many important taxonomic groups have remained recalcitrant to inclusion into broader scale studies. Here, we focus on collection of 9 new 454 transcriptome data sets from Ostracoda, an ancient and diverse group with a dense fossil record, which is often under-sampled in broader studies. We combine the new transcriptomes with a new morphological matrix (including fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome, nuclear genome and rDNA data. Our analyses lead to new insights into ostracod and pancrustacean phylogeny. We obtained support for three epic pancrustacean clades that likely originated in the Cambrian: Oligostraca (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Within the Oligostraca clade, our results support the unresolved question of ostracod monophyly. Within Multicrustacea, we find support for Thecostraca plus Copepoda, for which we suggest the name Hexanauplia. Within Allotriocarida, some analyses support the hypothesis that Remipedia is the sister taxon to Hexapoda, but others support Branchiopoda+Cephalocarida as the sister group of hexapods. In multiple different analyses, we see better support for equivocal nodes using slow-evolving genes or when excluding distant outgroups, highlighting the increased importance of conditional data combination in this age of abundant, often anonymous data. Yet, when we analyze the same set of species and ignore rate of gene evolution, we find higher support when including all data, more in line with a ‘total evidence’ philosophy. By concatenating molecular and morphological data, we place pancrustacean fossils in the phylogeny, which can be used for studies of divergence times in Pancrustacea, Arthropoda, or Metazoa. Our results and new data will allow for attributes of Ostracoda, such as its amazing fossil record and diverse biology, to be leveraged in broader scale comparative studies. Further, we illustrate how adding extensive next-generation sequence data from understudied groups can yield important new phylogenetic insights into long-standing questions, especially when carefully analyzed in combination with other data.

We used mitochondrial gene sequences to infer phylogenetic relationships among North American snakes of the colubrid tribe Lampropeltini (Arizona, Bogertophis, Cemophora, New World Elaphe, Lampropeltis, Pituophis, Rhinocheilus, Senticolis, Stilosoma), and assessed the implications of our findings for the biogeography and evolution of food habits among these serpents. The maximum likelihood phylogeny identified Rhinocheilus as the sister taxon to all other lampropeltinines, and supported the monophyly of Lampropeltis (including Stilosoma), New World Elaphe, and Pituophis, but not that of Bogertophis. This phylogeny also suggested a sister group relationship between Cemophora and Lampropeltis, and between New World Elaphe and Pituophis, and strongly supported that Senticolis belongs within Lampropeltini, thus contradicting previous suggestions that Senticolis is not a lampropeltinine. Using a method for approximating ancestral areas of clades, we determined that western North America was most likely the ancestral area of lampropeltinines. Our survey of published studies, combined with unpublished data, indicated that lampropeltinines as a group feed mainly on mammals, less frequently on lizards, birds, and bird eggs, and only rarely on squamate eggs, snakes, anurans, and insects. Some individual species indeed emphasize mammals in their diets, but others most frequently eat lizards, squamate eggs, bird eggs, or snakes, whereas others take two prey types with similar frequency. Our reconstruction of the evolution of food habits among lampropeltinines suggests that a diet emphasizing lizards is ancestral, and therefore diets that mostly consist of mammals, squamate and bird eggs, and snakes are derived within the clade. In at least some species, smaller individuals prey mostly on lizards and larger ones add mammals to their diets.

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, and Zoopagomycota. The placement of all fungal genera is provided at the class-, order-and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi.

