Stratigraphic tests of cladistic hypotheses

Paleobiology ◽  
1995 ◽  
Vol 21 (2) ◽  
pp. 153-178 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Confidence Intervals ◽  
Fossil Record ◽  
Evolutionary Dynamics ◽  
Test Group ◽  
Individual Species ◽  
Stratigraphic Record ◽  
Long Time ◽  
Morphologic Evolution ◽  
Phylogenetic Hypotheses ◽  
Stratigraphic Ranges

Cladograms predict the order in which fossil taxa appeared and, thus, make predictions about general patterns in the stratigraphic record. Inconsistencies between cladistic predictions and the observed stratigraphic record reflect either inadequate sampling of a clade's species, incomplete estimates of stratigraphic ranges, or homoplasy producing an incorrect phylogenetic hypothesis. A method presented in this paper attempts to separate the effects of homoplasy from the effects of inadequate sampling. Sampling densities of individual species are used to calculate confidence intervals on their stratigraphic ranges. The method uses these confidence intervals to test the order of branching predicted by a cladogram. The Lophospiridae (“Archaeogastropoda”) of the Ordovician provide a useful test group because the clade has a good fossil record and it produced species over a long time. Confidence intervals reject several cladistic hypotheses that postulate improbable “ghost lineages.” Other hypotheses are acceptable only with explicit ancestor-descendant relationships. The accepted cladogram is the shortest one that stratigraphic data cannot reject. The results caution against evaluating phylogenetic hypotheses of fossil taxa without considering both stratigraphic data and the possible presence of ancestral species, as both factors can affect interpretations of a clade's evolutionary dynamics and its patterns of morphologic evolution.

Confidence intervals on stratigraphic ranges

Paleobiology ◽  
1990 ◽  
Vol 16 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Confidence Intervals ◽  
Fossil Record ◽  
Morphological Evolution ◽  
Radiometric Dating ◽  
Phylogenetic Hypotheses ◽  
Stratigraphic Ranges ◽  
Taxonomic Assignments ◽  
Fossil Records ◽  
Source Of Error ◽  
Stratigraphic Range

Observed stratigraphic ranges almost always underestimate true longevities. Strauss and Sadler (1987, 1989) provide a method for calculating confidence intervals on the endpoints of local stratigraphic ranges. Their method can also be applied to composite sections; confidence intervals may be placed on times of origin and extinction for entire species or lineages. Confidence interval sizes depend only on the length of the stratigraphic range and the number of fossil horizons. The technique's most important assumptions are that fossil horizons are distributed randomly and that collecting intensity has been uniform over the stratigraphic range. These assumptions are more difficult to test and less likely to be fulfilled for composite sections than for local sections.Confidence intervals give useful baseline estimates of the incompleteness of the fossil record, even if the underlying assumptions cannot be tested. Confidence intervals, which can be very large, should be calculated when the fossil record is used to assess absolute rates of molecular or morphological evolution, especially for poorly preserved groups. Confidence intervals have other functions: to determine how rich the fossil record has to be before radiometric dating errors become the dominant source of error in estimated times of origin or extinction; to predict future fossil finds; to predict which species with fossil records should be extant; and to assess phylogenetic hypotheses and taxonomic assignments.

Confidence intervals on stratigraphic ranges: partial relaxation of the assumption of randomly distributed fossil horizons

Paleobiology ◽  
1994 ◽  
Vol 20 (4) ◽  
pp. 459-469 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Confidence Intervals ◽  
Fossil Record ◽  
Continuous Distribution ◽  
Random Processes ◽  
Upper Bounds ◽  
Restrictive Assumption ◽  
End Points ◽  
New Approach ◽  
Stratigraphic Position ◽  
Stratigraphic Ranges

The equations for calculating classical confidence intervals on the end points of stratigraphic ranges are based on the restrictive assumption of randomly distributed fossil finds. Herein, a method is presented for calculating confidence intervals on the end-points of stratigraphic ranges that partially relaxes this assumption: the method will work for any continuous distribution of gap sizes, not just those generated by random processes. The price paid for the generality of the new approach is twofold: (1) there are uncertainties associated with the sizes of the confidence intervals, and (2) for large confidence values (e.g., 95%) a rich fossil record is required to place upper bounds on the corresponding confidence intervals. This new method is not universal; like the method for calculating classical confidence intervals it is based on the assumption that there is no correlation between gap size and stratigraphic position. The fossil record of the Neogene Caribbean bryozoan Metrarabdotos is analyzed with the new approach. The equations developed here, like those for classical confidence intervals, should not be applied to stratigraphic ranges based on discrete sampling regimes, such as those typically established from deep-sea drilling cores, though there are exceptions to this rule.

