Higher-level Systematics of the Millipedes (Arthropoda: Myriapoda: Diplopoda) Evaluated Using Transcriptomic Data, Mitochondrial Genomics, and Classification Analyses PDF Download
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Author: Michael Scott Brewer Publisher: ISBN: Category : Animals Languages : en Pages : 136
Book Description
Knowledge of deep level phylogenetic relationships within and between many animal groups is currently lacking. Past attempts to reconstruct these ancient evolutionary relationships once relied chiefly on morphological characters and consequently suffered from deficiencies inherent to these data (homoplasy, few diagnostic characters, etc.). Advances in molecular biology over the last 20 years (namely PCR and high-throughput sequencing) have provided a whole other facet of potential characters via a vast array of loci, both nuclear and mitochondrial, which represent unlinked regions spanning entire genomes. The class Diplopoda (the millipedes) is a diverse group, 12,000 described species, which has suffered a long and convoluted taxonomic and systematic history. Containing many overinflated groups (numerous monotypic taxa) while other groups are vastly understudied, the current scheme of classification does not reflect the evolutionary history of the group but instead exists primarily for identification purposes. A classification constructed in such a manner can be characterized as an "unnatural classification". This work represents an attempt to: 1) ascertain the uniformity of millipede taxa at the ordinal level by evaluating species diversity contained in higher taxa (orders, families, genera); 2) achieve a robust and empirically derived estimate of millipede global diversity; 3) reconstruct the higher level relationships among all major millipede taxa using genomic scale molecular data; 4) map the ancestral states of key millipede characteristics; and 5) date the divergences of major diplopod lineages. Full mitochondrial genomes and transcriptomic data obtained via second-generation sequencing for exemplar taxa representing the ordinal taxa were used to reconstruct the relationships between the higher millipede taxa. Our work uncovered interesting and potentially alarming trends in millipede taxonomy. Additionally, we demonstrated the utility, or lack thereof, of using mitochondrial sequence data to reconstruct deep evolutionary relationships. Transcriptomic data analyses yielded well- supported trees containing relationships that have not been suggested previously. The transcriptome-based phylogeny was used to reconstruct the evolutionary changes of key millipede characteristics and, consequently, to assess their utility in delineating millipede taxa. This information provides a basis for future work within the Diplopoda including but not limited to: character evolution, biogeography, divergence time estimations, and comparative genomics.
Author: Michael Scott Brewer Publisher: ISBN: Category : Animals Languages : en Pages : 136
Book Description
Knowledge of deep level phylogenetic relationships within and between many animal groups is currently lacking. Past attempts to reconstruct these ancient evolutionary relationships once relied chiefly on morphological characters and consequently suffered from deficiencies inherent to these data (homoplasy, few diagnostic characters, etc.). Advances in molecular biology over the last 20 years (namely PCR and high-throughput sequencing) have provided a whole other facet of potential characters via a vast array of loci, both nuclear and mitochondrial, which represent unlinked regions spanning entire genomes. The class Diplopoda (the millipedes) is a diverse group, 12,000 described species, which has suffered a long and convoluted taxonomic and systematic history. Containing many overinflated groups (numerous monotypic taxa) while other groups are vastly understudied, the current scheme of classification does not reflect the evolutionary history of the group but instead exists primarily for identification purposes. A classification constructed in such a manner can be characterized as an "unnatural classification". This work represents an attempt to: 1) ascertain the uniformity of millipede taxa at the ordinal level by evaluating species diversity contained in higher taxa (orders, families, genera); 2) achieve a robust and empirically derived estimate of millipede global diversity; 3) reconstruct the higher level relationships among all major millipede taxa using genomic scale molecular data; 4) map the ancestral states of key millipede characteristics; and 5) date the divergences of major diplopod lineages. Full mitochondrial genomes and transcriptomic data obtained via second-generation sequencing for exemplar taxa representing the ordinal taxa were used to reconstruct the relationships between the higher millipede taxa. Our work uncovered interesting and potentially alarming trends in millipede taxonomy. Additionally, we demonstrated the utility, or lack thereof, of using mitochondrial sequence data to reconstruct deep evolutionary relationships. Transcriptomic data analyses yielded well- supported trees containing relationships that have not been suggested previously. The transcriptome-based phylogeny was used to reconstruct the evolutionary changes of key millipede characteristics and, consequently, to assess their utility in delineating millipede taxa. This information provides a basis for future work within the Diplopoda including but not limited to: character evolution, biogeography, divergence time estimations, and comparative genomics.
