Systematic biostratigraphy: A solution to problematic classification systems in biostratigraphy

Systematic biostratigraphy is based on the exclusive use of monophyletic marker taxa. Non-monophyletic, or artificial, marker taxa have been shown to change biostratigraphic correlations, a situation that can be rectified by using systematics to ensure that marker taxa are monophyletic or natural. Both hypothetical and real examples demonstrate the validity of the methodology. The foraminiferal genera Praemurica and Parvularugoglobigerina are examples of non-monophyletic marker taxa. Cladistic results permit the reclassification of both genera, and a revision of foraminiferal biostratigraphy. Systematic biostratigraphy ensures the use of monophyletic marker taxa, preventing artificial classifications from hindering biostratigraphic correlations and producing more accurate, and stable, biostratigraphic zonations.     

The probability of correctly resolving a split as an experimental design criterion in phylogenetics

We illustrate how recently developed large sequence-length approximations to probabilities of correct phylogenetic reconstruction for maximum likelihood estimation can be used to evaluate experimental design strategies. The specific criterion of interest is the probability of correctly resolving an a priori defined split of interest in a phylogenetic tree. Design strategies considered include increased taxon sampling and increasing sequence length. Our analyses of specific examples strongly suggest that it is better to sample taxa that connect as close as possible to the split of interest. Assuming this can be done, these examples suggest it is better to sample additional taxa than to add a comparable number of sites for the existing taxa. If the rates of evolution in the added taxa are slow, it is better to choose taxa connecting to a long edge, but if rates are comparable to a sister lineage, it is not necessarily the best strategy to sample taxa connected to a long edge. We also examined deleting taxa while increasing the number of sites. Although deleting a small number of taxa distant from the split of interest can be beneficial, deleting too many or making poor choices as to what should be deleted can lead to smaller probabilities of correct reconstruction than for the original sequence data.     

Diskontinuierlich aktive Gene und Evolution Eine Diskussion am Beispiel der Archaeognatha (Insecta)

Discontinuous activity of genes and evolution - a discussion based on examples of the Archaeognatha (Insecta) On the basis of examples, mainly from the group of Archaeognatha (Insecta) it seems probable that, in multicellular organisms, there is not only a discontinuous activity of genes and groups of genes during the individual development, but also during the phylogenesis. The possibility that silent genes can be reactivated is probably an essential reason for the existence of parallelisms and homologous tendencies. Both conceptions have a complementary importance for an establishment of taxa ana the reconstruction of phylogenesis and are defined according to evolutionary genetics. The examples are discussed and the necessity of similar comparative studies in other supraspecific taxa is emphasized.     

Behaviour is not Reliably Inferred from End-Product Structure in Caddisflies

Many animals engage in elaborate behavioural sequences in order to build structures. The ‘end‐products’ (e.g., nests of birds, cases of caddisflies) of these behaviours have occasionally been used either to infer details of building behaviour or to infer that structures similar in appearance are constructed by similar behavioural sequences. However, behavioural information can be extrapolated from end‐products only if there is congruence between the end‐product structure and the animal's movements. Case building behaviour was studied in caddisflies (Trichoptera) to examine the relationship between end‐products and behaviour. We found examples of taxa that built similar structures using different behavioural patterns, and taxa that built different structures using similar behaviours, regardless of whether these taxa were closely or distantly related. These findings question the reliability of behavioural inferences based solely on details of their associated end‐products and suggest that end‐product structure should be removed from the definition of animal behaviour.     

Functional inference from gastropod shell morphology - some caveats

The dangers of making broad paleobiological inferences from shell morphology, based on limited observations of a few taxa, are indicated using as examples the secondary protoconchs of Colina species (Cerithiidae), and the ratchet sculpture of some surface dwelling species of Cerithium. Secondary protoconchs are not indicative of types of development and ratchet sculpture does not always indicate burrowing. □ Protoconch, shell morphology, functional morphology, burrowing, Cerithiidae.     

