Abstract— Science progresses through the development of integrative theories that unify more and more subsidiary theories. Progress in phylogenetic theory comes from mutual reconciliation with the theoretical structure of other branches of evolutionary biology, such as developmental biology, population biology, and population genetics. The notions of species, individuality, and scalar hierarchy are keys to this reconciliation. Conflation of the results and simplifying assumptions of particular discovery operations with the nature of the entities that we search for is a continuing problem in inferential biology. Other problems extend from the fact that scientific discovery operations address sets of entities and sets of interactions, even when the definitions employed by the operations are not rigorous set-definers, but rather generalized descriptive approximations which summarize similarities among the parts of hierarchically more general entities. As an example, in the discovery methods of phylogenetic systematics, organisms (parts of species) are treated as if they are extensions of a set (the lineage considered as a set), rather than as indefinable parts of a particular (the lineage as a system). This simplifying assumption constitutes treating scalar hierarchies as if they are specification hierarchies and, although this may be necessary for scientific progress, it can lead to over-reductionism if applied uncritically. We expect all analytical techniques to fail at some frequency in part because the limits and reality of the entities that scientists attempt to discover do not extend from definitions used in discovery operations, For this reason, all operational definitions in systematics must be patched by theoretical (= process) claims to one degree or another to give us a more complete representation of evolutionary history. In our view, ontology is the result of reconciliation of theoretical expectations and lines of operational evidence (both of “direct” observation and logical techniques). This “consilience of inductions” provides a general picture of the world and illuminates the limitations of particular discovery operations. As our understanding of the lawful nature of the universe improves, we are able to refine the definitions used by our discovery operations. Against the backdrop of the payoffs to evolutionary biology, the various definitions of species are most starkly compared. In cases where tokogeny is not inherently hierarchical, the level of organization chosen as the basic unit that maximizes the explanatory power of phylogenetic hypotheses is the level of Evolutionary Species, which is that of largest integrating lineages, rather than the level of individual organisms. Nevertheless, we recognize that our discovery operations rest on observations of organismal characteristics. The Phylogenetic Species Concept is, at best, the operational equivalent of Evolutionary Species, but may identify parts of Evolutionary Species that are only temporarily isolated. The cost of this kind of error is judged to be small compared with the alternative of recognizing paraphyletic “species” on the basis of potential to recombine. Metaphyly, concerns about exclusiveness of lineages as something more than an analytical issue, and “an escape from species” through operationalism are judged to stem from errors of overreduction.
Abstract: Conservation biology is linked inextricably with systematic biology. The principles of systematic biology, however, have not been integrated completely into the practice and principles of conservation biology. Systematists have recognized for some time that a number of evolutionary processes lead to the diversification of lineages. Yet some present units of conservation, such as the evolutionarily significant unit ( Waples 1991), primarily emphasize only one of these processes, adaptation. Allopatric speciation produces biodiversity without requiring any adaptive shift (and consequent adaptive differences between daughter species), so definitions of conservation units that emphasize adaptation may underestimate biodiversity. We estimated the frequency of different modes of speciation for three groups of vertebrates. The frequency of allopatric speciation varies among these groups, but is an important type of speciation in two of the three groups studied. Our results, and the results of other published studies of the frequency of modes of speciation, demonstrate that any unit of conservation defined solely in terms of adaptation is likely to underestimate biological diversity.
ABSTRACT The bony-tongue fishes, Osteoglossomorpha, have been the focus of a great deal of morphological, systematic, and evolutionary study, due in part to their basal position among extant teleostean fishes. This group includes the mooneyes (Hiodontidae), knifefishes (Notopteridae), the abu (Gymnarchidae), elephantfishes (Mormyridae), arawanas and pirarucu (Osteoglossidae), and the African butterfly fish (Pantodontidae). This morphologically heterogeneous group also has a long and diverse fossil record, including taxa from all continents and both freshwater and marine deposits. The phylogenetic relationships among most extant osteoglossomorph families are widely agreed upon. However, there is still much to discover about the systematic biology of these fishes, particularly with regard to the phylogenetic affinities of several fossil taxa, within Mormyridae, and the position of Pantodon. In this paper we review the state of knowledge for osteoglossomorph fishes. We first provide an overview of the diversity of Osteoglossomorpha, and then discuss studies of the phylogeny of Osteoglossomorpha from both morphological and molecular perspectives, as well as biogeographic analyses of the group. Finally, we offer our perspectives on future needs for research on the systematic biology of Osteoglossomorpha.
