Pattern and process in paleobiology: the role of cladistic analysis in systematic paleontology

Paleobiology ◽  
1981 ◽  
Vol 7 (4) ◽  
pp. 456-468 ◽  
Author(s):  
Joel Cracraft
Keyword(s):  
Natural Selection ◽  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
Evolutionary Process ◽  
Taxonomic Diversity ◽  
Logical Structure ◽  
Ecological Processes ◽  
Systematic Paleontology ◽  
History Of ◽  
Natural Groups

Systematics and paleontology have had a long conceptual relationship, united by the common goal of reconstructing the history of life. Yet, with few exceptions, paleontologists have had little input into formulating systematic theory and methodology. The reasons for this apparently relate to two conceptual-philosophical traditions of post-Darwinian paleontology: (1) the widespread adoption of a species concept in which taxa are viewed as nondiscrete, arbitrarily designated segments of evolutionary continua, and (2) the belief that phylogenetic reconstruction is primarily an empirical matter of tracing evolutionary change through the stratigraphic record.Available systematic evidence supports the hypothesis that species are real, discrete units in space and time and that, unless they are postulated to be directly ancestral to another species, they can be defined by the possession of one or more evolutionary novelties (derived characters). Species beginnings are delineated by speciation (vicariance) events and their terminations by subsequent speciation events or by extinctions.Natural groups are composed of taxa that have shared a common genealogical history. Cladistic analysis is a method to construct and test hypotheses of monophyly and thereby define natural groups. Cladistic hypotheses are necessary to investigate many of the major questions within contemporary paleobiology. Virtually no studies of evolutionary rates, patterns of taxonomic diversity, modes of taxic evolution, and patterns of morphological diversification can be undertaken without reference to cladistic hypotheses about the composition of natural groups.Because paleobiology is historical in its content, paleontologists are greatly limited in their ability to use paleontological data to investigate questions about the evolutionary process. According to current evolutionary theory, the concepts of adaptation and natural selection relate to genetic and ecological processes that take place within local populations (microevolution). If so, then data relevant to examining these phenomena are likely to be lacking in paleontological samples. Consequently, explanations of paleontological pattern that include process-related concepts such as adaptation and natural selection are axiomatic in their logical structure and thus cannot be falsified or critically evaluated by that paleontological pattern.

Getting Beyond the Apemen

2021 ◽  
pp. 1-18
Author(s):  
Lesley Newson ◽  
Peter J. Richerson
Keyword(s):  
At Risk ◽  
Natural Selection ◽  
Human Evolution ◽  
Evolutionary Process ◽  
Adult Males ◽  
Evolutionary Processes ◽  
Complex Information ◽  
History Of ◽  
Evolution By Natural Selection

This introductory chapter explains why a new story of human evolution is needed, and also lays the foundations of the story told in this book. One of the reasons we need a new story is that previous stories have concentrated on what our male ancestors were doing. Since survival is most at risk in the first years of life, it makes much more sense to concentrate on children and their mothers than on adult males. A brief account of the history of ideas in evolution by natural selection and human evolution provides readers with a background in evolutionary processes. Humans are a product of evolution, but we are not like other animals, because we are connected and readily share complex information. We are unique and our evolution was the result of a unique evolutionary process. To understand ourselves in evolutionary terms, it’s necessary to consider two intertwined evolutionary processes—genes and culture.

Phylogenetic Reconstruction of Character Development in Physciaceae

2001 ◽  
Vol 33 (1) ◽  
pp. 3-23 ◽  
Author(s):  
A. Nordin ◽  
J.-E. Mattsson
Keyword(s):  
Phylogenetic Trees ◽  
Character Development ◽  
Phylogenetic Reconstruction ◽  
Cladistic Analysis ◽  
The Other ◽  
New Genera ◽  
Secondary Chemistry ◽  
The Family ◽  
History Of ◽  
Basal Position