Pengembangan Media Pembelajaran Interaktif Berdasarkan Teori Apos pada Materi Fungsi Kuadrat

2018 ◽  
Vol 6 (1) ◽  
pp. 1-10
Author(s):  
Arie Gusman ◽  
Kamid Kamid ◽  
Syamsurizal Syamsurizal
Keyword(s):  
Learning Theory ◽  
Teaching And Learning ◽  
Quadratic Function ◽  
Test Group ◽  
Quadratic Functions ◽  
High School Mathematics ◽  
Constructivist Learning Theory ◽  
Average Value ◽  
Long Time ◽  
Action Process

Learning quadratic functions that had been performed by the majority of vocational school and high school mathematics teacher in Kuala Tungkal is still using conventional learning media. The use of conventional learning media is experiencing a lot of obstacles, such as: a fairly long time in describing the graph function, especially when analyzing some quadratic function graphs with various characteristics. APOS is one of the constructivist learning theory which states that students learn through several stages, namely: action – process – object – schema. And to integrate into media APOS writer adapting ADDIE development model. The effectiveness of the use of media-based learning theory APOS seen from the student activity sheet can be concluded more increased activity of students in the learning process. Study of the test results, students were able to meet the completeness criteria stipulated minimum is 75. With an average value of learning outcomes, namely 87.14. It can be seen from the students' responses on a test group of small and large groups where it is concluded that researchers develop learning media can be categorized as good / interesting in the teaching and learning of mathematics.

The tale of the headless turtle

Zootaxa ◽  
2016 ◽  
Vol 4200 (2) ◽  
pp. 327 ◽  
Author(s):  
PEDRO S. R. ROMANO
Keyword(s):  
New Species ◽  
Phenotypic Plasticity ◽  
Lower Cretaceous ◽  
Fossil Record ◽  
Diagnostic Features ◽  
Fossil Species ◽  
The Past ◽  
Early Paleocene ◽  
Phylogenetic Hypotheses ◽  
A New Species

Pelomedusoides is the most diverse clade of side-necked turtles and there is an extensive fossil record (de Broin, 1988; Lapparent de Broin, 2000; Gaffney et al., 2006, 2011) that dates back at least to the Barremian (Lower Cretaceous) (Romano et al., 2014). Its large fossil record evidences a greater diversity in the past, particularly at the end of the Mesozoic, and exhibits a good sampling of species that are represented by skull material (Gaffney et al., 2006, 2011). As a consequence, the most complete and recent phylogenetic hypotheses for this clade (e.g. Romano et al., 2014; Cadena, 2015) are based on matrices comprising a great amount of cranial characters derived largely from Gaffney et al. (2006, 2011). In addition, it is well established that shell characters show a lot of phenotypic plasticity, even in the fossil species (Romano, 2008; Gaffney et al., 2006, 2011). In most cases it consequently is not justified to rely on “diagnostic features” of poorly informative shell-only material for describing a new species. Because of that, most authors remark new morphotypes in the literature when such aberrant specimens are recovered, but do not make any nomenclatural act by proposing a new yet poorly supported species (e.g. Romano et al., 2013; Ferreira & Langer, 2013; Menegazzo et al., 2015). Unfortunately, such a supposedly new bothremydid turtle (Pleurodira: Bothremydidae) from the Early Paleocene of Brazil was recently described based on poorly diagnostic remains (Carvalho et al., 2016; hereafter CGB, for the authors initials) and a correction of this unfounded nomenclatural act is required. In addition I present some comments on shell only material from Brazil in order to guide splitter-taxonomists to stop describing poorly preserved fossil specimens as new species. 

