Biological Systematics

Understanding the history and philosophy of biological systematics (phylogenetics, taxonomy and classification of living things) is key to successful practice of the discipline. In this thoroughly revised third edition, the authors provide an updated account of cladistic principles and techniques, emphasizing their empirical and epistemological clarity. The book covers the history and philosophy of systematics; the mechanics and methods of character analysis, phylogenetic inference, and evaluation of results; the practical application of systematic results to biological classification, adaptation and coevolution, biodiversity, and conservation; along with new chapters on species and molecular clocks. The book is both a textbook for students studying systematic biology and a desk reference for practicing systematists. Part explication of concepts and methods, part exploration of the underlying epistemology of systematics, the edition addresses why some methods are more empirically sound than others.

Ready Species One: Exploring the Use of Augmented Reality to Enhance Systematic Biology with a Revision of Fijian Strumigenys (Hymenoptera: Formicidae)

Advances in technology are rapidly changing the way people transmit, view, and interact with information. These advances offer new opportunities for researchers to share scientific discoveries with each other and the general public as never before. The field of revisionary biology has audiences confined to small groups of specialists, but the core task of systematic biology—documenting the endless forms of nature—is particularly well suited to capitalize on innovations in the realm of virtual, mixed and augmented reality. Interactive three-dimensional (3D) digital models of biological specimens can help bridge barriers across scientific disciplines by circumventing technical jargon, and also promise to open exciting new vistas for public engagement. Here, we explore the potential of augmented reality for communicating the discovery of new species. As a test case, we revise a radiation of Strumigenys Smith (Hymenoptera: Formicidae) miniature trap-jaw ants in Fiji. In addition to traditional revisionary elements, we present the augmented reality application ‘Insects3D’ built specifically for this study. The application runs on mobile devices and allows users to interact with X-ray microtomography-derived 3D specimen models and visualize 3D geographic distribution maps. We recognize 23 species in Fiji, including 6 new species: S. anorak n. sp., S. artemis n. sp., S. avatar n. sp., S. gunter n. sp., S. oasis n. sp., and S. parzival n. sp. This study demonstrates the potential of leveraging 3D data and technology for a more interactive systematic biology, and the need for research programs to develop robust and generalized tools to realize this potential.

A note on Brazeau et al.'s (2017) algorithm for characters with inapplicable data, illustrated with an analysis of their Fig. 3d using anagallis, a program for parsimony analysis of character hierarchies

Brazeau et al. (2017) recently published a paper with a single-character algorithm to calculate the score of a character with inapplicable data on a tree, aiming to maximize homology in such characters. In this note, I show by example (using their Fig. 3d) that their algorithm is insufficient to find all optimal inner node state reconstructions in such characters. The root cause seems to be a inherent built-in constraint on the evaluation of implied absence/presence characters in their algorithm. In more complex cases, this constraint can lead to an overestimation of the optimal minimal score of character hierarchies and to errors in the trees that are selected as optimal during tree search.[Note added on 26 January 2019: the paper of Brazeau at al. is now available as Brazeau, Guillerme, and Smith. An algorithm for Morphological Phylogenetic Analysis with Inapplicable Data. Systematic Biology, syy083, https://doi.org/10.1093/sysbio/syy083; more information about the anagallis program can be found at www.anagallis.be.]

A review of the systematic biology of fossil and living bony-tongue fishes, Osteoglossomorpha (Actinopterygii: Teleostei)

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.

Críticas ao "Tree Thinking": elucidando o significado das relações filogenéticas

<p>O "Tree Thinking" é tido como a metodologia dominante na Biologia Sistemática atual. Todavia, críticas aos procedimentos executados pela mesma são diversas. Neste trabalho serão apresentadas e defendidas aquelas feitas por Fitzhugh no que tange a sua base filosófica e as consequências de tais modificações. Assim, o presente trabalho tem como objetivo demonstrar que o "Tree Thinking" é incompleto, por não reconhecer que as relações filogenéticas são do tipo causal, i.e., são hipóteses explanatórias, sumarizadas de forma prévia em um esquete explanatório (cladograma). Além disso, para embasar tal argumentação, será apresentada uma discussão sobre a definição e os objetivos da Biologia Sistemática e do "Tree Thinking". Como resultado, será possível observar uma confusão entre classificar e sistematizar o conhecimento por aqueles que seguem o "Tree Thinking". Ademais, o "Tree Thinking" falha na aquisição de explicações causais quanto à origem e fixação das características estudadas. Desta forma, o "Tree Thinking" pode ser considerado como uma prática incompleta dentro da Biologia Sistemática e, portanto, recomenda-se a aplicação das propostas de Fitzhugh.</p><p><strong>Palavras chave</strong>: Biologia Sistemática, Cladística, Fitzhugh, Hennig, Sistemática Filogenética, Zimmerman.</p><p><strong>"Tree Thinking" Criticism: elucidating the meaning of phylogenetic relationships</strong></p><p><strong>Abstract</strong>: The "Tree Thinking" is regarded as the dominant methodology in current Systematic Biology. However, criticisms of the procedures carried out by it are diverse. Here the criticisms made by Fitzhugh regarding its philosophical basis and the consequences of such modifications are presented and defended. Thus, the present work aims to demonstrate that "Tree Thinking", as it has been used, is incomplete because it does not recognize that phylogenetic relationships are of the causal type previously summarized in an explanatory sketch (cladogram). In addition, to support such an argument, a discussion on the definition and objectives of Systematic Biology and "Tree Thinking" is provided. As a result, it is possible to observe confusion between classifying and systematizing the knowledge by those who follow "Tree Thinking". In addition, "Tree Thinking" fails to provide causal explanations regarding the origin and fixation of the characteristics studied. In this way, "Tree Thinking" can be considered an incomplete practice within Systematic Biology and, therefore, the application of the proposals of Fitzhugh are recommended.</p><p><strong>Key words</strong>: Systematic Biology, Cladistics, Fitzhugh, Hennig, Systematic Phylogenetics, Zimmerman.</p>