We evaluated the house mouse (Mus musculus species complex) and its laboratory descendents as models for three aspects of systematic biology: hybrid zone biology, chromosomal evolution and speciation, and tests for methods of phylogenetic reconstruction. The taxonomy and genetic relationships of the species in the complex are summarized. The comparative phylogenetic method was used to illucidate biogeographical, ecological, and chromosomal events in the group. Hybridization in house mice was evaluated with respect to the emerging discipline of hybrid zone biology. Inter- and intraspecific contact zones are described and compared. Zonespecific electrophoretic alleles, new metacentric chromosomes, and increased levels of parasitism are explained as consequences of genome disruption. The interspecific zone is widest in the area of most recent contact between species. Variation in the widths of individual clines is discussed. Chromosomal evolution is proceeding along alternative paths in different commensal lineages of house mice. A karyotypic revolution occurred within the species M. domesticus that led to the reproductive isolation between two local populations. The recency of this karyotypic revolution permits a study of how Robertsonian populations evolve and an evaluation of whether the stasipatric model of speciation is a good explanation for this case. The genealogical history of the inbred strains of mice is well known, and this information has been used to test how faithfully different kinds of data and different kinds of analytical techniques recreate the known phylogeny. Molecular data recapture the correct phylogeny better than do morphological data, and the commonly used analytical methods are all equally robust in producing this phylogeny.
BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. METHODOLOGY/PRINCIPAL FINDINGS: We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. CONCLUSIONS/SIGNIFICANCE: The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.
Joel Cracraft, The Seven Great Questions of Systematic Biology: An Essential Foundation for Conservation and the Sustainable Use of Biodiversity, Annals of the Missouri Botanical Garden, Vol. 89, No. 2 (Spring, 2002), pp. 127-144
In the wake of the Rio Convention on Biological Diversity, much attention has centered on our poor current state of knowledge about the diversity of life on Earth. This Policy Forum reviews the challenges that confront the systematic biology community. Whereas new collection-based institutes are being established in several tropical collections, resources are failing for many long-established centers of excellence. Given the exciting prospect of exploring Mars for life, it is too easy to forget the urgent need to discover and understand effectively the diversity of life on our own planet.
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Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.
Members of the form genus Rhizoctonia D.C. are considered as a complex mixture of filamentous fungi, having in common the possession of a non-spored imperfect state, usually referred to as the Rhizoctonia anamorph. The group includes several of the most devastating crop pathogens like Thanatephorus cucumeris (Frank) Donk (anamorph=Rhizoctonia solani Kühn), the majority of orchid mycorrhizal symbionts (mainly belonging to genus Ceratobasidium D.P. Rogers) and a collection of saprotrophic organisms of different systematic placement. The Rhizoctonia anamorph is characterized by several common features present among members of the entire Rhizoctonia species complex. Taxa from the group have been rearranged into several groups of higher fungi, including both Ascomycota and Basidiomycota, and split into several genera, employing criteria such as the analysis and ultrastructural comparison of septal apparatus. Until very recently, classification for some of the groups within the complex has been exclusively based on criteria such as hyphal anastomosis, since other types of diagnostic features are usually scarce in these fungi. Phytopathological studies in the complex have represented the major contingent of contributions in the group, especially in the case of R. solani. Some members of the complex have been reported to be protective isolates against pathogenic members of Rhizoctonia and some other fungal pathogens. This review focuses on the knowledge of several aspects of the species of Rhizcotonia s. lato, such as its current taxonomic placement, the biology and systematics of some groups of the complex, and a revision of the methodologies employed in studying it.
▪ Abstract Polymorphism, or variation within species, is common in all kinds of data and is the major focus of research on microevolution. However, polymorphism is often ignored by those who study macroevolution: systematists and comparative evolutionary biologists. Polymorphism may have a profound impact on phylogeny reconstruction, species-delimitation, and studies of character evolution. A variety of methods are used to deal with polymorphism in phylogeny reconstruction, and many of these methods have been extremely controversial for more than 20 years. Recent research has attempted to address the accuracy of these methods (their ability to estimate the true phylogeny) and to resolve these issues, using computer simulation, congruence, and statistical analyses. These studies suggest three things: that (a) the exclusion of polymorphic characters (as is commonly done in morphological phylogenetics) is unjustified and may greatly decrease accuracy relative to analyses that include these characters; (b) methods that incorporate frequency information on polymorphic characters tend to perform best, and (c) distance and likelihood methods designed for polymorphic data may often outperform parsimony methods. Although rarely discussed, polymorphism may also have a major impact on comparative studies of character evolution, such as the reconstruction of ancestral character states. Finally, polymorphism is an important issue in the delimitation of species, although this area has been somewhat neglected methodologically. The integration of within-species variation and microevolutionary processes into studies of systematics and comparative evolutionary biology is another example of the benefits of exchange of ideas between the fields of population genetics and systematics.
A limited diversity of character states for reproductive traits and a robust phylogeny make scleractinian corals an ideal model organism with which to explore the evolution of life-history traits. Here, we explore systematic and biogeographical patterns in the reproductive biology of the Scleractinia within the context of a new molecular phylogeny and using reproductive traits from nearly 400 species. Our analyses confirm that coral sexuality is highly conserved, and mode of larval development is relatively plastic. An overabundance of species with autotrophic larvae in the eastern Pacific and Atlantic is most likely the result of increased capacity for long-distance dispersal conferred by vertical transmission of symbiotic zooxanthellae. Spawning records from diverse biogeographical regions indicate that multispecies spawning occurs in all speciose coral assemblages. A new quantitative index of spawning synchrony shows peaks at mid-tropical latitudes in the Indo-Pacific, influenced in part by two spawning seasons in many species on equatorial reefs.