Fossil preservation and the stratigraphic ranges of taxa

Paleobiology ◽  
1996 ◽  
Vol 22 (2) ◽  
pp. 121-140 ◽  
Author(s):  
Mike Foote ◽  
David M. Raup
Keyword(s):  
Fossil Record ◽  
Mammalian Species ◽  
Evolutionary Rates ◽  
Extinction Rate ◽  
Mammal Species ◽  
Original Distribution ◽  
Lower Ordovician ◽  
Stratigraphic Ranges ◽  
Fossil Preservation ◽  
Rule Out

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy.Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased. (3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

Using Confidence Intervals to Quantify the Uncertainty in the End-Points of Stratigraphic Ranges

2010 ◽  
Vol 16 ◽  
pp. 291-316 ◽  
Author(s):  
Charles R. Marshall
Keyword(s):  
Environmental Change ◽  
Confidence Intervals ◽  
Mass Extinction ◽  
Relative Importance ◽  
End Points ◽  
Western Tethys ◽  
Space And Time ◽  
Biotic Events ◽  
Stratigraphic Ranges ◽  
The Many

One of the many contributions paleontology makes to our understanding of the biosphere and its evolution is a direct temporal record of biotic events. However, assuming fossils have been correctly identified and accurately dated, stratigraphic ranges underestimate true temporal ranges: observed first occurrences are too young, and observed last occurrences are too old. Here I introduce the techniques developed for placing confidence intervals on the end-points of stratigraphic ranges. I begin with the analysis of single taxa in local sections – with the simplest of assumptions – random fossilization. This is followed by a discussion of the methods developed to handle the fact that the recovery of fossils is often non-random in space and time. After discussion of how confidence intervals can be used to test for simultaneous origination and extinctions, I conclude with an example application of confidence intervals to unravel the relative importance of background extinction, environmental change and mass extinction of ammonite species at the end of the Cretaceous in western Tethys.

Community Replacement Pathways: What Do Fossil Sequences Reveal About Marine Ecosystem Transitions?

1990 ◽  
Vol 5 ◽  
pp. 262-272
Author(s):  
William Miller
Keyword(s):  
Fossil Record ◽  
Large Scale ◽  
Marine Ecosystem ◽  
Small Scale ◽  
Data Sets ◽  
Mass Extinctions ◽  
Ultimate Cause ◽  
Long Time ◽  
History Of ◽  
Time And Energy

Paleontologists have lavished much time and energy on description and explanation of large-scale patterns in the fossil record (e.g., mass extinctions, histories of monophyletic taxa, deployment of major biogeographic units), while paying comparatively little attention to biologic patterns preserved only in local stratigraphic sequences. Interpretation of the large-scale patterns will always be seen as the chief justification for the science of paleontology, but solving problems framed by long time spans and large areas is rife with tenuous inference and patterns are prone to varied interpretation by different investigators using virtually the same data sets (as in the controversy over ultimate cause of the terminal Cretaceous extinctions). In other words, the large-scale patterns in the history of life are the true philosophical property of paleontology, but there will always be serious problems in attempting to resolve processes that transpired over millions to hundreds-of-millions of years and encompassed vast areas of seafloor or landscape. By contrast, less spectacular and more commonplace changes in local habitats (often related to larger-scale events and cycles) and attendant biologic responses are closer to our direct experience of the living world and should be easier to interpret unequivocally. These small-scale responses are reflected in the fossil record at the scale of local outcrops.

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

scholarly journals Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

2011 ◽  
Vol 279 (1732) ◽  
pp. 1300-1309 ◽  
Author(s):  
Rampal S. Etienne ◽  
Bart Haegeman ◽  
Tanja Stadler ◽  
Tracy Aze ◽  
Paul N. Pearson ◽  
...  
Keyword(s):  
Standard Model ◽  
Fossil Record ◽  
Evolutionary Dynamics ◽  
Planktonic Foraminifera ◽  
Fossil Evidence ◽  
Rate Of Increase ◽  
The Standard Model ◽  
Molecular Phylogenies ◽  
Biological Realism

The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence ( Dendroica , Plethodon and Heliconius ). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.

Exploring new uses for measures of fit of phylogenetic hypotheses to the fossil record

Paleobiology ◽  
2006 ◽  
Vol 32 (1) ◽  
pp. 147-165 ◽  
Author(s):  
Kenneth D. Angielczyk ◽  
David L. Fox
Keyword(s):  
Fossil Record ◽  
Phylogenetic Hypotheses
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