AbstractA cladistic analysis of the Physciaceae, based on morphological and chemical data, is presented. In the resulting phylogenetic reconstruction two major clades are formed, one containing the foliose genera (Anaptychia, Dirinana, Heterodermia, Hyperphyscia, Physcia, Phaeophyscia, Physconia, Pyxine) and the fruticose Tornabea and the other containing the remaining, mainly crustose genera. Rinodina appears as paraphyletic with representatives both at the base of the tree, at the same level as the two major clades and at the base of the crustose clade. Also Mobergia has a basal position. The characters used and their distribution in the phylogenetic trees are discussed as well as their significance for the identification of monophyletic groups. The history of the family is also briefly hinted at and characters of importance for the recognition of new genera are surveyed. Relevant publications and the variation in secondary chemistry are presented in tables.

Effects of Relaxed Natural Selection on the Evolution of Behavior

1999 ◽  
Author(s):  
Richard G. Coss
Keyword(s):  
Natural Selection ◽  
Related Species ◽  
Empirical Test ◽  
Parallel Evolution ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Behavioral Differences ◽  
Relaxed Selection ◽  
Herbert Spencer ◽  
Habitat Properties

Theoretical discussion of the role of natural selection in shaping behavioral variation in different habitats has been an integral part of the study of animal behavior since the late 19th century. Herbert Spencer (1888) was among the first to argue that migrating populations that fail to adjust to environmental circumstances “are the first to disappear.” A common rationale for comparing populations or related species is the desire to identify behavioral differences that correspond with habitat properties providing different patterns of selection (Tuomi 1981, Riechert 1993, this volume). Behavioral similarities are often ignored or are treated as less interesting because the thrust of the research program emphasizes behavioral differences as an empirical test of the theory of natural selection. Nevertheless, these similarities can be as revealing of evolutionary process as are differences when they reflect behavioral convergence or slow disintegration of behavior under relaxed selection (Coss and Goldthwaite 1995). When populations invade novel habitats, they not only experience new selective regimes; they can also experience relaxed selection on specific behavioral phenotypes. This is particularly common when the new habitat is missing a class of predators that was abundant in the ancestral habitat (e.g., Curio 1975, Pressley 1981). Under relaxed selection, characters may disintegrate, presumably because mutations that result in loss of the phenotype are not at a selective disadvantage. Disintegration is not always observed, however. Instead, behavioral characters are sometimes retained for long periods of time after selection has been relaxed (Coss 1991b, Kaneshiro 1989). Inferring relaxed selection requires that the history of the contrasted populations be relatively well known. Both ancestral selective regimes and behavioral characters must be known if character polarity is to be established. Character polarity must be established to distinguish disintegration from parallel evolution of novel behavior patterns. This often is a problem in population contrasts because differentiation is usually too recent to have resulted in the evolution of enough derived characters for the use of standard cladistic methods of phylogenetic reconstruction, although recent advances in statistical and molecular techniques are promising (Foster 1994, Foster and Cameron 1996). Instead, inference of character polarity has typically relied on geological evidence and comparison with closely related species.

Contingency and determinism in evolution: Replaying life’s tape

Science ◽  
2018 ◽  
Vol 362 (6415) ◽  
pp. eaam5979 ◽  
Author(s):  
Zachary D. Blount ◽  
Richard E. Lenski ◽  
Jonathan B. Losos
Keyword(s):  
Natural Selection ◽  
Evolutionary Biology ◽  
Empirical Studies ◽  
Evolutionary Process ◽  
Random Mutation ◽  
Ongoing Research ◽  
Adaptive Landscapes ◽  
Historical Processes ◽  
History Of ◽  
Evolutionary Paths

Historical processes display some degree of “contingency,” meaning their outcomes are sensitive to seemingly inconsequential events that can fundamentally change the future. Contingency is what makes historical outcomes unpredictable. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by the deterministic force of natural selection, but natural selection works upon variation that arises unpredictably through time by random mutation, and even beneficial mutations can be lost by chance through genetic drift. Moreover, evolution has taken place within a planetary environment with a particular history of its own. This tension between determinism and contingency makes evolutionary biology a kind of hybrid between science and history. While philosophers of science examine the nuances of contingency, biologists have performed many empirical studies of evolutionary repeatability and contingency. Here, we review the experimental and comparative evidence from these studies. Replicate populations in evolutionary “replay” experiments often show parallel changes, especially in overall performance, although idiosyncratic outcomes show that the particulars of a lineage’s history can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. Ongoing research on the structure of adaptive landscapes is providing additional insight into the interplay of fate and chance in the evolutionary process.