Ecological integrity of supraspecific taxa and the arctic biota

Some specific features of the development of concepts about integrity (systemic organization) of supraspecific taxa are considered. Several forms of integrity can be distinguished: taxonomic, or genealogical; evolutionary (considering a taxon as a developing system); ecological, or eco-adaptive (manifestation of the properties of a united system in the course of exploring the various conditions and types of environment by the phyletically specified biota). Taxa of different level “behave” as whole units or blocks, forming structural parts of the cenotic and biotic forms of life. The properties of integrity, systemic organization of supraspecific taxa can be displayed by analysis of changes in the structural parameters of the biota related to latitudinal gradients of climatic factors, in phenomena of individualistic distribution, ecological substitution (vicariance) of taxa, and preservation of their ecological functions (adaptive zone) despite the reduced species diversity. The variants of adaptive exploration of high-latitude landscape-zonal conditions are considered using examples from the Arctic flora and fauna.     

Pure numbers,invariants and symmetry in the evolution of life histories

Summary Certain dimensionless numbers related to life histories are approximately conserved within some taxa; this suggests that the underlying life-history tradeoffs satisfy yet-to-be-discovered symmetry principles. Some possible examples are discussed.     

Barbula cylindrica (Tayl.) Schimp. with rhizoidal tubers

Abstract

Reviews in the 1970s concluded that African moss taxonomy was in a poor state. A comparison is made between the position then and that of today, using examples of recent taxonomic revisions. It is projected that the eventual number of moss taxa in the area may be reduced from over 3000 taxa to around 1300 if a full taxonomic revision is completed. Collecting activity has been greater in recent years, and is continuing. The need for further collecting and a dramatic increase in taxonomic work is emphasised.     

Comments on detecting rogue taxa using RogueNaRok

Rogues are relatively unstable taxa in phylogenetic analyses that are of concern if they obfuscate relationships, or support for relationships, of interest among more stable taxa. RogueNaRok is a recently developed heuristic solution to the problem of identifying rogue taxa. We illustrate the performance of RogueNaRok with simple examples designed to clarify its behaviour. We argue that the optimality criterion currently used by RogueNaRok may sometimes be poorly suited to the task of detecting rogues and that the scores reported by RogueNaRok should not be interpreted as measures of taxon instability. We suggest how RogueNaRok might be enhanced and recommend that it not be relied upon exclusively for detecting rogues.     

Deep-sea food bonanzas: early Cenozoic whale-fall communities resemble wood-fall rather than seep communities

The evolutionary history of invertebrate communities utilizing whale carcasses and sunken wood in the deep-sea is explored using fossil evidence. Compared to modern whale-fall communities, the Eo-Oligocene examples lack those vent-type taxa that most heavily rely on sulphide produced by anaerobic breakdown of bone lipids, but are very similar in their trophic structure to contemporaneous wood-falls. This sheds doubt on the hypothesis that whale-falls were evolutionary stepping stones for taxa that now inhabit hydrothermal vents and seeps. We suggest that the whale-fall communities reported here represent a new ecologic stage among whale-falls, which we have coined the 'chemosymbiotic opportunist stage' and that the 'sulphophilic stage' of modern whale-falls developed during the Early Miocene, resulting from a significant increase in both body size and/or oil content of bones among cetaceans during this time.     

Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods

The use of supraspecific terminal taxa to represent groups of species in phylogenetic analyses can result in changes to inferred relationships as compared to a complete species level analysis. These changes in topology result from interactions among (1) the cladistic status of the supraspecific taxa; (2) the method used to represent the taxa as single terminals, and (3) incongruence in the data set. We examine the effects of using supraspecific terminal taxa using a parallel analysis of hypothetical examples and an actual data matrix for the true seals (Mammalia: Phocidae). Incongruence among characters can produce changes in topology by shifting the ‘balance of power’ among groups of characters when supraspecific taxa are represented as single terminals. In the absence of homoplasy, the correct topology is maintained. Of the three methods for representing supraspecific taxa, the ‘ancestral’ method, which explicidy infers the common ancestor of the group corresponding to the taxon, performed the best, always maintaining the correct topology when monophyletic taxa were represented. This agrees with theoretical predictions. The ‘democratic’ and ‘exemplar’ methods, which represent the higher level taxon through a survey of all or one of its extant constituent species, respectively, were not as effective in maintaining the correct topology. Although both occasionally provided correct answers, their occurrences were largely unpredictable. The success of the exemplar method varies with the species selected. The simultaneous representation of two or more higher level taxa produced interactive effects where the resultant topology included different clades than when the taxa were collapsed individually. Interactive effects occurred with all three methods, albeit to a lesser degree for the ancestral method. Changes in topology were observed regardless of whether the higher group was monophyletic or not, but were more prevalent when it was paraphyletic. Unfortunately, there does not seem to be a reliable way to determine when a paraphyletic group has been included in the analysis (e.g. through bootstrap values or indices measuring homoplasy). The implications of these findings for phylogenetic analyses of molecular data are also discussed.     

Evaluating reasons for biased sex ratios in Crustacea

ABSTRACT

While equal ratios of males and females are normal, crustacean sex ratios are frequently biased. Here I review potential reasons for sex ratio biases in animals, and evaluate how likely they apply to crustaceans. I introduce crustacean examples and highlight promising crustacean taxa for future studies where examples are lacking. I conclude that ecological differences between the sexes appear to be the dominant reason for sex ratio bias in crustaceans. Major life history patterns limit the importance of evolutionary drivers to sedentary taxa with limited dispersal. Still largely unresolved is the question whether females can bias their offspring sex ratio, and given the diversity of sex determining systems, answers will vary from case to case.

Abbreviations: LMC: local mate competition; LSC: local sperm competition.     

Pronophiline butterflies (Satyridae) of the three Andean Cordilleras of Colombia

The 125 species of the satyrid butterfly tribe Pronophilini known from the three Andean Cordilleras of Colombia are listed, together with two species whose Colombian status is doubtful. The biological, ecological and biogeographical features of the tribe are described, using the listed species as examples. The features include restriction to moist conditions at high altitudes, endemism in the Cordilleras and in areas and on slopes within them, allopatric speciation and subspeciation, parapatric distributions of related species up the altitude gradients, intraspecific variation and polymorphism and apparent mimicry. The criteria used for classifying the taxa and assessing their relationships are discussed. Seventeen new species, three new subspecies and one new form are described. At the species level, 11 new synonymies are established, two synonymies are rejected, the status of 15 other taxa is revised, and 23 new combinations are made. At the generic level, two new synonymies are established, and one genus is resurrected.     

Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa

Molecular data offer great potential to resolve the phylogeny of living taxa but can molecular data improve our understanding of relationships of fossil taxa? Simulations suggest that this is possible, but few empirical examples have demonstrated the ability of molecular data to change the placement of fossil taxa. We offer such an example here. We analyze the placement of snakes among squamate reptiles, combining published morphological data (363 characters) and new DNA sequence data (15,794 characters, 22 nuclear loci) for 45 living and 19 fossil taxa. We find several intriguing results. First, some fossil taxa undergo major changes in their phylogenetic position when molecular data are added. Second, most fossil taxa are placed with strong support in the expected clades by the combined data Bayesian analyses, despite each having >98% missing cells and despite recent suggestions that extensive missing data are problematic for Bayesian phylogenetics. Third, morphological data can change the placement of living taxa in combined analyses, even when there is an overwhelming majority of molecular characters. Finally, we find strong but apparently misleading signal in the morphological data, seemingly associated with a burrowing lifestyle in snakes, amphisbaenians, and dibamids. Overall, our results suggest promise for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa.     