Pliocene shallow-water marine sediments at Marine Plain (centred on 68°37.7ʹS; 78°07.8ʹE) and covering approximately 10 km² in the Vestfold
Hills, East Antarctica, have yielded six species of gastropods, and 11 species of bivalves from two beds within the Sørsdal Formation. Most of the material is close to in situ but some specimens have been disturbed from their life position; there is no evidence of significant transport. The gastropods include Nacella concinna (Strebel, 1908), Falsimargarita parvispira Quilty, Darragh, Gallagher & Harding sp. nov., indeterminate species of trochids and naticids, Chlanidota (Chlanidota) sp. cf. C. signeyana Powell, 1951, and two species of Trophon/Trophonella. Bivalves include Ennucula sp. aff. E. grayi (d’Orbigny, 1846), Aequiyoldia defossata Quilty, Darragh, Gallagher & Harding, sp. nov., ‘Pectunculina’ sp., Lissarca sp., Austrochlamys anderssoni (Hennig, 1911), Ruthipecten campestris Quilty, Darragh, Gallagher & Harding sp. nov., Adamussium necopinatum Quilty, Darragh, Gallagher & Harding sp. nov., Limatula (Antarctolima) sp. cf. L. hodgsoni (Smith, 1907), Cyclocardia magna Quilty, Darragh, Gallagher & Harding sp. nov., ?Hiatella sp. cf. H. arctica (Linnaeus, 1767) and Laternula elliptica (King, 1832). Preservation varies considerably owing to recrystallization, dissolution or distortion through compaction, so several species are left in open nomenclature. Oxygen isotope data indicate that water temperature was 4–7.5°C at the time of shell growth. Many species or species groups are now extinct or have migrated away from the Antarctic to the sub-Antarctic region. An Antarctic mollusc fauna has been characteristic of the region for much of the Cenozoic.

Pleistocene fragmentation of the Amazonian rainforest has been hypothesized to be a major cause of Neotropical speciation and diversity. However, the role and even the reality of Pleistocene forest refugia have attracted much scepticism. In Amazonia, previous phylogeographical studies have focused mostly on organisms found in the forests themselves, and generally found speciation events to have predated the Pleistocene. However, molecular studies of open-formation taxa found both north and south of the Amazonian forests, probably because of vicariance resulting from expansion of the rainforests, may provide novel insights into the age of continuous forest cover across the Amazon basin. Here, we analyse three mitochondrial genes to infer the phylogeography of one such trans-Amazonian vicariant, the Neotropical rattlesnake (Crotalus durissus), which occupies primarily seasonal formations from Mexico to Argentina, but avoids the rainforests of Central and tropical South America. The phylogeographical pattern is consistent with gradual dispersal along the Central American Isthmus, followed by more rapid dispersal into and across South America after the uplift of the Isthmus of Panamá. Low sequence divergence between populations from north and south of the Amazon rainforest is consistent with mid-Pleistocene divergence, approximately 1.1 million years ago (Ma). This suggests that the Amazonian rainforests must have become fragmented or at least shrunk considerably during that period, lending support to the Pleistocene refugia theory as an important cause of distribution patterns, if not necessarily speciation, in Amazonian forest organisms. These results highlight the potential of nonforest species to contribute to an understanding of the history of the Amazonian rainforests themselves.

The Osmundales (Royal Fern order) originated in the late Paleozoic and is the most ancient surviving lineage of leptosporangiate ferns. In contrast to its low diversity today (less than 20 species in six genera), it has the richest fossil record of any extant group of ferns. The structurally preserved trunks and rhizomes alone are referable to more than 100 fossil species that are classified in up to 20 genera, four subfamilies, and two families. This diverse fossil record constitutes an exceptional source of information on the evolutionary history of the group from the Permian to the present. However, inconsistent terminology, varying formats of description, and the general lack of a uniform taxonomic concept renders this wealth of information poorly accessible. To this end, we provide a comprehensive review of the diversity of structural features of osmundalean axes under a standardized, descriptive terminology. A novel morphological character matrix with 45 anatomical characters scored for 15 extant species and for 114 fossil operational units (species or specimens) is analysed using networks in order to establish systematic relationships among fossil and extant Osmundales rooted in axis anatomy. The results lead us to propose an evolutionary classification for fossil Osmundales and a revised, standardized taxonomy for all taxa down to the rank of (sub)genus. We introduce several nomenclatural novelties: (1) a new subfamily Itopsidemoideae (Guaireaceae) is established to contain Itopsidema, Donwelliacaulis, and Tiania; (2) the thamnopteroid genera Zalesskya, Iegosigopteris, and Petcheropteris are all considered synonymous with Thamnopteris; (3) 12 species of Millerocaulis and Ashicaulis are assigned to modern genera (tribe Osmundeae); (4) the hitherto enigmatic Aurealcaulis is identified as an extinct subgenus of Plenasium; and (5) the poorly known Osmundites tuhajkulensis is assigned to Millerocaulis. In addition, we consider Millerocaulis stipabonettiorum a possible member of Palaeosmunda and Millerocaulis estipularis as probably constituting the earliest representative of the (Todea-)Leptopteris lineage (subtribe Todeinae) of modern Osmundoideae.