Author: Chad Lee Spruill Publisher: ISBN: Category : Andrognathidae Languages : en Pages : 59
Book Description
The genus Brachycybe Wood, 1864 (Platydesmida: Andrognathidae) belongs to an ancient millipede lineage that has persisted since the Miocene. The group displays a Holarctic distribution with species in the eastern Nearctic, western Nearctic, and eastern Palaearctic. Like many millipede groups, its taxonomy to date has been based solely on morphology, which may under represent species richness by ignoring cryptic species. Here we present the first phylogenetic analyses for Brachycybe based on molecular data obtained from the mitochondrial genes cytochrome c oxidase 1 and cytochrome b. Standard phylogenetic methods were used to reconstruct the evolutionary relationships of the group. Using the internal phylogenetic framework, we evaluated geographic associations among clades; species boundaries were evaluated using the cohesion species concept. The application of molecular phylogenetics, phylogeographic methods, and the cohesion species concept to the genus Brachycybe is used to evaluate its species diversity. The mitochondrial genome of Brachycybe lecontii Wood, 1864 (Platydesmida: Andrognathidae) is also presented here along with the phylogeny of Myriapoda, produced using the amino acid sequences from the entire mitochondrial genome. The complete mitochondrial genome sequence of Brachycybe lecontii comprises 15,465 base pairs and includes 13 protein-encoding genes, 21 tRNA genes, two rRNA genes, and two large non coding regions that are approximately 436 and 464 bp in length. The genome is uncharacteristic of typical Diplopods and varies dramatically from other sequenced members of the Arthropoda. The unique gene synteny is novel among others because of the rearrangement of two protein coding genes (nad1 and nad5) along with their retained transcriptional polarity. The phylogeny produced from these data recover the monophyly of the Myriapoda classes. However, support values within the Diplopoda are low, possibly due to the inclusion of atp8 in the analysis. This will have important implications for taxonomic research because it will expand the growing bank of complete millipede mitochondrial genomes, allow more robust phylogenetic analyses, and aid in the development of more genetic markers and consequently larger nucleotide datasets.
Author: Alessandro Minelli Publisher: BRILL ISBN: 9004156119 Category : Science Languages : en Pages : 547
Book Description
"The Myriapoda” is the first comprehensive monograph ever on all aspects of myriapod biology, including external and internal morphology, physiology, reproduction, development, distribution, ecology, phylogeny and taxonomy. It is thus of major interest for all zoologists and soil biologists.
Author: Alessandro Minelli Publisher: Springer Science & Business Media ISBN: 3642361609 Category : Science Languages : en Pages : 530
Book Description
More than two thirds of all living organisms described to date belong to the phylum Arthropoda. But their diversity, as measured in terms of species number, is also accompanied by an amazing disparity in terms of body form, developmental processes, and adaptations to every inhabitable place on Earth, from the deepest marine abysses to the earth surface and the air. The Arthropoda also include one of the most fashionable and extensively studied of all model organisms, the fruit-fly, whose name is not only linked forever to Mendelian and population genetics, but has more recently come back to centre stage as one of the most important and more extensively investigated models in developmental genetics. This approach has completely changed our appreciation of some of the most characteristic traits of arthropods as are the origin and evolution of segments, their regional and individual specialization, and the origin and evolution of the appendages. At approximately the same time as developmental genetics was eventually turning into the major agent in the birth of evolutionary developmental biology (evo-devo), molecular phylogenetics was challenging the traditional views on arthropod phylogeny, including the relationships among the four major groups: insects, crustaceans, myriapods, and chelicerates. In the meantime, palaeontology was revealing an amazing number of extinct forms that on the one side have contributed to a radical revisitation of arthropod phylogeny, but on the other have provided evidence of a previously unexpected disparity of arthropod and arthropod-like forms that often challenge a clear-cut delimitation of the phylum.