Heterogeneity in Bacterial Specialized Metabolism

Specialized metabolites (SMs) like typical antibiotics, signaling molecules or other bioactive compounds of bacterial origin (sometimes also used in human therapy) are often complex natural products that are costly for the cell to make. Several bacterial taxa are known to produce multiple SM classes in parallel and therefore a division of labor within a clonal population of bacteria might be beneficial. In this review, examples of SM of gram-negative and gram-positive bacterial taxa that are produced by different cell types are presented, and the possibility that such a heterogeneity is more widespread in SM biosynthesis is discussed. In addition, tools to study SM production at the single cell level are presented.     

Disaster taxa in microbially mediated metazoans: how endosymbionts and environmental catastrophes influence the adaptive capacity of reef corals

Reef corals are examples of metazoans that engage in mutualisms with a variety of microorganisms, including dinoflagellates, Bacteria, Archaea, and viruses. The high adaptive capacity of these microbial symbionts can be co‐opted by their coral hosts, and various emergent traits of these associations, such as thermotolerance, are undergoing strong selection due to climate change. This selection may spur the rise of microbial ‘disaster taxa’: opportunistic, cosmopolitan generalists that can proliferate and increase host survivorship following disturbances. Coral bleaching (a stress‐induced loss of dinoflagellates) constitutes one type of catastrophic disturbance for resident symbiont communities, and opens novel patches of host for colonization by microbial disaster taxa. Moreover, the compartmentalization of microbial symbionts within coral polyps reduces their effective population size and thus facilitates the spread of disaster taxa during times of environmental change. These phenomena suggest that, despite widespread loss of coral cover as a result of climate disturbances, the potential spread of resilient microbial disaster taxa in surviving colonies can have important implications for coral reef persistence over the coming decades.     

Uncovering hidden phylogenetic consensus in large data sets

Many of the steps in phylogenetic reconstruction can be confounded by “rogue” taxa—taxa that cannot be placed with assurance anywhere within the tree, indeed, whose location within the tree varies with almost any choice of algorithm or parameters. Phylogenetic consensus methods, in particular, are known to suffer from this problem. In this paper, we provide a novel framework to define and identify rogue taxa. In this framework, we formulate a bicriterion optimization problem, the relative information criterion, that models the net increase in useful information present in the consensus tree when certain taxa are removed from the input data. We also provide an effective greedy heuristic to identify a subset of rogue taxa and use this heuristic in a series of experiments, with both pathological examples from the literature and a collection of large biological data sets. As the presence of rogue taxa in a set of bootstrap replicates can lead to deceivingly poor support values, we propose a procedure to recompute support values in light of the rogue taxa identified by our algorithm; applying this procedure to our biological data sets caused a large number of edges to move from “unsupported” to “supported” status, indicating that many existing phylogenies should be recomputed and reevaluated to reduce any inaccuracies introduced by rogue taxa. We also discuss the implementation issues encountered while integrating our algorithm into RAxML v7.2.7, particularly those dealing with scaling up the analyses. This integration enables practitioners to benefit from our algorithm in the analysis of very large data sets (up to 2,500 taxa and 10,000 trees, although we present the results of even larger analyses).     

古生物多样性统计中的偏差及其校正

地质历史时期生物多样性统计中的偏差是普遍存在的。文中以奥陶纪海洋生物和二叠纪腕足动物分异度为例介绍和讨论古生物多样性统计中的偏差问题。认为在研究某些时段分异度时不能依靠单一的种、属或科的数量来建立分异度模式,而需要用生物分异度、灭绝率和新生率等多种计算方法来综合分析。同时古生物分异度的研究受到化石记录的完整性、研究、保存和采集程度、时间段的不均一性等多种因素影响,因此,大多需要应用稀疏标准化法等对不同时段或化石群在同等量化标准的基础上进行比较和校正后,才能得到比较符合实际的分异度模式。