Scale insects (Hemiptera: Coccoidea) are small herbivorous insects found on all continents except Antarctica. They are extremely invasive, and many species are serious agricultural pests. They are also emerging models for studies of the evolution of genetic systems, endosymbiosis and plant-insect interactions. ScaleNet was launched in 1995 to provide insect identifiers, pest managers, insect systematists, evolutionary biologists and ecologists efficient access to information about scale insect biological diversity. It provides comprehensive information on scale insects taken directly from the primary literature. Currently, it draws from 23,477 articles and describes the systematics and biology of 8194 valid species. For 20 years, ScaleNet ran on the same software platform. That platform is no longer viable. Here, we present a new, open-source implementation of ScaleNet. We have normalized the data model, begun the process of correcting invalid data, upgraded the user interface, and added online administrative tools. These improvements make ScaleNet easier to use and maintain and make the ScaleNet data more accurate and extendable. Database URL: http://scalenet.info.
Michael D. Sorenson, Thomas W. Quinn; Numts: A Challenge For Avian Systematics And Population Biology, The Auk, Volume 115, Issue 1, 1 January 1998, Pages
The braconid parasitoid wasp subfamily Microgastrinae is perhaps the most species-rich subfamily of animals on Earth. Despite their small size, they are familiar to agriculturalists and field ecologists alike as one of the principal groups of natural enemies of caterpillars feeding on plants. Their abundance and nearly ubiquitous terrestrial distribution, their intricate interactions with host insects, and their historical association with mutualistic polydnaviruses have all contributed to Microgastrinae becoming a key group of organisms for studying parasitism, parasitoid genomics, and mating biology. However, these rich sources of data have not yet led to a robust genus-level classification of the group, and some taxonomic confusion persists as a result. We present the current status of understanding of the general biology, taxonomic history, diversity, geographical patterns, host relationships, and phylogeny of Microgastrinae as a stimulus and foundation for further study. Current progress in elucidating the biology and taxonomy of this important group is rapid and promises a revolution in the classification of these wasps in the near future.
Introduction - an overview of microbiology and cell biology cell chemistry cell biology metabolism, biosynthesis and nutrition macromolecules and molecular genetics viruses microbial genetics genetic engineering and biotechnology growth and its control industrial microbiology host-parasite relationships immunology and immunity clinical and diagnostic mibrobiology epidemiology and public health microbiology major microbial diseases metabolic diversity among the microorganisms microbial ecology molecular systematics and microbial evolution the bacteria archaea eukarya - eukaryotic microorganisms.
G. E. Gates, Burmese Earthworms: An Introduction to the Systematics and Biology of Megadrile Oligochaetes with Special Reference to Southeast Asia, Transactions of the American Philosophical Society, Vol. 62, No. 7 (1972), pp. 1-326
R. E. Woodruff, Citrus Weevils in Florida and the West Indies: Preliminary Report on Systematics, Biology, and Distribution (Coleoptera: Curculionidae), The Florida Entomologist, Vol. 68, No. 3 (Sep., 1985), pp. 370-379
Solutions to problems move only very slowly between different disciplines. Transfer can be greatly speeded up with suitable abstraction and classification of problems. Russian researchers working on the TRIZ (Teoriya Resheniya Izobretatelskikh Zadatch) method for inventive problem solving have identified systematic means of transferring knowledge between different scientific and engineering disciplines. With over 1500 person years of effort behind it, TRIZ represents the biggest study of human creativity ever conducted, whose aim has been to establish a system into which all known solutions can be placed, classified in terms of function. At present, the functional classification structure covers nearly 3 000 000 of the world's successful patents and large proportions of the known physical, chemical and mathematical knowledge-base. Additional tools are the identification of factors which prevent the attainment of new technology, leading directly to a system of inventive principles which will resolve the impasse, a series of evolutionary trends of development, and to a system of methods for effecting change in a system (Su-fields). As yet, the database contains little biological knowledge despite early recognition by the instigator of TRIZ (Genrich Altshuller) that one day it should. This is illustrated by natural systems evolved for thermal stability and the maintenance of cleanliness.
Introduction: Introduction to Plant Nematology History of Plant Nematology Agricultural Importance of Plant Nematodes?Methodology: Sampling for Nematode Assay Storage of Samples Extraction of Nematodes from Soil Extraction of Nematodes from Plant Tissue Extraction of Sedentary Nematodes and Eggs Extraction of Entomopathogenic Nematodes from Soil Processing of Nematodes Preparation of Enface View, Perineal Pattern and Vulval Cone Staining of Nematodes in Plant Tissue Electron Microscopy of Nematodes Biochemical and Molecular Techniques Gel Electrophoresis?Morphology of Nematodes: General Structure of Nematodes Cuticular Markings Head Tail?Systematics and Classification of Nematodes?Biology of Nematodes: Egg Development Reproduction Digestive System Excretory System Nervous System and Sensory Structures Nematode Physiology?Feeding and Trophic Relationship of Nematodes: Feeding and Feeding Behaviour Mode of Parasitism Host Parasite Relationship?Ecology of Nematodes: Population Dynamics of Plant Nematodes Interaction of Nematodes with other Organisms