Author: Akshay Kumar Chakravarthy Publisher: Springer ISBN: 9811015244 Category : Science Languages : en Pages : 431
Book Description
Arthropods are invertebrates that constitute over 90% of the animal kingdom, and their bio-ecology is closely linked with global functioning and survival. Arthropods play an important role in maintaining the health of ecosystems, provide livelihoods and nutrition to human communities, and are important indicators of environmental change. Yet the population trends of several arthropods species show them to be in decline. Arthropods constitute a dominant group with 1.2 million species influencing earth’s biodiversity. Among arthropods, insects are predominant, with ca. 1 million species and having evolved some 350 million years ago. Arthropods are closely associated with living and non-living entities alike, making the ecosystem services they provide crucially important. In order to be effective, plans for the conservation of arthropods and ecosystems should include a mixture of strategies like protecting key habitats and genomic studies to formulate relevant policies for in situ and ex situ conservation. This two-volume book focuses on capturing the essentials of arthropod inventories, biology, and conservation. Further, it seeks to identify the mechanisms by which arthropod populations can be sustained in terrestrial and aquatic ecosystems, and by means of which certain problematic species be managed without producing harmful environmental side-effects. This edited compilation includes chapters contributed by over 80 biologists on a wide range of topics embracing the diversity, distribution, utility and conservation of arthropods and select groups of insect taxa. More importantly, it describes in detail the mechanisms of sustaining arthropod ecosystems, services and populations. It addresses the contribution of modern biological tools such as molecular and genetic techniques regulating gene expression, as well as conventional, indigenous practices in arthropod conservation. The contributors reiterate the importance of documenting and understanding the biology of arthropods from a holistic perspective before addressing conservation issues at large. This book offers a valuable resource for all zoologists, entomologists, ecologists, conservation biologists, policy makers, teachers and students interested in the conservation of biological resources.
Author: Gonzalo Giribet Publisher: Princeton University Press ISBN: 0691197067 Category : Science Languages : en Pages : 608
Book Description
The most up-to-date book on invertebrates, providing a new framework for understanding their place in the tree of life In The Invertebrate Tree of Life, Gonzalo Giribet and Gregory Edgecombe, leading authorities on invertebrate biology and paleontology, utilize phylogenetics to trace the evolution of animals from their origins in the Proterozoic to today. Phylogenetic relationships between and within the major animal groups are based on the latest molecular analyses, which are increasingly genomic in scale and draw on the soundest methods of tree reconstruction. Giribet and Edgecombe evaluate the evolution of animal organ systems, exploring how current debates about phylogenetic relationships affect the ways in which aspects of invertebrate nervous systems, reproductive biology, and other key features are inferred to have developed. The authors review the systematics, natural history, anatomy, development, and fossil records of all major animal groups, employing seminal historical works and cutting-edge research in evolutionary developmental biology, genomics, and advanced imaging techniques. Overall, they provide a synthetic treatment of all animal phyla and discuss their relationships via an integrative approach to invertebrate systematics, anatomy, paleontology, and genomics. With numerous detailed illustrations and phylogenetic trees, The Invertebrate Tree of Life is a must-have reference for biologists and anyone interested in invertebrates, and will be an ideal text for courses in invertebrate biology. A must-have and up-to-date book on invertebrate biology Ideal as both a textbook and reference Suitable for courses in invertebrate biology Richly illustrated with black-and-white and color images and abundant tree diagrams Written by authorities on invertebrate evolution and phylogeny Factors in the latest understanding of animal genomics and original fossil material
Author: Ward C. Wheeler Publisher: Wiley-Blackwell ISBN: 9780470671702 Category : Science Languages : en Pages : 0
Book Description
Systematics: A Course of Lectures is designed for use in an advanced undergraduate or introductory graduate level course in systematics and is meant to present core systematic concepts and literature. The book covers topics such as the history of systematic thinking and fundamental concepts in the field including species concepts, homology, and hypothesis testing. Analytical methods are covered in detail with chapters devoted to sequence alignment, optimality criteria, and methods such as distance, parsimony, maximum likelihood and Bayesian approaches. Trees and tree searching, consensus and super-tree methods, support measures, and other relevant topics are each covered in their own sections. The work is not a bleeding-edge statement or in-depth review of the entirety of systematics, but covers the basics as broadly as could be handled in a one semester course. Most chapters are designed to be a single 1.5 hour class, with those on parsimony, likelihood, posterior probability, and tree searching two classes (2 x 1.5 hours).