scholarly journals Current understanding on the Cambrian Explosion: questions and answers

PalZ ◽  
2021 ◽  
Author(s):  
Xingliang Zhang ◽  
Degan Shu
Keyword(s):  
Environmental Changes ◽  
Size Variation ◽  
Progressive Increase ◽  
Cambrian Explosion ◽  
Time Interval ◽  
Early Cambrian ◽  
Ecological Processes ◽  
Questions And Answers ◽  
Evolutionary Event ◽  
History Of

AbstractThe Cambrian Explosion by nature is a three-phased explosion of animal body plans alongside episodic biomineralization, pulsed change of generic diversity, body size variation, and progressive increase of ecosystem complexity. The Cambrian was a time of crown groups nested by numbers of stem groups with a high-rank taxonomy of Linnaean system (classes and above). Some stem groups temporarily succeeded while others were ephemeral and underrepresented by few taxa. The high number of stem groups in the early history of animals is a major reason for morphological gaps across phyla that we see today. Most phylum-level clades achieved their maximal disparity (or morphological breadth) during the time interval close to their first appearance in the fossil record during the early Cambrian, whereas others, principally arthropods and chordates, exhibit a progressive exploration of morphospace in subsequent Phanerozoic. The overall envelope of metazoan morphospace occupation was already broad in the early Cambrian though it did not reach maximal disparity nor has diminished significantly as a consequence of extinction since the Cambrian. Intrinsic and extrinsic causes were extensively discussed but they are merely prerequisites for the Cambrian Explosion. Without the molecular evolution, there could be no Cambrian Explosion. However, the developmental system is alone insufficient to explain Cambrian Explosion. Time-equivalent environmental changes were often considered as extrinsic causes, but the time coincidence is also insufficient to establish causality. Like any other evolutionary event, it is the ecology that make the Cambrian Explosion possible though ecological processes failed to cause a burst of new body plans in the subsequent evolutionary radiations. The Cambrian Explosion is a polythetic event in natural history and manifested in many aspects. No simple, single cause can explain the entire phenomenon.

scholarly journals The Botanical, Chemical and Ethnobotanical Diversity of Southern African Lamiaceae

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3712
Author(s):  
Ryan D. Rattray ◽  
Ben-Erik Van Wyk
Keyword(s):  
Southern Africa ◽  
Folk Medicine ◽  
Taxonomic Diversity ◽  
Volatile Oils ◽  
Edible Plant ◽  
Flora Of Southern Africa ◽  
Traditional Uses ◽  
History Of ◽  
Pharmaceutical Industries ◽  
History Of Use

The Lamiaceae is undoubtedly an important plant family, having a rich history of use that spans the globe with many species being used in folk medicine and modern industries alike. Their ability to produce aromatic volatile oils has made them valuable sources of materials in the cosmetic, culinary, and pharmaceutical industries. A thorough account of the taxonomic diversity, chemistry and ethnobotany is lacking for southern African Lamiaceae, which feature some of the region’s most notable medicinal and edible plant species. We provide a comprehensive insight into the Lamiaceae flora of southern Africa, comprising 297 species in 42 genera, 105 of which are endemic to the subcontinent. We further explore the medicinal and traditional uses, where all genera with documented uses are covered for the region. A broad review of the chemistry of southern African Lamiaceae is presented, noting that only 101 species (34%) have been investigated chemically (either their volatile oils or phytochemical characterization of secondary metabolites), thus presenting many and varied opportunities for further studies. The main aim of our study was therefore to present an up-to-date account of the botany, chemistry and traditional uses of the family in southern Africa, and to identify obvious knowledge gaps.