The natural world demonstrates signs of spatialtemporal order, an order that appears to us through a series of recognizable, recurring and consecutive patterns, i.e. regularities in forms, functions, behaviors, events and processes. These patterns lend insight into the modes and tempos of evolution and thus into the units, levels, and mechanisms that underlie the evolutionary hierarchy. Contributors to this special issue analyze converging patterns in the biological and sociocultural realm across and beyond classic divisions between micro-and macro-evolution; horizontal/reticulate and vertical evolution; phylogeny, ontogeny and ecology; synchronic and diachronic sociocultural and linguistic research; and tree and network diagrams. Explanations are sought in complexity theory, major transitions of evolution, and process and mechanism approaches to change; and consequences for notions such as

Chalcidoidea (Hymenoptera) is extremely diverse with an estimated 500 000 species. We present the first phylogenetic analysis of the superfamily based on both morphological and molecular data. A web-based, systematics workbench mx was used to score 945 character states illustrated by 648 figures for 233 morphological characters for a total of 66 645 observations for 300 taxa. The matrix covers 22 chalcidoid families recognized herein and includes 268 genera within 78 of 83 subfamilies. Morphological data were analysed alone and in combination with molecular data from ribosomal 18S (2105 bp) and 28S D2-D5 expansion regions (1812 bp). Analyses were analysed alone and in combined datasets using implied-weights parsimony and likelihood. Proposed changes in higher classification resulting from the analyses include: (i) recognition of Eriaporidae, revised status; (ii) recognition of Cynipencyrtidae, revised status; (iii) recognition of Azotidae, revised status; (iv) inclusion of Sycophaginae in Agaonidae, revised status; (v) reclassification of Aphelinidae to include Aphelininae, Calesinae, Coccophaginae, Eretmocerinae and Eriaphytinae; (vi) inclusion of Cratominae and Panstenoninae within Pteromalinae (Pteromalidae), new synonymy; (vii) inclusion of Epichrysomallinae in Pteromalidae, revised status. At a higher level, Chalcidoidea was monophyletic, with Mymaridae the sister group of Rotoitidae plus the remaining Chalcidoidea. A eulophid lineage was recovered that included Aphelinidae, Azotidae, Eulophidae, Signiphoridae, Tetracampidae and Trichogrammatidae. Eucharitidae and Perilampidae were monophyletic if Eutrichosomatinae (Pteromalidae) was included, and Eupelmidae was monophyletic if Oodera (Pteromalidae: Cleonyminae) was included. Likelihood recovered a clade of Eupelmidae + (Tanaostigmatidae + (Cynipencyrtus + Encyrtidae). Support for other lineages and their impact on the classification of Chalcidoidea is discussed. Several life-history traits are mapped onto the new phylogeny.

Aconsolidated list of available generic names introduced since the beginning of the binomial
nomenclature system for trilobites is presented for the first time. Each entry is accompanied
by the author and date of availability, by the name of the type species, by a lithostratigraphic
or biostratigraphic and geographic reference for the type species, by a family assignment and
by an age indication of the type species at the Period level (e.g. MCAM, LDEV). A second
listing of these names is taxonomically arranged in families with the families listed
alphabetically, higher level classification being outside the scope of this work. We also
provide a list of names that have apparently been applied to trilobites but which remain
nomina nuda within the ICZN definition.