Author: Ephraim Cohen Publisher: Springer ISBN: 3030129195 Category : Science Languages : en Pages : 822
Book Description
The extracellular matrix (ECM) is an acellular three-dimensional network composed of proteins, glycoproteins, proteoglycans and exopolysaccharides. It primarily serves as a structural component in the tissues and organs of plants and animals, or forms biofilms in which bacterial cells are embedded. ECMs are highly dynamic structures that undergo continuous remodeling, and disruptions are frequently the result of pathological processes associated with severe diseases such as arteriosclerosis, neurodegenerative illness or cancer. In turn, bacterial biofilms are a source of concern for human health, as they are associated with resistance to antibiotics. Although exopolysaccharides are crucial for ECM formation and function, they have received considerably little attention to date. The respective chapters of this book comprehensively address such issues, and provide reviews on the structural, biochemical, molecular and biophysical properties of exopolysaccharides. These components are abundantly produced by virtually all taxa including bacteria, algae, plants, fungi, invertebrates and vertebrates. They include long unbranched homopolymers (cellulose, chitin/chitosan), linear copolymers (alginate, agarose), peptoglycans such as murein, heteropolymers like a variety of glycosaminoglycans (hyaluronan, dermatan, keratin, heparin, Pel), and branched heteropolymers such as pectin and hemicellulose. A separate chapter is dedicated to modern industrial and biomedical applications of exopolysaccharides and polysaccharide-based biocomposites. Their unique chemical, physical and mechanical properties have attracted considerable interest, inspired basic and applied research, and have already been harnessed to form structural biocomposite hybrids for tailor-made applications in regenerative medicine, bioengineering and biosensor design. Given its scope, this book provides a substantial source of basic and applied information for a wide range of scientists, as well as valuable textbook for graduate and advanced undergraduate students.
Author: Lothar A. Beck Publisher: Springer ISBN: 3319443216 Category : Science Languages : en Pages : 730
Book Description
This book is devoted to the knowledge of up to 250 years of collecting, organizing and preserving animals by generations of scientists. Zoological Collections are a huge resource for modern animal research and should be available for national and international scientists and institutions, as well as prospective public and private customers. Moreover, these collections are an important part of the scientific enterprise, supporting scientific research, human health, public education, and the conservation of biodiversity. Much of what we are beginning to understand about our world, we owe to the collection, preservation, and ongoing study of natural specimens. Properly preserved collections of marine or terrestrial animals are libraries of Earth's history and vital to our ability to learn about our place in its future. The approach employed by the editor involves not only an introduction to the topic, but also an external view on German collections including an assessment of their value in the international and national context, and information on the international and national collection networks. Particular attention is given to new approaches of sorting, preserving and researching in Zoological Collections as well as their neglect and/or threat. In addition, the book provides information on all big Public Research Museums, on important Collections in regional Country and local District Museums, and also on University collections. This is a highly informative and carefully presented book, providing scientific insight for readers with an interest in biodiversity, taxonomy, or evolution, as well as natural history collections at large.
Author: Michael Scott Brewer
Author: Michael Scott Brewer
Author: Chad Lee Spruill
Author: Alessandro Minelli
Author: Alessandro Minelli
Author: A. P. Gupta
Author: Akshay Kumar Chakravarthy
Author: Gonzalo Giribet
Author: Ward C. Wheeler
Author: Ephraim Cohen
Author: Lothar A. Beck