scholarly journals Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

2018 ◽  
Vol 44 (1) ◽  
pp. 20
Author(s):  
Eloiza Teles Caldart ◽  
Helena Mata ◽  
Cláudio Wageck Canal ◽  
Ana Paula Ravazzolo
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Molecular Epidemiology ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Evolutionary Process ◽  
Amino Acid Sequences ◽  
Evolutionary Models ◽  
Reconstruction Methods ◽  
Basic Concepts

Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.

scholarly journals Biological Transmission of Arboviruses: Reexamination of and New Insights into Components, Mechanisms, and Unique Traits as Well as Their Evolutionary Trends

2005 ◽  
Vol 18 (4) ◽  
pp. 608-637 ◽  
Author(s):  
Goro Kuno ◽  
Gwong-Jen J. Chang
Keyword(s):  
Biological Sciences ◽  
Host Range ◽  
Disease Transmission ◽  
Evolutionary Process ◽  
Field Research ◽  
Diverse Range ◽  
Unique Mode ◽  
History Of ◽  
Mode Of Transmission ◽  
Available Information

SUMMARY Among animal viruses, arboviruses are unique in that they depend on arthropod vectors for transmission. Field research and laboratory investigations related to the three components of this unique mode of transmission, virus, vector, and vertebrate host, have produced an enormous amount of valuable information that may be found in numerous publications. However, despite many reviews on specific viruses, diseases, or interests, a systematic approach to organizing the available information on all facets of biological transmission and then to interpret it in the context of the evolutionary process has not been attempted before. Such an attempt in this review clearly demonstrates tremendous progress made worldwide to characterize the viruses, to comprehend disease transmission and pathogenesis, and to understand the biology of vectors and their role in transmission. The rapid progress in molecular biologic techniques also helped resolve many virologic puzzles and yielded highly valuable data hitherto unavailable, such as characterization of virus receptors, the genetic basis of vertebrate resistance to viral infection, and phylogenetic evidence of the history of host range shifts in arboviruses. However, glaring gaps in knowledge of many critical subjects, such as the mechanism of viral persistence and the existence of vertebrate reservoirs, are still evident. Furthermore, with the accumulated data, new questions were raised, such as evolutionary directions of virus virulence and of host range. Although many fundamental questions on the evolution of this unique mode of transmission remained unresolved in the absence of a fossil record, available observations for arboviruses and the information derived from studies in other fields of the biological sciences suggested convergent evolution as a plausible process. Overall, discussion of the diverse range of theories proposed and observations made by many investigators was found to be highly valuable for sorting out the possible mechanism(s) of the emergence of arboviral diseases.

III.—The Life-history and Cytology of Didymium nigripes Fr.

1932 ◽  
Vol 57 (1) ◽  
pp. 93-142 ◽  
Author(s):  
Elsie J. Cadman
Keyword(s):  
Life History ◽  
Life Histories ◽  
Important Research ◽  
Great Work ◽  
Animal Kingdom ◽  
History Of ◽  
Natural Groups

Since 1860, in which year De Bary published his great work Die Mycetozoen, the investigation of the life-history of members of the Mycetozoa has aroused a considerable amount of interest, and a great deal of important research has been carried out in this connection. The group of organisms is particularly interesting, because it lies on the borderline between plant and animal kingdoms, and it is very possible that a detailed investigation of several species of the Mycetozoa might be of considerable assistance in elucidating certain obscure points in the life-histories of higher members of both the great natural groups. The term “Mycetozoa,” which we owe to De Bary, will be used throughout in preference to the older term “Myxogastres” invented by Fries (32, p. 2), and that of “Myxomycetes” first employed by Link (32, p. 2). “Mycetozoon,” or “fungus-like animal,” is a very appropriate description of a member of the group, since during part of its life-history it exhibits distinctly animal-like characters, and the individuals move rapidly by means of flagella, whilst later, during the development of the sporangium, a plant-like form is assumed. The combination of plant and animal characters has given rise to much discussion as to the position of the Mycetozoa in plant or animal kingdom, and the group has been claimed by both zoologists and botanists.

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